Journal of Genomics最新文献

Modern medicine is unthinkable without antibiotics; yet, growing issues with microbial drug resistance require intensified search for new active compounds. Natural products generated by Actinobacteria have been a rich source of candidate antibiotics, for example anthracimycin that, so far, is only known to be produced by Streptomyces species. Based on sequence similarity with the respective biosynthetic cluster, we sifted through available microbial genome data with the goal to find alternative anthracimycin-producing organisms. In this work, we report about the prediction and experimental verification of the production of anthracimycin derivatives by Nocardiopsis kunsanensis, a non-Streptomyces actinobacterial microorganism. We discovered N. kunsanensis to predominantly produce a new anthracimycin derivative with methyl group at C-8 and none at C-2, labeled anthracimycin BII-2619, besides a minor amount of anthracimycin. It displays activity against Gram-positive bacteria with similar low level of mammalian cytotoxicity as that of anthracimycin.

The sex determination systems of fish are highly diverse compared with those of mammals. Thus, performing investigations using nonmodel fish species helps to understand the highly diverse sex determination systems of fish. Because greater amberjack (Seriola dumerili) is one of the most important edible fish globally and knowledge of its sex determination system is economically important in the field of aquaculture, we are interested in the mechanisms of sex determination of Seriola species. In this study, we identified sex-associated SNPs of greater amberjack using SNP information of 10 males and 10 females by an association test. We determined that the sex-associated SNPs were on chromosome 12 and mainly covered with two scaffolds (about 7.1 Mbp). Genotypes of sex-associated SNPs indicated that females are the heterogametic sex (ZZ/ZW). Furthermore, we compared the genomic structure of greater amberjack with those of Japanese amberjack (Seriola quinqueradiata), California yellowtail (Seriola dorsalis), and medaka (Oryzias latipes). Whole-genome alignments and synteny analysis indicated that the sex determination system of greater amberjack is markedly different from that of medaka and implied that the sex determination system is conserved in the Seriola species.

Rarity in reporting whole genome sequence of Dengue virus from dengue endemic countries leaves lacunae in understanding regional pattern of virus mutation and ultimately leading to non-understanding of transmission pattern and clinical outcomes emerging at regional levels. Due to inter-serotype genomic similarity and intra-serotype genomic diversity, appropriate designing of primer pairs appears as an exhaustive exercise. Present paper reports new Dengue virus type-specific primer which may help in characterizing virus specific to Asian origin. Genomes of dengue virus serotypes of Asian region were searched and using advanced bioinformatics tools, serotype specific primers were designed and tested for their targeted amplification efficiency. 19 primers sets for DENV-1, 18 primer sets for DENV-2, 17 for DENV-3 and 18 for DENV-4 were designed. In-silico and experimental testing of the designed primers were performed on virus isolated from both clinical isolates and passaged cultures. While all 17 and 18 primer sets of DENV-3 and DENV-2 respectively yielded good quality sequencing results; in case of DENV-4, 16 out of 18 primer sets and in DENV-1, 16 out of 19 primer sets yielded good results. Average sequencing read length was 382 bases and around 82% nucleotide bases were Phred quality QV20 bases (representing an accuracy of circa one miscall every 100 bases) or higher. Results also highlighted importance of use of primer development algorithm and identified genomic regions which are conservative, yet specific for developing primers to achieve efficiency and specificity during experiments.

Burying beetles (Nicrophorus spp.) are among the relatively few insects that provide parental care while not belonging to the eusocial insects such as ants or bees. This behavior incurs energy costs as evidenced by immune deficits and shorter life-spans in reproducing beetles. In the absence of an assembled transcriptome, relatively little is known concerning the molecular biology of these beetles. This work details the assembly and analysis of the Nicrophorus orbicollis transcriptome at multiple developmental stages. RNA-Seq reads were obtained by next-generation sequencing and the transcriptome was assembled using the Trinity assembler. Validation of the assembly was performed by functional characterization using Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Differential expression analysis highlights developmental stage-specific expression patterns, and immunity-related transcripts are discussed. The data presented provides a valuable molecular resource to aid further investigation into immunocompetence throughout this organism's sexual development.

Microcystis aeruginosa is a freshwater bloom-forming cyanobacterium that is distributed worldwide. M. aeruginosa can be divided into at least 8 phylogenetic groups (A-G and X) at the intraspecific level. Here, we report the complete genome sequence of M. aeruginosa NIES-2481, which was isolated from Lake Kasumigaura, Japan, and is assigned to group G. The complete genome sequence of M. aeruginosa NIES-2481 comprises a 4.29-Mbp circular chromosome and a 147,539-bp plasmid; the circular chromosome and the plasmid contain 4,332 and 167 protein-coding genes, respectively. Comparative analysis with the complete genome of M. aeruginosa NIES-2549, which belongs to the same group with NIES-2481, showed that the genome size is the smallest level in previously sequenced M. aeruginosa strains, and the genomes do not contain a microcystin biosynthetic gene cluster in common. Synteny analysis revealed only small-scale rearrangements between the two genomes.

Methyl tert-butyl ether (MTBE) is a ground water contaminant with plausible carcinogenic properties. Mycobacterium sp. strain ENV421 cometabolically degrades MTBE and other ethers during the growth on propane as a carbon source. In this study, the 6.2 Mb genome of strain ENV421 was deciphered. The genome sequence revealed the presence of numerous putative propane catabolic genes including genes encoding hydrocarbon oxygenases and short chain alcohol dehydrogenases. These data provide the basis for the elucidation of propane metabolic pathways in strain ENV421 and its application for the remediation of ground water contaminated with toxic ethers.

The thermophilic 'Geobacilli' are important sources of thermostable enzymes and other biotechnologically relevant macromolecules. The present work reports the high quality draft genome sequences of previously unsequenced type strains of Geobacillus uzenensis (DSM 23175^T), G. thermocatenulatus (DSM 730^T) and Parageobacillus galactosidasius (DSM 18751^T). Phylogenomic analyses revealed that DSM 18751^T and DSM 23175^T represent later heterotypic synonyms of P. toebii and G. subterraneus, respectively, while DSM 730^T represents the type strain for the species G. thermocatenulatus. These genome sequences will contribute towards a deeper understanding of the ecological and biological diversity and the biotechnological exploitation of the 'geobacilli'.

DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak. In-silico functional analysis with PANTHER predicted putative deleterious functional impact of c.161 T>A; p. V54Q while alignment of bovine and human NTR-J domains revealed that p.Q19H, p.E20Q and p. E21X mutations occurred in helix 2 and p.V54Q missense mutation occurred in helix 3 respectively. The 124 bp insertion found in the yak DNAJA1 ortholog may have significant functional relevance warranting further investigation. Our results suggest that these genetic differences may be concomitant with population genetic history and possible functional consequences for climate adaptation in bovidae.

To investigate chromosome evolution in fish species, we newly mapped 181 markers that allowed us to construct a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map with 1,713 DNA markers, which was far denser than a previous map, and we anchored the de novo assembled sequences onto the RH physical map. Finally, we mapped a total of 13,977 expressed sequence tags (ESTs) on a genome sequence assembly aligned with the physical map. Using the high-density physical map and anchored genome sequences, we accurately compared the yellowtail genome structure with the genome structures of five model fishes to identify characteristics of the yellowtail genome. Between yellowtail and Japanese medaka (Oryzias latipes), almost all regions of the chromosomes were conserved and some blocks comprising several markers were translocated. Using the genome information of the spotted gar (Lepisosteus oculatus) as a reference, we further documented syntenic relationships and chromosomal rearrangements that occurred during evolution in four other acanthopterygian species (Japanese medaka, zebrafish, spotted green pufferfish and three-spined stickleback). The evolutionary chromosome translocation frequency was 1.5-2-times higher in yellowtail than in medaka, pufferfish, and stickleback.

Gene expression depends on sex and environment. We stringently explored the contributions of these effects in Drosophila melanogaster by rearing three distinct wildtype genotypes on isocaloric diets either high in protein or sugar followed by expression profiling of heads from the sexes. By using different genotypes as replicates we developed robust sex- and diet-biased expression responses.