The complete mitogenome of Bombyx mori strain Dazao (Lepidoptera: Bombycidae) and comparison with other lepidopteran insects

The complete mitochondrial genome (mitogenome) of Bombyx mori strain Dazao (Lepidoptera: Bombycidae) was determined to be 15,653 bp, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a A + T-rich region. It has the typical gene organization and order of mitogenomes from lepidopteran insects. The AT skew of this mitogenome was slightly positive and the nucleotide composition was also biased toward A + T nucleotides (81.31%). All PCGs were initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which was initiated by CGA. The cox1 and cox2 genes had incomplete stop codons consisting of just a T. All the tRNA genes displayed a typical clover-leaf structure of mitochondrial tRNA. The A + T-rich region of the mitogenome was 495 bp in length and consisted of several features common to the lepidopteras. Phylogenetic analysis showed that the B. mori Dazao was close to Bombycidae.     

Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: An ultra-large metazoan mitochondrial genome

The complete mitochondrial (mt) genome of the ark shell Scapharca broughtonii was determined using long PCR and a genome walking sequencing strategy with genus-specific primers. The S. broughtonii mt genome (GenBank accession number AB729113) contained 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 2 ribosomal RNA genes, and 42 transfer tRNA genes, in a length of 46,985 nucleotides for the size of mtDNA with only one copy of the heteroplasmic tandem repeat (HTR) unit. Moreover the S. broughtonii mt genome shows size variation; these genomes ranged in size from about 47 kb to about 50 kb because of variation in the number of repeat sequences in the non-coding region. The mt-genome of S. broughtonii is, to date, the longest reported metazoan mtDNA sequence. Sequence duplication in non-coding region and the formation of HTR arrays were two of the factors responsible for the ultra-large size of this mt genome. All the tRNA genes were found within the S. broughtonii mt genome, unlike the other bivalves usually lacking one or more tRNA genes. Twelve additional specimens were used to analyze the patterns of tandem repeat arrays by PCR amplification and agarose electrophoresis. Each of the 12 specimens displayed extensive heteroplasmy and had 8–10 length variants. The motifs of the HTR arrays are about 353–362 bp and the number of repeats ranges from 1 to 11.     

Characterisation of the complete mitochondrial genome of Helice wuana (Grapsoidea: Varunidae) and comparison with other Brachyuran crabs

The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterised the mitogenome of the crab Helice wuana to better understand its molecular evolution and phylogeny. The 16,359 bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The genome composition is highly A + T biased 68.42%, and exhibits a negative AT–skew (? 0.036) and GC–skew (? 0.269) among Brachyura crabs. Gene rearrangements were detected, as was tandem duplication followed by random loss, which explains the translocation of mitochondrial genes. Phylogenetic analysis showed that H. wuana and H. tientsinensis clustered on one branch with high nodal support values. These results confirm that the placement of H. wuana within the Varunidae family of Thoracotrematan crabs. This study will provided a better understanding for gene rearrangements and crab evolution in the further.     

Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections

The scabies mite, Sarcoptes scabiei, is an obligate parasite of the skin that infects humans and other animal species, causing scabies, a contagious disease characterized by extreme itching. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where co-infection of epidermal scabies lesions by Group A Streptococci or Staphylococcus aureus is thought to be responsible for the high rate of rheumatic heart disease and chronic kidney disease. We collected and separately sequenced mite DNA from several pools of thousands of whole mites from a porcine model of scabies (S. scabiei var. suis) and two human patients (S. scabiei var. hominis) living in different regions of northern Australia. Our sequencing samples the mite and its metagenome, including the mite gut flora and the wound micro-environment. Here, we describe the mitochondrial genome of the scabies mite. We developed a new de novo assembly pipeline based on a bait-and-reassemble strategy, which produced a 14 kilobase mitochondrial genome sequence assembly. We also annotated 35 genes and have compared these to other Acari mites. We identified single nucleotide polymorphisms (SNPs) and used these to infer the presence of six haplogroups in our samples, Remarkably, these fall into two closely-related clades with one clade including both human and pig varieties. This supports earlier findings that only limited genetic differences may separate some human and animal varieties, and raises the possibility of cross-host infections. Finally, we used these mitochondrial haplotypes to show that the genetic diversity of individual infections is typically small with 1–3 distinct haplotypes per infestation.     

Complete nucleotide sequence and organization of the mitochondrial genome of eri-silkworm,Samia cynthia ricini (Lepidoptera: Saturniidae)

Samia cynthia ricini is a commercial silk-producing insect that is now reared year-round in Korea, with the expectation of being utilized for diverse purposes. In this report, we present the complete mitochondrial genome (mitogenome) of S. c. ricini. The 15,384-bp long S. cynthia ricini mitogenome was amplified into 26 short fragments using three long overlapping fragments using primers designed from reported lepidopteran mitogenome sequences. The genome comprises 37 genes (13 protein-coding genes, two rRNA genes, and 22 tRNA genes), and one large non-coding region termed the A + T-rich region. The A/T content of the third codon position was 91.7%, which was 18.8% and 21.6% higher than those of first and second codon positions, respectively. The high A/T content in the genome is reflected in codon usage, accounting for 39.5% of A/T-composed codons (TTA, ATT, TTT, and ATA). Unlike a previous report on the start codon for the COI gene, the S. c. ricini COI gene commences with a typical ATT codon. A total of 221 bp of non-coding sequences are dispersed in 17 regions, ranging in size from 1 to 54 bp, which comprise 1.4% of the total genome. One of the non-coding sequence located between tRNA^Gln and ND2 (54 bp) has 77% sequence homology with the 5′-sequence of the neighboring ND2 gene, suggesting partial duplication of the sequence during evolution. The 361-bp long A + T-rich region contains an 18 bp-long poly-T stretch, ATAGA motif, ATTTA element, microsatellite-like A/T sequence, poly-A stretch and one tRNA-like sequence, as typically found in Lepidoptera including Bombycoidea.     

The complete mitochondrial genome and phylogenetic analysis of Nyctereutes procyonoides

The complete mitochondrial genome sequence of the raccoon dog (Nyctereutes procyonoides) was determined by using the long and accurate polymerase chain reaction. The entire mitochondrial genome sequence is 16,713 bp in length contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 control region. Most mitochondrial genes are encoded on the H strand, except for the ND6 gene and 8 tRNA genes. The base compositions of mitochondrial genomes present clearly A–T skew. All the transfer RNA genes can be folded into the typical cloverleaf-shaped structure except tRNA-Ser (AGY), which lacks the dihydrouridine arm. Protein-coding genes mainly initiate with ATG and terminate with TAA. Some reading frame intervals and overlaps are found in the mitochondrial genome. The control region can be divided into three domains: the extended termination associated sequences (ETASs) domain, the central conserved domain and the conserved sequence blocks (CSBs) domain. Three conserved sequence blocks (CSBs) and one extended termination associated sequences (ETAS-1) is found in the control region. The phylogenetic analysis based on the concatenated data set of 14 genes in the mitochondrial genome of Canidae shows that the raccoon dog has close phylogenetic position with the red fox (Vulpes vulpes) and they constitute a clade which has an equil evolutionary position with the clade formed by the genera Canis and Cuon.     

Complete mitochondrial genome of Coelomactra antiquata (Mollusca: Bivalvia): The first representative from the family Mactridae with novel gene order and unusual tandem repeats

The complete mitochondrial genome plays an important role in the accurate inference of phylogenetic relationships among metazoans. Mactridae, also known as trough shells or duck clams, is an important family of marine bivalve clams in the order Veneroida. Here we present the complete mitochondrial genome sequence of the Xishishe Coelomactra antiquata (Mollusca: Bivalvia), which is the first representative from the family Mactridae. The mitochondrial genome of C. antiquata is of 17,384 bp in length, and encodes 35 genes, including 12 protein-coding, 21 transfer RNA, and 2 ribosomal RNA genes. Compared with the typical gene content of animal mitochondrial genomes, atp8 and tRNAS₂ are missing. Gene order of the mitochondrial genome of C. antiquata is unique compared with others from Veneroida. In the mitochondrial genome of the C. antiquata, a total of 2189 bp of non-coding nucleotides are scattered among 26 non-coding regions. The largest non-coding region contains one section of tandem repeats (99 bp × 11), which is the second largest tandem repeats found in the mitochondrial genomes from Veneroida. The phylogenetic trees based on mitochondrial genomes support the monophyly of Veneridae and Lucinidae, and the relationship at the family level: ((Veneridae + Mactridae) + (Cardiidae + Solecurtidae)) + Lucinidae. The phylogenetic result is consistent with the morphological classification. Meanwhile, bootstrap values are very high (BP = 94–100), suggesting that the evolutionary relationship based on mitochondrial genomes is very reliable.     

Preliminary Molecular Characterizations of Sarcoptes scaibiei (Acari: Sarcoptidae) from Farm Animals in Egypt

Little is known about the genetic diversity of Sarcoptes scabiei mites in farm animals in Egypt. In this study, we characterized S. scabiei in 25 skin scrapes from water buffalo, cattle, sheep, and rabbits at the nuclear marker ITS2 and mitochondrial markers COX1 and 16S rRNA. Sequences of the ITS2 showed no host segregation or geographical isolation, whereas those of the mitochondrial COX1 and 16S rRNA genes indicated the presence of both host-adapted and geographically segregated populations of S. scabiei. Host adaptation may limit inter-species transmission of. S. scabiei, thus restrict gene flow among S. scabiei from different hosts. This is the first report on the molecular characterization of sarcoptic mites in Egypt. Further genetic studies involving larger numbers of specimens, especially those from humans and companion animals, are needed to understand the molecular epidemiology of sarcoptic mange in Egypt.     

Complete mitochondrial genome of Odontobutis haifengensis (Perciformes,Odontobutiae): A unique rearrangement of tRNAs and additional non-coding regions identified in the genus Odontobutis

Herein, the complete mitochondrial genome of Odontobutis haifengensis was sequenced for the first time. The O. haifengensis mitogenome was 17,016 bp in length and included 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The genome organization, base composition, codon usage, and gene rearrangement was similar to other Odontobutis species. Furthermore, a tRNA gene rearrangement within the SLH cluster was found to be identical to other Odontobutis species. Moreover, the gene order and the positions of additional intergenic non-coding regions suggests that the observed unique gene rearrangement resulted from a tandem duplication and random loss of large-scale gene regions. Additionally, phylogenetic analysis showed that Odontobutis species form a monophyletic clade due to the conserved mitochondrial gene rearrangement. This study provides useful information that aids in a better understanding of mitogenomic diversity and evolutionary patterns of Odontobutidae species.     

Life history parameters of a commercially available Amblyseius swirskii (Acari: Phytoseiidae) fed on cattail (Typha latifolia) pollen and tomato russet mite (Aculops lycopersici)

Development, oviposition, and survival of a commercially available predatory mite, Amblyseius swirskii (Athias-Henriot), were investigated to determine the life history parameters when they consumed a diet of cattail (Typha latifolia L.) pollen or tomato russet mites (Aculops lycopersici [Massee]) at 25 ± 0.5 °C and 70 ± 10% RH. Both diets were favorable for development, oviposition, and survival of A. swirskii. Amblyseius swirskii reared on mite prey showed improved performance as compared to pollen. Females laid a total of 26.8 and 38.1 eggs on the pollen and mite diets, respectively. The mortality of female A. swirskii was very low during the first 20 days on both diets, and the cumulative Weibull models that were used to describe age-specific survival and fecundity of female showed a good fit to the data. The net reproductive rate (R₀), intrinsic rate of increase (r_m), and finite rate of increase (λ) of A. swirskii were higher on russet mites than when fed on the pollen diet due to their shorter immature development period and higher oviposition rate. The intrinsic rate of increase (r_m) of the predatory mite was 0.185 and 0.201 on the pollen and mite diet, respectively. The mean generation time (T) and the population doubling time (D_t) were not significantly different for A. swirskii on the two diets. Our results provide life history information for a commercially available A. swirskii using two favorable diets and can be used to compare population growth under other diet sources.     

Complete mitochondrial genome of Membranipora grandicella (Bryozoa: Cheilostomatida) determined with next-generation sequencing: The first representative of the suborder Malacostegina

Next-generation sequencing (NGS) has proven a valuable platform for fast and easy obtaining of large numbers of sequences at relatively low cost. In this study we use shot-gun sequencing method on Illumina HiSeq 2000, to obtain enough sequences for the assembly of the bryozoan Membranipora grandicella (Bryozoa: Cheilostomatida) mitochondrial genome, which is the first representative of the suborder Malacostegina. The complete mitochondrial genome is 15,861 bp in length, which is relatively larger than other studied bryozoans. The mitochondrial genome contains 13 protein-coding genes, 2 ribosomal RNAs and 20 transfer RNAs. To investigate the phylogenetic position and the inner relationships of the phylum Bryozoa, phylogenetic trees were constructed with amino acid sequences of 11 PCGs from 30 metazoans. Two superclades of protostomes, namely Lophotrochozoa and Ecdysozoa, are recovered as monophyletic with strong support in both ML and Bayesian analyses. Somewhat to surprise, Bryozoa appears as the sister group of Chaetognatha with moderate or high support. The relationship among five bryozoans is Tubulipora flabellaris + (M. grandicella + (Flustrellidra hispida + (Bugula neritina + Watersipora subtorquata))), which supports for the view that Cheilostomatida is not a natural, monophyletic clade. NGS proved to be a quick and easy method for sequencing a complete mitochondrial genome.     

Description of complete mitochondrial genome of the black-veined white,Aporia crataegi (Lepidoptera: Papilionoidea), and comparison to papilionoid species

The black-veined white, Aporia crataegi (Lepidoptera: Papilionoidea) is nearly extinct in South Korea, although substantial numbers of dried specimens are available. One of the common practices used to rescue such endangered species is to launch a re-introduction program after a proper amount of genetic information is analyzed from donor and donee populations. In this study, we sequenced the complete mitochondrial genome (mitogenome) of A. crataegi to accumulate genetic information for subsequent population studies and to further understand the mitogenome evolution in true butterflies, Papilionoidea. The 15,140-bp long A. crataegi mitogenome has typical sets of 37 genes and is the smallest among the true butterfly species, with overall slightly smaller size genes and regions throughout the genome. The A/T content of the genome (81.3%) is the highest in Pieridae, where A. crataegi belongs, but lower than that of the lycaenid species (81.7%–82.7%). Unlike the diversified or modified usage of an anticodon for tRNA^Ser(AGN), the species of Pieridae including A. crataegi all contain GCT that has been hypothesized as being ancestral for Lepidoptera. A total of 111 bp of non-coding sequences are interspersed in 13 regions, ranging in size from 1–49 bp. Among these sequences, relatively longer ones (≥ 16 bp) all have relatively higher sequence identity to other regions of the genome, suggesting partial duplication of the sequences during A. crataegi evolution.     

Genetic variability of wildlife-derived <Emphasis Type="Italic">Sarcoptes scabiei</Emphasis> determined by the ribosomal ITS-2 and mitochondrial 16S genes

Infestation by the ectoparasitic mite Sarcoptes scabiei (Acari: Sarcoptidae) has important implications for global wildlife conservation and both animal and human health. Ribosomal and mitochondrial DNA sequences of parasites are useful to determine genetic diversity and to describe their likely dynamic evolution. In this study, we described the genetic diversity of S. scabiei individuals collected from wild animals in China by sequencing the ribosomal ITS-2 and mitochondrial 16S rRNA genes. A total of 13 Sarcoptes isolates of wildlife, coupled with one of rabbit origin, were subjected to genetic characteristics. After cloning and sequencing, 14 ITS-2 sequences and 12 16S rRNA sequences were obtained and analyzed. Further analysis of haplotype network and population genetic structure revealed that there were 79 haplotypes in ITS-2 (main haplotype H2) and 31 haplotypes in 16S rRNA (main haplotype C10). The phylogenetic trees showed some partial clustering by location and host, and the analysis of gene polymorphism may prompt that all isolates of S. scabiei have a similar origin. We speculate that the genetic evolution of S. scabiei may be related with that of the hosts, but more research is necessary to better understand the host-parasite co-evolutionary relationship in S. scabiei. These results provide new insights into understanding the population genetics and evolutionary biology of S. scabiei and therefore a better understanding of controlling its infestation pathways worldwide.     

Pseudomonas silesiensis sp. nov. strain A3T isolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence

Microorganisms classified in to the Pseudomonas genus are a ubiquitous bacteria inhabiting variety of environmental niches and have been isolated from soil, sediment, water and different parts of higher organisms (plants and animals). Members of this genus are known for their metabolic versatility and are able to utilize different chemical compounds as a source of carbon, nitrogen or phosphorus, which makes them an interesting microorganism for bioremediation or bio-transformation. Moreover, Pseudomonas sp. has been described as a microorganism that can easily adapt to new environmental conditions due to its resistance to the presence of high concentrations of heavy metals or chemical pollution. Here we present the isolation and analysis of Pseudomonas silesiensis sp. nov. strain A3^T isolated from peaty soil used in a biological wastewater treatment plant exploited by a pesticide packaging company. Phylogenetic MLSA analysis of 4 housekeeping genes (16S rRNA, gyrB, rpoD and rpoB), complete genome sequence comparison (ANIb, Tetranucleotide identity, digital DDH), FAME analysis, and other biochemical tests indicate the A3^T strain (type strain PCM 2856^T = DSM 103370^T) differs significantly from the closest relative species and therefore represents a new species within the Pseudomonas genus. Moreover, bioinformatic analysis of the complete sequenced genome showed that it consists of 6,823,539 bp with a 59.58 mol% G + C content and does not contain any additional plasmids. Genome annotation predicted the presence of 6066 genes, of which 5875 are coding proteins and 96 are RNA genes.     

Complete mitochondrial genome sequence of the Arctic gammarid,Onisimus nanseni (Crustacea; Amphipoda): Novel gene structures and unusual control region features

To analyze the mitogenome of the amphipod Onisimus nanseni, we amplified the complete mitogenome of O. nanseni using long-PCR and genome walking techniques. The mitogenome of O. nanseni is circular and contains all the typical mt genes (2 rRNAs, 22 tRNAs, and 13 protein-coding genes). It has two peculiar non-coding regions of 148 bp and 194 bp. The latter can be involved in replication and termination processes. The total length of the pooled protein-coding, rRNA, and tRNA genes is shorter than those of other crustaceans. In addition, the intergenic spacers of the O. nanseni mitogenome are considerably shorter in length than those of other crustaceans. Fourteen adjacent genes overlap, resulting in a compact mitogenomic structure. In the O. nanseni mitogenome, the AT composition is elevated, particularly in the control regions (78.9% AT), as has been demonstrated for two other amphipods. The tRNA order is highly rearranged compared to other arthropod mitogenomes, but the order of protein-coding genes and rRNAs is largely conserved. The gene cluster between the CO1 and CO3 genes is completely conserved among all amphipods compared. This provides insights into the evolution and gene structures of crustacean mitochondrial genomes, particularly in amphipods.     

Acaricidal properties of an Ailanthus altissima bark extract against Psoroptes cuniculi and Sarcoptes scabiei var. cuniculi in vitro

The potential acaricidal properties of an Ailanthus altissima bark extract were assessed against two common species of animal ectoparasitic mites, Psoroptes cuniculi and Sarcoptes scabiei var. cuniculi, in vitro. A. altissima bark extract was obtained by ethanol thermal circumfluence and tested at four concentrations (1.0, 0.5, 0.25 and 0.125 g/ml) on mites collected from rabbits. Compared to the fenvalerate treatment group, the A. altissima bark exhibited significant acaricidal properties for both mite species treated. The extract of concentrations of 1.0, 0.5 and 0.25 g/ml killed all tested S. scabiei within 7 h, however, only 1.0 and 0.5 g/ml of extract killed all treated P. cuniculi. The median lethal time (LT₅₀) values at 1, 0.5 and 0.25 g/ml were 0.60, 0.78, 1.48 h for S. scabiei and 0.74, 1.29, 3.33 h for P. cuniculi. The median lethal concentration (LC₅₀) for P. cuniculi was approximately 1.6 times that for S. scabiei var. cuniculi at 4 h. The extract showed stronger toxicity against S. scabiei than against P. cuniculi. Mortality rates increased with increasing concentration of extract administered and with increasing time post-treatment, indicating that the acaricidal activity of A. altissima bark extract is both time-dependent and dose-dependent. This is the first report on acaricidal activity of A. altissima against P. cuniculi and S. scabiei var. cuniculi. It indicates that A. altissima contain potential acaricidal compounds. Our study is the first step to develop potentially novel compounds from A. altissima for the effective control of mites in livestock.     

New nemadectin congeners with acaricidal and nematocidal activity from Streptomyces microflavus neau3 Y-3

Two nemadectin congeners 1 and 2 were isolated from the fermentation broth of a mutant strain (Y-3) of Streptomyces microflavus neau3. Their structures were determined on the basis of extensive spectroscopic analysis and comparison with data from the literature. Compound 2 possessed a 5-membered ring lactone that is unprecedented among known milbemycins and avermectins. Both compounds 1 and 2 exhibited potent acaricidal activity and nematocidal activity. Especially, compound 2 demonstrated impressive acaricidal activity against adult mites with an IC₅₀ of 2.3 ± 0.9 μg/mL and mite eggs with an IC₅₀ of 17.5 ± 2.1 μg/mL and nematocidal activity against Caenorhabditis elegans with an IC₅₀ of 0.7 ± 0.2 μg/mL, which are higher than those of nemadectin and the known commercial acaricide and nematocide milbemycin A3/A4.     

Comprehensive genomics and expression analysis of eceriferum (CER) genes in sunflower (Helianthus annuus)

Sunflower occupies the fourth position among oilseed crops the around the world. Eceriferum (CER) is an important gene family that plays critical role in very-long-chain fatty acids elongation and biosynthesis of epicuticular waxes under both biotic and abiotic stress conditions. The aim of present study was to investigate the effect of sunflower CER genes during drought stress condition. Thus, comparative analysis was undertaken for sunflower CER genes with Arabidopsis genome to determine phylogenetic relationship, chromosomal mapping, gene structures, gene ontology and conserved motifs. Furthermore, we subjected the sunflower cultivars under drought stress and used qRT-PCR analysis to explore the expression pattern of CER genes during drought conditions. We identified thirty-seven unevenly distributed CER genes in the sunflower genome. The phylogenetic analysis revealed that CER genes were grouped into seven clades in Arabidopsis, Helianthus annuus, and Gossypium hirsutum. Expression analysis showed that genes CER10 and CER60 were upregulated in sunflower during drought conditions, indicating that these genes are activated during drought stress. The results obtained will serve to characterize the CER gene family in sunflower and exploit the role of these genes in wax biosynthesis under limited water conditions.Key messageCuticular waxes protect the plants from drought stress, so we observed the expression of wax bio synthesis genes in recently sequences genome of Helianthus annuus. We observed that expression of wax biosynthesis genes CER10 and CER60 was upregulated when the plants were subjected to drought stress.