De novo sequencing and initial annotation of the Mongolian gerbil (Meriones unguiculatus) genome

The Mongolian gerbil (Meriones unguiculatus) is a member of the rodent family that displays several features not found in mice or rats, including sensory specializations and social patterns more similar to those in humans. These features have made gerbils a valuable animal for research studies of auditory and visual processing, brain development, learning and memory, and neurological disorders. Here, we report the whole gerbil annotated genome sequence, and identify important similarities and differences to the human and mouse genomes. We further analyze the chromosomal structure of eight genes with high relevance for controlling neural signaling and demonstrate a high degree of homology between these genes in mouse and gerbil. This homology increases the likelihood that individual genes can be rapidly identified in gerbil and used for genetic manipulations. The availability of the gerbil genome provides a foundation for advancing our knowledge towards understanding evolution, behavior and neural function in mammals.Accession numberThe Whole Genome Shotgun sequence data from this project has been deposited at DDBJ/ENA/GenBank under the accession NHTI00000000. The version described in this paper is version NHTI01000000. The fragment reads, and mate pair reads have been deposited in the Sequence Read Archive under BioSample accession SAMN06897401.     

Extensive Gene Order Rearrangement in the Mitochondrial Genome of the Centipede Scutigera coleoptrata

We describe the complete mitochondrial genome of the house centipede Scutigera coleoptrata. Its gene order is unique among characterized arthropod mitochondrial genomes. Comparison to the gene order in the horseshoe crab mtDNA implies 10 or more translocations. By extending comparisons to 30 arthropod mitochondrial genomes plus two outgroups, we identify two different patterns of gene order change. The first, only affecting position and orientation of tRNAs, is much more frequent than the second, which also involves protein encoding and ribosomal genes. The analysis of the same data set using available algorithms for phylogenetic reconstruction based on gene order results in unreliable trees. This indicates that the current methods for analyzing gene order rearrangement are not suitable for wide-ranging phylogenetic studies. Data deposition: The fully annotated mtDNA sequence of Scutigera coleoptrata is available at the DDBJ/GenBank/EBI Data Bank under accession number AJ507061.     

Rhodopirellula aestuarii sp. nov., a novel member of the genus Rhodopirellula isolated from brackish sediments collected in the Tagus River estuary,Portugal

Bacteria within the phylum Planctomycetota are biologically relevant due to unique characteristics among prokaryotes. Members of the genus Rhodopirellula can be abundant in marine habitats, however, only six species are currently validly described. In this study, we expand the explored genus diversity by formally describing a novel species. The pink-coloured strain ICT_H3.1^T was isolated from brackish sediments collected in the Tagus estuary (Portugal) and a 16S rRNA gene sequence-based analysis placed this strain into the genus Rhodopirellula (family Pirellulaceae). The closest type strain is Rhodopirellula rubra LF2^T, suggested by a similarity of 98.4% of the 16S rRNA gene sequence. Strain ICT_H3.1^T is heterotrophic, aerobic and able to grow under microaerobic conditions. The strain grows between 15 and 37 °C, over a range of pH 6.5 to 11.0 and from 1 to 8% (w/v) NaCl. Several nitrogen and carbon sources were utilized by the novel isolate. Cells have an elongated pear-shape with 2.0 ± 0.3 × 0.9 ± 0.2 µm in size. Cells of strain ICT_H3.1^T cluster in rosettes through a holdfast structure and divide by budding. Younger cells are motile. Ultrathin cell sections show cytoplasmic membrane invaginations and polar fimbriae. The genome size is 9,072,081 base pairs with a DNA G + C content of 56.1 mol%. Genomic, physiological and morphological comparison of strain ICT_H3.1^T with its relatives suggest that it belongs to a novel species within the genus Rhodopirellula. Hence, we propose the name Rhodopirellula aestuarii sp. nov., represented by ICT_H3.1^T (=CECT30431^T = LMG32464^T) as the type strain of this novel species.16S rRNA gene accession number: GenBank = OK001858.Genome accession number: The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAMQBK000000000. The version described in this paper is version JAMQBK010000000.     

Draft genome sequence of the human pathogen Streptomyces somaliensis, a significant cause of actinomycetoma

We report the draft genome sequence of the human pathogen Streptomyces somaliensis (DSM 40738), a pathogen within a genus of largely saprophytic organisms. S. somaliensis causes severe and debilitating deep tissue and bone infections. The genome sequence is deposited in DDBJ/EMBL/GenBank with the accession number AJJM01000000.     

Complete mitochondrial genome of Malaysian Mahseer (Tor tambroides)

This is the first documentation of the complete mitochondrial genome sequence of the Malaysian Mahseer, Tor tambroides. The 16,690 bp mitogenome with GenBank accession number JX444718 contains 13 protein genes, 22 tRNAs, two rRNAs, and a noncoding control region (D-loop) as is typical of most vertebrates. The phylogenomic reconstruction of this newly generated data with 21 Cypriniformes GenBank accession ID concurs with the recognized status of T. tambroides within the subfamily Cyprininae. This is in agreement with previous hypotheses based on morphological and partial mitochondrial analyses.     

Whole genome scan detects an allelic variant of <Emphasis Type="Italic">fad2</Emphasis> associated with increased oleic acid levels in maize

We used whole genome scan association mapping to identify loci with major effect on oleic acid content in maize kernels. Single nucleotide polymorphism haplotypes at 8,590 loci were tested for association with oleic acid content in 553 maize inbreds. A single locus with major effect on oleic acid was mapped between 380 and 384 cM in the IBM2 neighbors genetic map on chromosome 4 and confirmed in a biparental population. A fatty acid desaturase, fad2, identified ∼2 kb from the associated genetic marker, is the most likely candidate gene responsible for the differences in the phenotype. The fad2 alleles with high- and low-oleic acid content were sequenced and allelic differences in fad2 RNA level in developing embryos was investigated. We propose that a non-conservative amino acid polymorphism near the active site of fad2 contributes to the effect on oleic acid content. This is the first report of the use of a high resolution whole genome scan association mapping where a putative gene responsible for a quantitative trait was identified in plants. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number EF687907.     

Nucleotide sequence of the psaD gene from the thermophilic cyanobacterium Synechococcus vulcanus

The nucleotide sequence was determined for the psaD gene of a thermophilic cyanobacterium, Synechococcus vulcanus, which encoded the PsaD subunit (Subunit II) of the Photosystem I reaction center complex. Except for some differences in the peripherals, the nucleotide sequence of the gene encoding PsaD was identical to that of another thermophilic cyanobacterium Synechococcus elongatus reported previously. Relationship between these primary structures and thermostability was also discussed.Abbreviations ORF open reading frame - PS I Photosystem I - SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis This paper is dedicated to commemorate the late Professor D.I. Arnon with whom the senior author (T.H.) spent five years from 1974 to 1979 as his last postdoctoral fellow at the Department of Cell Physiology, University of California, Berkeley.The sequence data presented here have been submitted to DDBJ/EMBL/GenBank under the accession number D17355.     

Draft Genome Sequence of Corynebacterium diphtheriae Biovar Intermedius NCTC 5011

We report an annotated draft genome of the human pathogen Corynebacterium diphtheriae bv. intermedius NCTC 5011. This strain is the first C. diphtheriae bv. intermedius strain to be sequenced, and our results provide a useful comparison to the other primary disease-causing biovars, C. diphtheriae bv. gravis and C. diphtheriae bv. mitis. The sequence has been deposited at DDBJ/EMBL/GenBank with the accession number AJVH01000000.     

Genome analysis of <Emphasis Type="Italic">Acidiplasma</Emphasis> sp. MBA-1, a polyextremophilic archaeon predominant in the microbial community of a bioleaching reactor

Results of genome analysis of a member of the family Ferroplasmaceae, Acidiplasma sp. strain MBA-1, an extremely acidophilic, moderately thermophilic archaeon oxidizing ferrous iron under oxic conditions and utilizing organic compounds. This strain was previously shown to predominate in the community carrying out biooxidation of pyrite-arsenopyrite gold-bearing concentrate. The genome was sequenced using the Illumina HiSeq 2000 platform. A total of 2306800 pairwise reads were obtained, corresponding to 300-fold coverage. Assembly was carried out by three programs in parallel. The optimal assembly contained nine contigs, the genome size was 1747364 bp, and N50 was 446845 bp. Annotation of the genome revealed 1749 protein-encoding sequences, as well as 46 tRNA genes and one rRNA gene copy. The results of genome analysis confirmed the previous data on the physiology of this organism. The gene of sulfocyanin (TZ01_06185), a blue copper-containing protein playing the key role in the iron-oxidizing electron transport chain, was identified in the genome. The genes encoding sulfur oxidoreductase (TZ01_04750) and sulfateadenilyl transferase (TZ01_04545), the enzymes of sulfur oxidation, were also identified. The genes involved in the transport and catabolism of organic compounds and the genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle were revealed. The genome of Acidiplasma sp. MBA-1 is the first genome of this genus deposited to a public database DDBJ/EMBL/GenBank (accession no. JYHS00000000) and is of interest for further investigation of Acidiplasma archaea.     

The complete chloroplast genome of Origanum vulgare L. (Lamiaceae)

Oregano (Origanum vulgare L., Lamiaceae) is a medicinal and aromatic plant maybe best known for flavouring pizza. New applications e.g. as natural antioxidants for food are emerging due to the plants' high antibacterial and antioxidant activity. The complete chloroplast (cp) genome of Origanum vulgare (GenBank/EBML/DDBJ accession number: JX880022) consists of 151,935 bp and includes a pair of inverted repeats (IR) of 25,527 bp separated by one small and one large single copy region (SSC and LSC) of 17,745 and 83,136 bp, respectively.     

Cloning,characterization and localization of <Emphasis Type="Italic">CHS</Emphasis> gene from blood orange, <Emphasis Type="Italic">Citrus sinensis</Emphasis> (L.) Osbeck cv. Ruby

Chalcone synthase (CHS) is involved in the biosynthesis of anthocyanin. In this study, a full-length DNA of CHS gene (named as CsCHS-bo) was cloned from the blood orange, Citrus sinensis (L.) Osbeck cv. Ruby. The gene was 1,512 bp in size containing an open reading frame (1,176 bp) encoding 391 amino acids. Comparative and bioinformatic analyses revealed that the deduced protein of CsCHS-bo was highly homologous to CHS from other plant species. The protein of CsCHS-bo had four CHS-specific conserved motifs and a CHS-family signature sequence GFGPG. Phylogenetic analysis indicated that the protein of CsCHS-bo was in a subgroup with CHS of Ruta Palmatum. The CsCHS-bo was localized to the chromosomes 2p, 4p and 6p by an improved fluorescence in situ hybridization technique, indicating that at least three copies of CsCHS-bo were present in the genome. The novel nucleotide sequence data published here have been deposited in the EMBL/DDBJ/GenBank databases under accession number EU410483.     

Two new polymorphisms in introns 2 and 3 of the human porphobilinogen deaminase gene

Sequencing of the polymerase chain reaction amplified exon 2–4 fragment of the human porphobilinogen deaminase gene revealed a G/T polymorphism (I2G and I2T) in intron 2, and a G/A polymorphism (I3G and I3A) in intron 3 of the gene. The frequencies of these alleles are presented.The nucleotide sequence data reported in this paper (the sequence of introns 2 and 3, and the polymorphic sites) will appear in the DDBJ, EMBL, and GenBank Nucleotide Sequence Database with accession nos. D10608 and D12722     

Cloning and Characterization of the Wx Gene Encoding a Granule-Bound Starch Synthase in Lotus (Nelumbo nucifera Gaertn)

The granule-bound starch synthase (GBSS) proteins were widely considered as one of the most important enzymes in plant amylose synthesis. However, understanding of the molecular basis of the GBSS protein in lotus remains fragmented. In this work, a lotus Wx gene, encoding a GBSS (GenBank accession no. EU938541), was isolated and characterized. This gene comprises 13 exons and 12 introns and covers 4152?bp (GenBank accession no. FJ602702). The exons of Wx gene have similar lengths, while the introns vary greatly. Phylogenetic tree indicated that the lotus GBSS protein belongs to a GBSS I subgroup. The expression of the Wx gene varies in different organs of the lotus during its development process and is also expressed differently in different cultivars. The Wx gene is expressed at a higher level in the rhizomes of cultivar Meirenhong than in those of cultivar Elian 4. This study elucidates more molecular information about the Wx gene in lotus and provides a theoretical foundation for the genes regulation and the modification of starch quality.     

Sequence of a cDNA encoding nitrite reductase from the tree Betula pendula and identification of conserved protein regions

Summary The sequence of an mRNA encoding nitrite reductase (NiR, EC 1.7.7.1.) from the tree Betula pendula was determined. A cDNA library constructed from leaf poly(A)⁺ mRNA was screened with an oligonucleotide probe deduced from NiR sequences from spinach and maize. A 2.5 kb cDNA was isolated that hybridized to an mRNA, the steady-state level of which increased markedly upon induction with nitrate. The nucleotide sequence of the cDNA contains a reading frame encoding a protein of 583 amino acids that reveals 79% identity with NiR from spinach. The transit peptide of the NiR precursor from birch was determined to be 22 amino acids in size by sequence comparison with NiR from spinach and maize and is the shortest transit peptide reported so far. A graphical evaluation of identities found in the NiR sequence alignment revealed nine well conserved sections each exceeding ten amino acids in size. Sequence comparisons with related redox proteins identified essential residues involved in cofactor binding. A putative binding site for ferredoxin was found in the N-terminal half of the protein.These sequence data appear in the EMBL/GenBank/DDBJ nucleotide sequence data bases under the accession number X60093     

cDNA cloning and expression analysis of a putative alternative oxidase HsAOX1 from wild barley (Hordeum spontaneum)

A novel alternative oxidase (AOX1) gene, designated HsAOX1 (GenBank accession number JF440341) was cloned by RT-PCR from wild barley (Hordeum spontaneum). The full length of HsAOX1 is 1115 bp with an open reading frame of 987 bp, encoding a protein of 328 amino acids with molecular weight of 36.89 kDa and a theoretical isoelectric point of 6.81. As found in other plant AOX1 proteins, sequence alignment showed that HsAOX1 had conserved metal binding and hydrophobic ??-helix regions and had high homology to other AOX1 in plants. The expression analysis by semi-quantitative RT-PCR revealed that HsAOX1 was induced in response to cold stress, H₂O₂ treatment, SA, antimycin A and KCN. These results showed that HsAOX1 functions not only during inhibition of cytochrome electron transport but also during oxidative stresses, thus suggesting a role of HsAOX1 in preventing the generation of free radicals by the mitochondrial electron transport chain. The cloning and characterization of the HsAOX1 gene will be useful for further studies of biological roles of HsAOX1 in plants.