Construction and Application of a Protein Interaction Map for White Spot Syndrome Virus (WSSV)

White spot syndrome virus (WSSV) is currently the most serious global threat for cultured shrimp production. Although its large, double-stranded DNA genome has been completely characterized, most putative protein functions remain obscure. To provide more informative knowledge about this virus, a proteomic-scale network of WSSV-WSSV protein interactions was carried out using a comprehensive yeast two-hybrid analysis. An array of yeast transformants containing each WSSV open reading frame fused with GAL4 DNA binding domain and GAL4 activation domain was constructed yielding 187 bait and 182 prey constructs, respectively. On screening of ∼28,000 pairwise combinations, 710 interactions were obtained from 143 baits. An independent coimmunoprecipitation assay (co-IP) was performed to validate the selected protein interaction pairs identified from the yeast two-hybrid approach. The program Cytoscape was employed to create a WSSV protein–protein interaction (PPI) network. The topology of the WSSV PPI network was based on the Barabási-Albert model and consisted of a scale-free network that resembled other established viral protein interaction networks. Using the RNA interference approach, knocking down either of two candidate hub proteins gave shrimp more protection against WSSV than knocking down a nonhub gene. The WSSV protein interaction map established in this study provides novel guidance for further studies on shrimp viral pathogenesis, host-viral protein interaction and potential targets for therapeutic and preventative antiviral strategies in shrimp aquaculture.White spot syndrome virus (WSSV)¹ is the causative agent of white spot disease (WSD) and is one of the most serious viral pathogens that threaten the shrimp culture industry worldwide. Because WSD causes rapid and high mortality up to 100% within 3–10 days after viral infection (1), it causes dramatic economic losses on farms. WSSV is a large enveloped, ovoid to bacilliform, double-stranded DNA (dsDNA) virus with a genome of ∼300 kb (See reviews in (2, 3)). The WSSV genome has been completely characterized for isolates from Thailand (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"AF369029","term_id":"58866698","term_text":"AF369029"}}AF369029), China (accession number {"type":"entrez-nucleotide","attrs":{"text":"AF332093","term_id":"721172032","term_text":"AF332093"}}AF332093) and Taiwan (accession number {"type":"entrez-nucleotide","attrs":{"text":"AF440570","term_id":"19481591","term_text":"AF440570"}}AF440570). To expand its basic genetic information, various genomic and proteomic approaches have been applied to gain more insight into the molecular mechanisms of WSSV pathogenesis (See reviews in (2, 3)). However, the roles of most of the WSSV proteins still remain to be elucidated. This is due to the fact that many of its putative open reading frames (ORFs) lack homology to known proteins in the database. Protein–protein interaction studies can provide a valuable framework for understanding the roles of protein functions. Interaction studies of WSSV proteins have particularly focused on viral structural proteins (4–15). However, so far there has been no report on a protein–protein interaction (PPI) network for WSSV or any other crustacean virus. By contrast, several PPI networks for cellular organisms such as Saccharomyces cerevisiae (16, 17), Helicobacter pylori (18), Drosophila melanogaster (19), Caenarhabitis elegans (20), Plasmodium falciparum (21), and Homo sapiens (22, 23) and pathogens such as bacteriophage T7 (24), vaccinia virus (25), hepatitis C virus (26), and herpesviruses (27–29) have already been established. Therefore, the present study aimed to obtain a more fundamental understanding of WSSV protein interactions. A comprehensive yeast two-hybrid assay was employed to generate viral fusion proteins with DNA binding (BD) and activation (AD) domains in an array format that effectively allowed searching every possible binary interaction in WSSV. The interaction results from the yeast two-hybrid assays were subsequently validated by coimmunoprecipitation (co-IP). Topological properties of the WSSV PPI network were assessed and compared with previously published viral networks. Candidate viral hub proteins with high numbers of interacting partners were identified in this study and their significance was investigated using an RNA interference approach.     

VP26 of white spot syndrome virus functions as a linker protein between the envelope and nucleocapsid of virions by binding with VP51

The envelopment of the nucleocapsid is an important step in white spot syndrome virus (WSSV) assembly. Previous studies showed that VP26, a major envelope protein of WSSV, can interact with viral nucleocapsid. In this study, using the biotin label transfer technique, we found that the biotin label was transferred from Bio-rVP26 to the viral capsid protein VP51 or from Bio-MBP-VP51 to VP26. Far-Western analyses provided further evidence for direct interaction between VP26 and VP51. Therefore, we conclude that VP26 functions as a matrix-like linker protein between the viral envelope and nucleocapsid, which suggests that VP26 is a key factor in the envelopment of WSSV virion.     

Extensive homologous recombination in classical swine fever virus: A re-evaluation of homologous recombination events in the strain AF407339

In this short report, the genome-wide homologous recombination events were re-evaluated for classical swine fever virus (CSFV) strain {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339. We challenged a previous study which suggested only one recombination event in {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339 based on 25 CSFV genomes. Through our re-analysis on the 25 genomes in the previous study and the 41 genomes used in the present study, we argued that there should be possibly at least two clear recombination events happening in {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339 through genome-wide scanning. The reasons for identifying only one recombination event in the previous study might be due to the limited number of available CSFV genome sequences at that time and the limited usage of detection methods. In contrast, as identified by most detection methods using all available CSFV genome sequences, two major recombination events were found at the starting and ending zones of the genome {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339, respectively. The first one has two parents {"type":"entrez-nucleotide","attrs":{"text":"AF333000","term_id":"13383931","term_text":"AF333000"}}AF333000 (minor) and {"type":"entrez-nucleotide","attrs":{"text":"AY554397","term_id":"49860681","term_text":"AY554397"}}AY554397 (major) with beginning and ending breakpoints located at 19 and 607 nt of the genome respectively. The second one has two parents {"type":"entrez-nucleotide","attrs":{"text":"AF531433","term_id":"22347661","term_text":"AF531433"}}AF531433 (minor) and {"type":"entrez-nucleotide","attrs":{"text":"GQ902941","term_id":"298113017","term_text":"GQ902941"}}GQ902941 (major) with beginning and ending breakpoints at 8397 and 11,078 nt of the genome respectively. Phylogenetic incongruence analysis using neighbor-joining algorithm with 1000 bootstrapping replicates further supported the existence of these two recombination events. In addition, we also identified additional 18 recombination events on the available CSFV strains. Some of them may be trivial and can be ignored. In conclusion, CSFV might have relatively high frequency of homologous recombination events. Genome-wide scanning of identifying recombination events should utilize multiple detection methods so as to reduce the risk of misidentification.     

Aberrantly Expressed lncRNAs in Primary Varicose Great Saphenous Veins

Long non-coding RNAs (lncRNAs) are key regulatory molecules involved in a variety of biological processes and human diseases. However, the pathological effects of lncRNAs on primary varicose great saphenous veins (GSVs) remain unclear. The purpose of the present study was to identify aberrantly expressed lncRNAs involved in the prevalence of GSV varicosities and predict their potential functions. Using microarray with 33,045 lncRNA and 30,215 mRNA probes, 557 lncRNAs and 980 mRNAs that differed significantly in expression between the varicose great saphenous veins and control veins were identified in six pairs of samples. These lncRNAs were sub-grouped and mRNAs expressed at different levels were clustered into several pathways with six focused on metabolic pathways. Quantitative real-time PCR replication of nine lncRNAs was performed in 32 subjects, validating six lncRNAs ({"type":"entrez-nucleotide","attrs":{"text":"AF119885","term_id":"7770206","term_text":"AF119885"}}AF119885, {"type":"entrez-nucleotide","attrs":{"text":"AK021444","term_id":"10432630","term_text":"AK021444"}}AK021444, {"type":"entrez-nucleotide","attrs":{"text":"NR_027830","term_id":"240255595","term_text":"NR_027830"}}NR_027830, {"type":"entrez-nucleotide","attrs":{"text":"G36810","term_id":"2734477","term_text":"G36810"}}G36810, {"type":"entrez-nucleotide","attrs":{"text":"NR_027927","term_id":"242246950","term_text":"NR_027927"}}NR_027927, uc.345-). A coding-non-coding gene co-expression network revealed that four of these six lncRNAs may be correlated with 11 mRNAs and pathway analysis revealed that they may be correlated with another 8 mRNAs associated with metabolic pathways. In conclusion, aberrantly expressed lncRNAs for GSV varicosities were here systematically screened and validated and their functions were predicted. These findings provide novel insight into the physiology of lncRNAs and the pathogenesis of varicose veins for further investigation. These aberrantly expressed lncRNAs may serve as new therapeutic targets for varicose veins. The Human Ethnics Committee of Shanghai East Hospital, Tongji University School of Medicine approved the study (NO.: 2011-DF-53).     

Identification of the nucleocapsid, tegument, and envelope proteins of the shrimp white spot syndrome virus virion

The protein components of the white spot syndrome virus (WSSV) virion have been well established by proteomic methods, and at least 39 structural proteins are currently known. However, several details of the virus structure and assembly remain controversial, including the role of one of the major structural proteins, VP26. In this study, Triton X-100 was used in combination with various concentrations of NaCl to separate intact WSSV virions into distinct fractions such that each fraction contained envelope and tegument proteins, tegument and nucleocapsid proteins, or nucleocapsid proteins only. From the protein profiles and Western blotting results, VP26, VP36A, VP39A, and VP95 were all identified as tegument proteins distinct from the envelope proteins (VP19, VP28, VP31, VP36B, VP38A, VP51B, VP53A) and nucleocapsid proteins (VP664, VP51C, VP60B, VP15). We also found that VP15 dissociated from the nucleocapsid at high salt concentrations, even though DNA was still present. These results were confirmed by CsCl isopycnic centrifugation followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and liquid chromatography-nanoelectrospray ionization-tandem mass spectrometry, by a trypsin sensitivity assay, and by an immunogold assay. Finally, we propose an assembly process for the WSSV virion.     

Small molecule sensitization to TRAIL is mediated via nuclear localization,phosphorylation and inhibition of chaperone activity of Hsp27

The small chaperone protein Hsp27 confers resistance to apoptosis, and therefore is an attractive anticancer drug target. We report here a novel mechanism underlying the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) sensitizing activity of the small molecule {"type":"entrez-nucleotide","attrs":{"text":"LY303511","term_id":"1257646067","term_text":"LY303511"}}LY303511, an inactive analog of the phosphoinositide 3-kinase inhibitor inhibitor {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002, in HeLa cells that are refractory to TRAIL-induced apoptosis. On the basis of the fact that {"type":"entrez-nucleotide","attrs":{"text":"LY303511","term_id":"1257646067","term_text":"LY303511"}}LY303511 is derived from {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002, itself derived from quercetin, and earlier findings indicating that quercetin and {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002 affected Hsp27 expression, we investigated whether {"type":"entrez-nucleotide","attrs":{"text":"LY303511","term_id":"1257646067","term_text":"LY303511"}}LY303511 sensitized cancer cells to TRAIL via a conserved inhibitory effect on Hsp27. We provide evidence that upon treatment with {"type":"entrez-nucleotide","attrs":{"text":"LY303511","term_id":"1257646067","term_text":"LY303511"}}LY303511, Hsp27 is progressively sequestered in the nucleus, thus reducing its protective effect in the cytosol during the apoptotic process. {"type":"entrez-nucleotide","attrs":{"text":"LY303511","term_id":"1257646067","term_text":"LY303511"}}LY303511-induced nuclear translocation of Hsp27 is linked to its sustained phosphorylation via activation of p38 kinase and MAPKAP kinase 2 and the inhibition of PP2A. Furthermore, Hsp27 phosphorylation leads to the subsequent dissociation of its large oligomers and a decrease in its chaperone activity, thereby further compromising the death inhibitory activity of Hsp27. Furthermore, genetic manipulation of Hsp27 expression significantly affected the TRAIL sensitizing activity of {"type":"entrez-nucleotide","attrs":{"text":"LY303511","term_id":"1257646067","term_text":"LY303511"}}LY303511, which corroborated the Hsp27 targeting activity of {"type":"entrez-nucleotide","attrs":{"text":"LY303511","term_id":"1257646067","term_text":"LY303511"}}LY303511. Taken together, these data indicate a novel mechanism of small molecule sensitization to TRAIL through targeting of Hsp27 functions, rather than its overall expression, leading to decreased cellular protection, which could have therapeutic implications for overcoming chemotherapy resistance in tumor cells.     

Both STING and MAVS Fish Orthologs Contribute to the Induction of Interferon Mediated by RIG-I

Viral infections are detected in most cases by the host innate immune system through pattern-recognition receptors (PRR), the sensors for pathogen-associated molecular patterns (PAMPs), which induce the production of cytokines, such as type I interferons (IFN). Recent identification in mammalian and teleost fish of cytoplasmic viral RNA sensors, RIG-I-like receptors (RLRs), and their mitochondrial adaptor: the mitochondrial antiviral signaling (MAVS) protein, also called IPS-1, highlight their important role in the induction of IFN at the early stage of a virus infection. More recently, an endoplasmic reticulum (ER) adaptor: the stimulator of interferon genes (STING) protein, also called MITA, ERIS and MPYS, has been shown to play a pivotal role in response to both non-self-cytosolic RNA and dsDNA. In this study, we cloned STING cDNAs from zebrafish and showed that it was an ortholog to mammalian STING. We demonstrated that overexpression of this ER protein in fish cells led to a constitutive induction of IFN and interferon-stimulated genes (ISGs). STING-overexpressing cells were almost fully protected against RNA virus infection with a strong inhibition of both DNA and RNA virus replication. In addition, we found that together with MAVS, STING was an important player in the RIG-I IFN-inducing pathway. This report provides the demonstration that teleost fish possess a functional RLR pathway in which MAVS and STING are downstream signaling molecules of RIG-I. The Sequences presented in this article have been submitted to GenBank under accession numbers: Zebrafish STING ({"type":"entrez-nucleotide","attrs":{"text":"HE856619","term_id":"410810118","term_text":"HE856619"}}HE856619); EPC STING ({"type":"entrez-nucleotide","attrs":{"text":"HE856620","term_id":"410810120","term_text":"HE856620"}}HE856620); EPC IRF3 ({"type":"entrez-nucleotide","attrs":{"text":"HE856621","term_id":"410810122","term_text":"HE856621"}}HE856621); EPC IFN promoter ({"type":"entrez-nucleotide","attrs":{"text":"HE856618","term_id":"410810117","term_text":"HE856618"}}HE856618).     

Virtual Screening as a Strategy for the Identification of Xenobiotics Disrupting Corticosteroid Action

Background

Impaired corticosteroid action caused by genetic and environmental influence, including exposure to hazardous xenobiotics, contributes to the development and progression of metabolic diseases, cardiovascular complications and immune disorders. Novel strategies are thus needed for identifying xenobiotics that interfere with corticosteroid homeostasis. 11β-hydroxysteroid dehydrogenase 2 (11β-HSD2) and mineralocorticoid receptors (MR) are major regulators of corticosteroid action. 11β-HSD2 converts the active glucocorticoid cortisol to the inactive cortisone and protects MR from activation by glucocorticoids. 11β-HSD2 has also an essential role in the placenta to protect the fetus from high maternal cortisol concentrations.

Methods and Principal Findings

We employed a previously constructed 3D-structural library of chemicals with proven and suspected endocrine disrupting effects for virtual screening using a chemical feature-based 11β-HSD pharmacophore. We tested several in silico predicted chemicals in a 11β-HSD2 bioassay. The identified antibiotic lasalocid and the silane-coupling agent {"type":"entrez-nucleotide","attrs":{"text":"AB110873","term_id":"44885399","term_text":"AB110873"}}AB110873 were found to concentration-dependently inhibit 11β-HSD2. Moreover, the silane {"type":"entrez-nucleotide","attrs":{"text":"AB110873","term_id":"44885399","term_text":"AB110873"}}AB110873 was shown to activate MR and stimulate mitochondrial ROS generation and the production of the proinflammatory cytokine interleukin-6 (IL-6). Finally, we constructed a MR pharmacophore, which successfully identified the silane {"type":"entrez-nucleotide","attrs":{"text":"AB110873","term_id":"44885399","term_text":"AB110873"}}AB110873.

Conclusions

Screening of virtual chemical structure libraries can facilitate the identification of xenobiotics inhibiting 11β-HSD2 and/or activating MR. Lasalocid and {"type":"entrez-nucleotide","attrs":{"text":"AB110873","term_id":"44885399","term_text":"AB110873"}}AB110873 belong to new classes of 11β-HSD2 inhibitors. The silane {"type":"entrez-nucleotide","attrs":{"text":"AB110873","term_id":"44885399","term_text":"AB110873"}}AB110873 represents to the best of our knowledge the first industrial chemical shown to activate MR. Furthermore, the MR pharmacophore can now be used for future screening purposes.     

Shotgun identification of the structural proteome of shrimp white spot syndrome virus and iTRAQ differentiation of envelope and nucleocapsid subproteomes

White spot syndrome virus (WSSV) is a major pathogen that causes severe mortality and economic losses to shrimp cultivation worldwide. The genome of WSSV contains a 305-kb double-stranded circular DNA, which encodes 181 predicted ORFs. Previous gel-based proteomics studies on WSSV have identified 38 structural proteins. In this study, we applied shotgun proteomics using off-line coupling of an LC system with MALDI-TOF/TOF MS/MS as a complementary and comprehensive approach to investigate the WSSV proteome. This approach led to the identification of 45 viral proteins; 13 of them are reported for the first time. Seven viral proteins were found to have acetylated N termini. RT-PCR confirmed the mRNA expression of these 13 newly identified viral proteins. Furthermore iTRAQ (isobaric tags for relative and absolute quantification), a quantitative proteomics strategy, was used to distinguish envelope proteins and nucleocapsid proteins of WSSV. Based on iTRAQ ratios, we successfully identified 23 envelope proteins and six nucleocapsid proteins. Our results validated 15 structural proteins with previously known localization in the virion. Furthermore the localization of an additional 12 envelope proteins and two nucleocapsid proteins was determined. We demonstrated that iTRAQ is an effective approach for high throughput viral protein localization determination. Altogether WSSV is assembled by at least 58 structural proteins, including 13 proteins newly identified by shotgun proteomics and one identified by iTRAQ. The localization of 42 structural proteins was determined; 33 are envelope proteins, and nine are nucleocapsid proteins. A comprehensive identification of WSSV structural proteins and their localization should facilitate the studies of its assembly and mechanism of infection.     

Angiopoietin-Like 4 Mediates PPAR Delta Effect on Lipoprotein Lipase-Dependent Fatty Acid Uptake but Not on Beta-Oxidation in Myotubes

Peroxisome proliferator-activated receptor (PPAR) delta is an important regulator of fatty acid (FA) metabolism. Angiopoietin-like 4 (Angptl4), a multifunctional protein, is one of the major targets of PPAR delta in skeletal muscle cells. Here we investigated the regulation of Angptl4 and its role in mediating PPAR delta functions using human, rat and mouse myotubes. Expression of Angptl4 was upregulated during myotubes differentiation and by oleic acid, insulin and PPAR delta agonist {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516. Treatment with {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516 or Angptl4 overexpression inhibited both lipoprotein lipase (LPL) activity and LPL-dependent uptake of FAs whereas uptake of BSA-bound FAs was not affected by either treatment. Activation of retinoic X receptor (RXR), PPAR delta functional partner, using bexarotene upregulated Angptl4 expression and inhibited LPL activity in a PPAR delta dependent fashion. Silencing of Angptl4 blocked the effect of {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516 and bexarotene on LPL activity. Treatment with {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516 but not Angptl4 overexpression significantly increased palmitate oxidation. Furthermore, Angptl4 overexpression did not affect the capacity of {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516 to increase palmitate oxidation. Basal and insulin stimulated glucose uptake, glycogen synthesis and glucose oxidation were not significantly modulated by Angptl4 overexpression. Our findings suggest that FAs-PPARdelta/RXR-Angptl4 axis controls the LPL-dependent uptake of FAs in myotubes, whereas the effect of PPAR delta activation on beta-oxidation is independent of Angptl4.     

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Phylum Crenarchaeota

• Pyrobaculum strain 1860, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003098","term_id":"356640791","term_text":"CP003098"}}CP003098 [1]

Phylum Deinococcus-Thermus

• “Thermus sp.” Strain CCB_US3_UF1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003126","term_id":"359289533","term_text":"CP003126"}}CP003126 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003127","term_id":"359291781","term_text":"CP003127"}}CP003127 (plasmid) [2]

Phylum Proteobacteria

• “Achromobacter arsenitoxydans” SY8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGUF00000000","term_id":"359366799","term_text":"AGUF00000000"}}AGUF00000000 [3]
• Acidovorax sp. Strain NO1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGTS00000000","term_id":"363417938","term_text":"AGTS00000000"}}AGTS00000000 [4]
• Acinetobacter baumannii AB4857, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAG00000000","term_id":"371492156","term_text":"AHAG00000000"}}AHAG00000000 [5]
• Acinetobacter baumannii AB5075, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAH00000000","term_id":"371492114","term_text":"AHAH00000000"}}AHAH00000000 [5]
• Acinetobacter baumannii AB5256, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAI00000000","term_id":"371492153","term_text":"AHAI00000000"}}AHAI00000000 [5]
• Acinetobacter baumannii AB5711, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAJ00000000","term_id":"371492197","term_text":"AHAJ00000000"}}AHAJ00000000 [5]
• Aeromonas salmonicida, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVO00000000","term_id":"356689990","term_text":"AGVO00000000"}}AGVO00000000 [6]
• Aggregatibacter actinomycetemcomitans RHAA1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHGR00000000","term_id":"359757447","term_text":"AHGR00000000"}}AHGR00000000 [7]
• Agrobacterium tumefaciens 5A, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVZ00000000","term_id":"358008163","term_text":"AGVZ00000000"}}AGVZ00000000 [8]
• Azoarcus sp. Strain KH32C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012304","term_id":"358635055","term_text":"AP012304"}}AP012304, {"type":"entrez-nucleotide","attrs":{"text":"AP012305","term_id":"358639587","term_text":"AP012305"}}AP012305 [9]
• Burkholderia sp. Strain YI23, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003087","term_id":"357934279","term_text":"CP003087"}}CP003087 (Chromosome 1), {"type":"entrez-nucleotide","attrs":{"text":"CP003088","term_id":"357937049","term_text":"CP003088"}}CP003088 (Chromosome 2), {"type":"entrez-nucleotide","attrs":{"text":"CP003089","term_id":"357938589","term_text":"CP003089"}}CP003089 (Chromosome 3), {"type":"entrez-nucleotide","attrs":{"text":"CP003090","term_id":"357939954","term_text":"CP003090"}}CP003090 (plasmid BYI23_D), {"type":"entrez-nucleotide","attrs":{"text":"CP003091","term_id":"357941606","term_text":"CP003091"}}CP003091 (plasmid BYI23_E) {"type":"entrez-nucleotide","attrs":{"text":"CP003092","term_id":"357941997","term_text":"CP003092"}}CP003092 (plasmid BYI23_F) [10]
• Brucella suis VBI22, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003128","term_id":"358257303","term_text":"CP003128"}}CP003128, {"type":"entrez-nucleotide","attrs":{"text":"CP003129","term_id":"358259429","term_text":"CP003129"}}CP003129 [11]
• Comamonas testosteroni ATCC 11996, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIL00000000","term_id":"371454882","term_text":"AHIL00000000"}}AHIL00000000 [12]
• “Commensalibacter intestini” A911^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFR00000000","term_id":"353673384","term_text":"AGFR00000000"}}AGFR00000000 [13]
• Edwardsiella ictaluri, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001600.1","term_id":"238867551","term_text":"CP001600.1"}}CP001600.1 [14]
• Enterobacter cloacae subsp. dissolvens SDM, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSY00000000","term_id":"357435944","term_text":"AGSY00000000"}}AGSY00000000 [15]
• “Gluconobacter morbifer” G707^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQV00000000","term_id":"356416073","term_text":"AGQV00000000"}}AGQV00000000 [16]
• Legionella dumoffii TEX-KL, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVT00000000","term_id":"358009168","term_text":"AGVT00000000"}}AGVT00000000 [17]
• Legionella dumoffii NY-23, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVU00000000","term_id":"358009167","term_text":"AGVU00000000"}}AGVU00000000 [17]
• Legionella pneumophila serogroup 12 Strain 570-CO-H, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003192","term_id":"364506764","term_text":"CP003192"}}CP003192 [18]
• Marinobacterium stanieri S30, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPL00000000","term_id":"339778849","term_text":"AFPL00000000"}}AFPL00000000 [19]
• “Marinobacter manganoxydans” MnI7-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CP001978 to CP001980","start_term":"CP001978","end_term":"CP001980","start_term_id":"311692891","end_term_id":"311697125"}}CP001978 to CP001980 [20]
• Mesorhizobium alhagi CCNWXJ12-2T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAM00000000","term_id":"359256606","term_text":"AHAM00000000"}}AHAM00000000 [21]
• Mesorhizobium amorphae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSN00000000","term_id":"355545111","term_text":"AGSN00000000"}}AGSN00000000 [22]
• Methylomicrobium alcaliphilum 20Z, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FO082060","term_id":"351716053","term_text":"FO082060"}}FO082060 and {"type":"entrez-nucleotide","attrs":{"text":"FO082061","term_id":"351720036","term_text":"FO082061"}}FO082061 [23]
• Mitsuaria sp. Strain H24L5A, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAFG01000001 to CAFG01000607","start_term":"CAFG01000001","end_term":"CAFG01000607","start_term_id":"354809229","end_term_id":"354808623"}}CAFG01000001 to CAFG01000607 [24]
• Novosphingobium pentaromativorans US6-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFM00000000","term_id":"357601355","term_text":"AGFM00000000"}}AGFM00000000 [25]
• Pantoea ananatis B1-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAEI01000001 to CAEI01000169","start_term":"CAEI01000001","end_term":"CAEI01000169","start_term_id":"344197887","end_term_id":"344197719"}}CAEI01000001 to CAEI01000169 [26]
• Pantoea ananatis LMG 5342, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE617160","term_id":"365184443","term_text":"HE617160"}}HE617160 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"HE617161","term_id":"365188784","term_text":"HE617161"}}HE617161 (pPANA10) [27]
• Pantoea ananatis Strain PA13, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003085","term_id":"354986417","term_text":"CP003085"}}CP003085 and {"type":"entrez-nucleotide","attrs":{"text":"CP003086","term_id":"354685304","term_text":"CP003086"}}CP003086 [28]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXI00000000","term_id":"343788111","term_text":"AFXI00000000"}}AFXI00000000 [29]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXJ00000000","term_id":"343788109","term_text":"AFXJ00000000"}}AFXJ00000000 [29]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXK00000000","term_id":"343788110","term_text":"AFXK00000000"}}AFXK00000000 [29]
• Pseudomonas chlororaphis GP72, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAY01000000","term_id":"359757954","term_text":"gb||AHAY01000000"}}AHAY01000000 [30]
• Pseudomonas fluorescens F113, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003150","term_id":"359757955","term_text":"CP003150"}}CP003150 [31]
• Pseudomonas fluorescens Wayne 1R, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CADX01000001 to CADX01000090","start_term":"CADX01000001","end_term":"CADX01000090","start_term_id":"354924103","end_term_id":"354924014"}}CADX01000001 to CADX01000090 [32]
• Pseudomonas fluorescens Wood1R, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAFF01000001","term_id":"354698772","term_text":"CAFF01000001"}}CAFF01000001 to {"type":"entrez-nucleotide","attrs":{"text":"CAFF01001437","term_id":"354697336","term_text":"CAFF01001437"}}CAFF01001437 [32]
• Pseudomonas psychrotolerans L19, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBD00000000","term_id":"359372666","term_text":"AHBD00000000"}}AHBD00000000 [33]
• Pseudoalteromonas rubra ATCC 29570^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHCD00000000","term_id":"540289291","term_text":"AHCD00000000"}}AHCD00000000 [34]
• Pseudomonas stutzeri SDM-LAC, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSX00000000","term_id":"357435965","term_text":"AGSX00000000"}}AGSX00000000 [35]
• Pseudoxanthomonas spadix BD-a59, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003093","term_id":"357433120","term_text":"CP003093"}}CP003093 [36]
• Rickettsia slovaca, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002428","term_id":"360041315","term_text":"CP002428"}}CP002428 [37]
• Salmonella enterica serovar Pullorum RKS5078, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003047","term_id":"357204415","term_text":"CP003047"}}CP003047 [38]
• Sinorhizobium meliloti CCNWSX0020, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVV00000000","term_id":"359507569","term_text":"AGVV00000000"}}AGVV00000000 [39]
• Sphingobium sp. Strain SYK-6, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012222","term_id":"345135066","term_text":"AP012222"}}AP012222 and {"type":"entrez-nucleotide","attrs":{"text":"AP012223","term_id":"345138980","term_text":"AP012223"}}AP012223 [40]
• Sphingomonas sp. Strain PAMC 26605, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIS00000000","term_id":"366040305","term_text":"AHIS00000000"}}AHIS00000000 [41]
• Stenotrophomonas maltophilia RR-10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGRB00000000","term_id":"359757773","term_text":"AGRB00000000"}}AGRB00000000 [42]
• Strain HIMB30, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIG00000000","term_id":"349602640","term_text":"AGIG00000000"}}AGIG00000000 [43]
• Taylorella equigenitalis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003059","term_id":"347973256","term_text":"CP003059"}}CP003059 [44]
• Vibrio campbellii DS40M4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIE00000000","term_id":"358251732","term_text":"AGIE00000000"}}AGIE00000000 [45]
• Vibrio fischeri SR5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIH00000000","term_id":"371496097","term_text":"AHIH00000000"}}AHIH00000000 [46]
• Yersinia enterocolitica, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQO00000000","term_id":"351780838","term_text":"AGQO00000000"}}AGQO00000000 [47]

Phylum Tenericutes

• Candidatus Mycoplasma haemominutum, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613254","term_id":"357978897","term_text":"HE613254"}}HE613254 [48]
• Mycoplasma haemocanis strain Illinois, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003199","term_id":"363988676","term_text":"CP003199"}}CP003199 [49]
• Mycoplasma iowae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFP00000000","term_id":"349504222","term_text":"AGFP00000000"}}AGFP00000000 [50]
• Mycoplasma pneumoniae Type 2a Strain 309, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012303","term_id":"358640274","term_text":"AP012303"}}AP012303 [51]

Phylum Firmicutes

• Bacillus cereus F837/76, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003187","term_id":"364509831","term_text":"CP003187"}}CP003187 (chromosome) {"type":"entrez-nucleotide","attrs":{"text":"CP003188","term_id":"364515227","term_text":"CP003188"}}CP003188 (pF837_55kb), {"type":"entrez-nucleotide","attrs":{"text":"CP003189","term_id":"364515372","term_text":"CP003189"}}CP003189 (pF837_10kb) [52]
• Brevibacillus laterosporus Strain GI-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGD01000001 to CAGD01000061","start_term":"CAGD01000001","end_term":"CAGD01000061","start_term_id":"359745324","end_term_id":"359745264"}}CAGD01000001 to CAGD01000061 [53]
• Clostridium sporogenes PA 3679, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGAH00000000","term_id":"364889226","term_text":"AGAH00000000"}}AGAH00000000 [54]
• Enterococcus mundtii CRL1656, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFWZ00000000.1","term_id":"354620965","term_text":"AFWZ00000000.1"}}AFWZ00000000.1 [55]
• Geobacillus thermoleovorans CCB_US3_UF5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003125","term_id":"359285645","term_text":"CP003125"}}CP003125 [56]
• Lactobacillus curvatus Strain CRL705, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGBU01000000","term_id":"354514905","term_text":"gb||AGBU01000000"}}AGBU01000000 [57]
• Lactobacillus rhamnosus ATCC 8530, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003094","term_id":"355393429","term_text":"CP003094"}}CP003094 [58]
• Lactobacillus rhamnosus R0011, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGKC00000000","term_id":"357540515","term_text":"AGKC00000000"}}AGKC00000000 [59]
• Lactococcus garvieae TB25, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQX01000000","term_id":"359031556","term_text":"gb||AGQX01000000"}}AGQX01000000 [60]
• Lactococcus garvieae LG9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQY01000000","term_id":"359031592","term_text":"gb||AGQY01000000"}}AGQY01000000 [60]
• Lactococcus lactis subsp. cremoris A76, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003132","term_id":"358748197","term_text":"CP003132"}}CP003132 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003136","term_id":"358750967","term_text":"CP003136"}}CP003136 (pQA505), {"type":"entrez-nucleotide","attrs":{"text":"CP003135","term_id":"358750954","term_text":"CP003135"}}CP003135 (PQA518), {"type":"entrez-nucleotide","attrs":{"text":"CP003134","term_id":"358750911","term_text":"CP003134"}}CP003134 (pQA549), {"type":"entrez-nucleotide","attrs":{"text":"CP003133","term_id":"358750841","term_text":"CP003133"}}CP003133 (pQA554) [61]
• Leuconostoc citreum LBAE C10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGE00000000","term_id":"365487970","term_text":"CAGE00000000"}}CAGE00000000 [62]
• Leuconostoc citreum LBAE C11, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGF00000000","term_id":"365512054","term_text":"CAGF00000000"}}CAGF00000000 [62]
• Leuconostoc citreum LBAE E16, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGG00000000","term_id":"365528100","term_text":"CAGG00000000"}}CAGG00000000 [62]
• Leuconostoc mesenteroides subsp. mesenteroides Strain J18, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003101","term_id":"948298071","term_text":"CP003101"}}CP003101 [63]
• Paenibacillus peoriae Strain KCTC 3763^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFX00000000","term_id":"359367787","term_text":"AGFX00000000"}}AGFX00000000 [64]
• Pediococcus acidilactici MA18/5M, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGKB00000000","term_id":"357540603","term_text":"AGKB00000000"}}AGKB00000000 [65]
• Pediococcus claussenii ATCC BAA-344^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003137","term_id":"361055534","term_text":"CP003137"}}CP003137 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003138","term_id":"361057275","term_text":"CP003138"}}CP003138 (pPECL-1), {"type":"entrez-nucleotide","attrs":{"text":"CP003139","term_id":"361057278","term_text":"CP003139"}}CP003139 (pPECL-2), {"type":"entrez-nucleotide","attrs":{"text":"CP003140","term_id":"361057281","term_text":"CP003140"}}CP003140 (pPECL-3), {"type":"entrez-nucleotide","attrs":{"text":"CP003141","term_id":"361057302","term_text":"CP003141"}}CP003141 (pPECL-4), {"type":"entrez-nucleotide","attrs":{"text":"CP003142","term_id":"361057319","term_text":"CP003142"}}CP003142 (pPECL-5), {"type":"entrez-nucleotide","attrs":{"text":"CP003143","term_id":"361057355","term_text":"CP003143"}}CP003143 (pPECL-6), {"type":"entrez-nucleotide","attrs":{"text":"CP003144","term_id":"361057377","term_text":"CP003144"}}CP003144 (pPECL-7), {"type":"entrez-nucleotide","attrs":{"text":"CP003145","term_id":"380450589","term_text":"CP003145"}}CP003145 (pPECL-8) [66]
• Staphylococcus aureus M013, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003166","term_id":"359829121","term_text":"CP003166"}}CP003166 [67]
• Staphylococcus aureus subsp. aureus TW20, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FN433596","term_id":"269939526","term_text":"FN433596"}}FN433596 [68]
• Weissella confusa LBAE C39-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGH00000000","term_id":"365549261","term_text":"CAGH00000000"}}CAGH00000000 [69]

Phylum Actinobacteria

• Corynebacterium casei, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAFW01000001 to CAFW01000106","start_term":"CAFW01000001","end_term":"CAFW01000106","start_term_id":"356609265","end_term_id":"356606462"}}CAFW01000001 to CAFW01000106 [70]
• Corynebacterium glutamicum, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQQ00000000","term_id":"658109743","term_text":"AGQQ00000000"}}AGQQ00000000 [71]
• Leucobacter chromiiresistens, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGCW00000000","term_id":"353529976","term_text":"AGCW00000000"}}AGCW00000000 [72]
• Mycobacterium abscessus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQU00000000","term_id":"353453148","term_text":"AGQU00000000"}}AGQU00000000 [73]
• Propionibacterium acnes ST9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003195","term_id":"365742920","term_text":"CP003195"}}CP003195 [74]
• Propionibacterium acnes ST22, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003196","term_id":"365740656","term_text":"CP003196"}}CP003196 [74]
• Propionibacterium acnes ST27, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003197","term_id":"365738411","term_text":"CP003197"}}CP003197 [74]
• Saccharomonospora azurea SZMC 14600, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBX00000000","term_id":"359740650","term_text":"AHBX00000000"}}AHBX00000000 [75]
• Streptomyces sp. Strain TOR3209, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGNH00000000","term_id":"359357427","term_text":"AGNH00000000"}}AGNH00000000 [76]
• Streptomyces sp. Strain W007, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSW00000000","term_id":"364010697","term_text":"AGSW00000000"}}AGSW00000000 [77]

Phylum Spirochaetes

• Borrelia valaisiana VS116, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABCY02000001","term_id":"224510974","term_text":"ABCY02000001"}}ABCY02000001 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001439","term_id":"224497263","term_text":"CP001439"}}CP001439 (plasmid Ip17), {"type":"entrez-nucleotide","attrs":{"text":"CP001437","term_id":"224497187","term_text":"CP001437"}}CP001437 (Ip25), {"type":"entrez-nucleotide","attrs":{"text":"CP001440","term_id":"224497290","term_text":"CP001440"}}CP001440 (plasmid Ip 28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP001442","term_id":"224497476","term_text":"CP001442"}}CP001442 (plasmid Ip28-8), {"type":"entrez-nucleotide","attrs":{"text":"CP001436","term_id":"224497148","term_text":"CP001436"}}CP001436 (Ip 36), {"type":"entrez-nucleotide","attrs":{"text":"CP001433","term_id":"224496993","term_text":"CP001433"}}CP001433 (plasmid Ip 54), {"type":"entrez-nucleotide","attrs":{"text":"CP001438","term_id":"224497250","term_text":"CP001438"}}CP001438 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP001432","term_id":"224496964","term_text":"CP001432"}}CP001432 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"CP001441","term_id":"224497433","term_text":"CP001441"}}CP001441 (plasmid cp32-5), {"type":"entrez-nucleotide","attrs":{"text":"CP001434","term_id":"224497064","term_text":"CP001434"}}CP001434 (plasmid cp32-7), {"type":"entrez-nucleotide","attrs":{"text":"CP001435","term_id":"224497109","term_text":"CP001435"}}CP001435 (plasmid cp32-10) [78]
• “Borrelia bissettii” DN127, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002746","term_id":"342222012","term_text":"CP002746"}}CP002746 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002756","term_id":"342223236","term_text":"CP002756"}}CP002756 (plasmid Ip12), {"type":"entrez-nucleotide","attrs":{"text":"CP002757","term_id":"342223270","term_text":"CP002757"}}CP002757 (plasmid Ip25), {"type":"entrez-nucleotide","attrs":{"text":"CP002758","term_id":"342223295","term_text":"CP002758"}}CP002758 (plasmid 28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP002759","term_id":"342223320","term_text":"CP002759"}}CP002759 (plasmid Ip 28-4), {"type":"entrez-nucleotide","attrs":{"text":"CP002760","term_id":"342223351","term_text":"CP002760"}}CP002760 (Ip28-7), {"type":"entrez-nucleotide","attrs":{"text":"CP002761","term_id":"342223388","term_text":"CP002761"}}CP002761 (plasmid Ip54), {"type":"entrez-nucleotide","attrs":{"text":"CP002762","term_id":"342223459","term_text":"CP002762"}}CP002762 (plasmid Ip56), {"type":"entrez-nucleotide","attrs":{"text":"CP002755","term_id":"342223223","term_text":"CP002755"}}CP002755 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP002747","term_id":"342222829","term_text":"CP002747"}}CP002747 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"CP002749","term_id":"342222904","term_text":"CP002749"}}CP002749 (plasmid cp32-3), {"type":"entrez-nucleotide","attrs":{"text":"CP002750","term_id":"342222947","term_text":"CP002750"}}CP002750 (plasmid cp32-4), {"type":"entrez-nucleotide","attrs":{"text":"CP002751","term_id":"342222990","term_text":"CP002751"}}CP002751 (plasmid 32-5), {"type":"entrez-nucleotide","attrs":{"text":"CP002752","term_id":"342223034","term_text":"CP002752"}}CP002752 (plasmid cp32-6), {"type":"entrez-nucleotide","attrs":{"text":"CP002753","term_id":"342223077","term_text":"CP002753"}}CP002753 (plasmid cp32-7), CP0027554 (plasmid cp32-9), {"type":"entrez-nucleotide","attrs":{"text":"CP002748","term_id":"342222857","term_text":"CP002748"}}CP002748 (plasmid cp32-11) [78]
• Borrelia spielmanii A14S, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000001","term_id":"224514548","term_text":"ABKB02000001"}}ABKB02000001 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001468","term_id":"224497637","term_text":"CP001468"}}CP001468 (plasmid Ip17), {"type":"entrez-nucleotide","attrs":{"text":"CP001471","term_id":"224497796","term_text":"CP001471"}}CP001471 (Ip28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP001470","term_id":"224497745","term_text":"CP001470"}}CP001470 (plasmid Ip28-4), {"type":"entrez-nucleotide","attrs":{"text":"CP001465","term_id":"224497532","term_text":"CP001465"}}CP001465 (plasmid Ip28-2), {"type":"entrez-nucleotide","attrs":{"text":"CP001466","term_id":"224497566","term_text":"CP001466"}}CP001466 (plasmid Ip36), {"type":"entrez-nucleotide","attrs":{"text":"CP001464","term_id":"224497496","term_text":"CP001464"}}CP001464 (plasmid Ip38), {"type":"entrez-nucleotide","attrs":{"text":"CP001469","term_id":"224497671","term_text":"CP001469"}}CP001469 (plasmid Ip54), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000016","term_id":"224513758","term_text":"ABKB02000016"}}ABKB02000016, {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000020","term_id":"224513743","term_text":"ABKB02000020"}}ABKB02000020 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP001467","term_id":"224497607","term_text":"CP001467"}}CP001467 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000026","term_id":"224513697","term_text":"ABKB02000026"}}ABKB02000026 (plasmid cp32-3), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000031","term_id":"224513641","term_text":"ABKB02000031"}}ABKB02000031 (plasmid 32-5), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000021","term_id":"224513736","term_text":"ABKB02000021"}}ABKB02000021 (plasmid cp32-12), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000014","term_id":"224513768","term_text":"ABKB02000014"}}ABKB02000014 (unidentified) [78]

Non-Bacterial genomes

• Aspergillus flavus, sequence accession {"type":"entrez-geo","attrs":{"text":"GSE32177","term_id":"32177"}}GSE32177 [79]
• Bacteriophage SPN3UB, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ288021","term_id":"378408798","term_text":"JQ288021"}}JQ288021 [80]
• Bamboo mitochondria, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"JQ235166 to JQ235179","start_term":"JQ235166","end_term":"JQ235179","start_term_id":"372861916","end_term_id":"372861969"}}JQ235166 to JQ235179 [81]
• Boea hygrometrica chloroplast, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN107811","term_id":"340549387","term_text":"JN107811"}}JN107811 [82]
• Boea hygrometrica mitochondrial, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN107812","term_id":"340549473","term_text":"JN107812"}}JN107812 [82]
• Canine Picornavirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN831356","term_id":"377826518","term_text":"JN831356"}}JN831356 [83]
• Chandipura virus (CHPV) CIN0327, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212856.1","term_id":"309261828","term_text":"GU212856.1"}}GU212856.1 [84]
• Chandipura virus (CHPV) CIN0451, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212857.1","term_id":"309261834","term_text":"GU212857.1"}}GU212857.1 [84]
• Chandipura virus (CHPV) CIN0751, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212858.1","term_id":"309261840","term_text":"GU212858.1"}}GU212858.1 [84]
• Chandipura virus (CHPV) CIN0755, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU190711.1","term_id":"309099431","term_text":"GU190711.1"}}GU190711.1 [84]
• Chinese Porcine Parvovirus Strain PPV2010, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN872448","term_id":"374676766","term_text":"JN872448"}}JN872448 [85]
• Common midwife toad megavirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ231222","term_id":"375281729","term_text":"JQ231222"}}JQ231222 [86]
• Dengue Virus Serotype 4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN983813","term_id":"372290533","term_text":"JN983813"}}JN983813 [87]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF270480","term_id":"367465451","term_text":"JF270480"}}JF270480 [88]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ314464","term_id":"377824036","term_text":"JQ314464"}}JQ314464 [88]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ314465","term_id":"377824038","term_text":"JQ314465"}}JQ314465 [88]
• Emiliania huxleyi Virus 202, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HQ634145","term_id":"356927554","term_text":"HQ634145"}}HQ634145 [89]
• Emiliania huxleyi Virus EhV-88, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974310","term_id":"347600450","term_text":"JF974310"}}JF974310 [89]
• Emiliania huxleyi EhV-201, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974311","term_id":"357972615","term_text":"JF974311"}}JF974311 [89]
• Emiliania huxleyi EhV-207, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974317","term_id":"347600924","term_text":"JF974317"}}JF974317 [89]
• Emiliania huxleyi EhV-208, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974318","term_id":"347601393","term_text":"JF974318"}}JF974318 [89]
• Glarea lozoyensis, sequence accession GUE00000000 [90]
• Nannochloropis gaditana, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGNI00000000","term_id":"366047505","term_text":"AGNI00000000"}}AGNI00000000 [91]
• Oryza sativa cv., sequence accession DRA000499 [92]
• Partetravirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN990269","term_id":"374718987","term_text":"JN990269"}}JN990269 [93]
• Porcine Bocavirus PBoV5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN831651","term_id":"371449604","term_text":"JN831651"}}JN831651 [94]
• Porcine epidemic diarrhea virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ282909","term_id":"377824029","term_text":"JQ282909"}}JQ282909 [95]
• Pseudomonas aeruginosa lytic bacteriophage PA1Ø, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HM624080","term_id":"315418954","term_text":"HM624080"}}HM624080 [96]
• Pseudomonas fluorescens phage OBP, sequence accesssion {"type":"entrez-nucleotide","attrs":{"text":"JN627160","term_id":"359842892","term_text":"JN627160"}}JN627160 [97]
• RNA Virus from Avocado, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN880414","term_id":"371444768","term_text":"JN880414"}}JN880414 [98]
• Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN391180","term_id":"370344404","term_text":"JN391180"}}JN391180 [99]
• Schistosoma haematobium, sequence accession PRJNA78265 [100]
• Schistosoma mansoni, sequence accession {"type":"entrez-protein","attrs":{"text":"ERP00038","term_id":"550209647","term_text":"ERP00038"}}ERP00038 [101]
• Stenopirates sp., sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN100019","term_id":"340008214","term_text":"JN100019"}}JN100019 [102]
• T7-Like Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN651747","term_id":"374713556","term_text":"JN651747"}}JN651747 [103]
• Vibrio harveyi siphophage VHS1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF713456","term_id":"334898816","term_text":"JF713456"}}JF713456 [104]
• Tyrolean ice man, sequence accession ERP001144 [105]

     

Genomic Basis of a Polyagglutinating Isolate of Neisseria meningitidis

Containment strategies for outbreaks of invasive Neisseria meningitidis disease are informed by serogroup assays that characterize the polysaccharide capsule. We sought to uncover the genomic basis of conflicting serogroup assay results for an isolate ({"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917) from a patient with acute meningococcal disease. To this end, we characterized the complete genome sequence of the {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917 isolate and performed a variety of comparative sequence analyses against N. meningitidis reference genome sequences of known serogroups. Multilocus sequence typing and whole-genome sequence comparison revealed that {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917 is a member of the ST-11 sequence group, which is most often associated with serogroup C. However, sequence similarity comparisons and phylogenetic analysis showed that the serogroup diagnostic capsule polymerase gene (synD) of {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917 belongs to serogroup B. These results suggest that a capsule-switching event occurred based on homologous recombination at or around the capsule locus of {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917. Detailed analysis of this locus uncovered the locations of recombination breakpoints in the {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917 genome sequence, which led to the introduction of an ∼2-kb serogroup B sequence cassette into the serogroup C genomic background. Since there is no currently available vaccine for serogroup B strains of N. meningitidis, this kind capsule-switching event could have public health relevance as a vaccine escape mutant.     

Construction of immune-related LncRNAs classifier to predict prognosis and immunotherapy response in thymic epithelial tumors

The primary objective of this study was to construct an immune-related long noncoding RNAs (IRLs) classifier to precisely predict the prognosis and immunotherapy response of patients with thymic epithelial tumors (TET). Based on univariable Cox regression analysis and Lasso regression, six prognosis-related IRLs (AC004466.3, {"type":"entrez-nucleotide","attrs":{"text":"AC138207.2","term_id":"29165571","term_text":"AC138207.2"}}AC138207.2, {"type":"entrez-nucleotide","attrs":{"text":"AC148477.2","term_id":"45504179","term_text":"AC148477.2"}}AC148477.2, {"type":"entrez-nucleotide","attrs":{"text":"AL450270.1","term_id":"11244554","term_text":"AL450270.1"}}AL450270.1, HOXB-AS1 and SNHG8) were selected to build an IRL classifier. Importantly, results of qRT-PCR validated that higher expression levels of {"type":"entrez-nucleotide","attrs":{"text":"AC138207.2","term_id":"29165571","term_text":"AC138207.2"}}AC138207.2, {"type":"entrez-nucleotide","attrs":{"text":"AC148477.2","term_id":"45504179","term_text":"AC148477.2"}}AC148477.2, {"type":"entrez-nucleotide","attrs":{"text":"AL450270.1","term_id":"11244554","term_text":"AL450270.1"}}AL450270.1 and SNHG8 as well as lower expression levels of AC004466.3, and HOXB-AS1 in TETs samples compared with normal controls. The IRL classifier could effectively classify patients into the low-risk and high-risk groups based on the different survival parameters. In terms of predictive ability and clinical utility, the IRL classifier was superior to Masaoka staging system. Additionally, IRL classifier is significantly associated with immune cells infiltration (dendritic cells, activated CD4 memory T cells and tumor-infiltrating lymphocyte (TIL), T cell subsets in particular), immune microenvironment (immune score and immune checkpoint inhibitors) and immunogenicity (TMB) in TETs, which hints that IRL classifier is tightly correlated with immune characteristics and might guide more effective immunotherapy strategies for TETs patients. Encouragingly, according to TIDE algorithm, there were more immunotherapy responders in the low-risk IRL subgroup and the IRL score was robustly negatively linked to the immunotherapeutic response. To sum up, the IRL classifier was established, which can be used to predict the prognosis, immune infiltration status, immunotherapy response in TETs patients, and may facilitate personalized counseling for immunotherapy.