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Auto Tag: Comparative genomics

July 7, 2019

Complete genome sequence of the poly-?-glutamate-synthesizing Bacterium Bacillus subtilis Bs-115.

Bacillus subtilis Bs-115 was isolated from the soil of a corn field in Yutai County, Jinan City, Shandong Province, People’s Republic of China, and is characterized by the efficient synthesis of poly-?-glutamate (?-PGA), with corn saccharification liquid as the sole energy and carbon source during the process of ?-PGA formation. Here, we report the complete genome sequence of Bacillus subtilis Bs-115 and the genes associated with poly-?-glutamate synthesis. Copyright © 2018 Wang et al.

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July 7, 2019

Genome sequences of five Mycobacterium bovis strains isolated from farmed animals and wildlife in Canada.

Mycobacterium bovis is the causative agent of bovine tuberculosis, an infectious disease that affects both animals and humans and thus presents a risk to public health and the livestock industry. Here, we report the genome sequences of five Mycobacterium bovis strains that represent major genotype clusters observed in farmed animals and wildlife in Canada.© Crown copyright 2018.

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July 7, 2019

The sequenced angiosperm genomes and genome databases.

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

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July 7, 2019

Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod.

Antifreeze glycoproteins (AFGPs) are a novel evolutionary innovation in members of the northern cod fish family (Gadidae), crucial in preventing death from inoculative freezing by environmental ice in their frigid Arctic and sub-Arctic habitats. However, the genomic origin and molecular mechanism of evolution of this novel life-saving adaptive genetic trait remained to be definitively determined. To this end, we constructed large insert genomic DNA BAC (bacterial artificial chromosome) libraries for two AFGP-bearing gadids, the high-Arctic polar cod Boreogadus saida and the cold-temperate Atlantic tomcod Microgadus tomcod, to isolate and sequence their AFGP genomic regions for fine resolution evolutionary analyses. The BAC library construction encountered poor cloning efficiency initially, which we resolved by pretreating the agarose-embedded erythrocyte DNA with a cationic detergent, a method that may be of general use to BAC cloning for teleost species and/or where erythrocytes are the source of input DNA. The polar cod BAC library encompassed 92,160 clones with an average insert size of 94.7?kbp, and the Atlantic tomcod library contained 73,728 clones with an average insert size of 89.6?kbp. The genome sizes of B. saida and M. tomcod were estimated by cell flow cytometry to be 836?Mbp and 645?Mbp respectively, thus their BAC libraries have approximately 10- and 9.7-fold genome coverage respectively. The inclusiveness and depth of coverage were empirically confirmed by screening the libraries with three housekeeping genes. The BAC clones that mapped to the AFGP genomic loci of the two gadids were then isolated by screening the BAC libraries with gadid AFGP gene probes. Eight minimal tiling path (MTP) clones were identified for B. saida, sequenced, and assembled. The B. saida AFGP locus reconstruction produced both haplotypes, and the locus comprises three distinct AFGP gene clusters, containing a total of 16 AFGP genes and spanning a combined distance of 512?kbp. The M. tomcod AFGP locus is much smaller at approximately 80?kbp, and contains only three AFGP genes. Fluorescent in situ hybridization with an AFGP gene probe showed the AFGP locus in both species occupies a single chromosomal location. The large AFGP locus with its high gene dosage in B. saida is consistent with its chronically freezing high Arctic habitats, while the small gene family in M. tomcod correlates with its milder habitats in lower latitudes. The results from this study provided the data for fine resolution sequence analyses that would yield insight into the molecular mechanisms and history of gadid AFGP gene evolution driven by northern hemisphere glaciation. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

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July 7, 2019

Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. áviolaceum

Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrum complex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3 and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrum and T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrum and T. violaceum was observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceum contains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrum and T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrum and T. violaceum underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.

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July 7, 2019

Probiotic genomes: Sequencing and annotation in the past decade

Probiotics are live microorganisms that confer many health benefits to the host when administered in adequate quantities. These health benefits have garnered much attention towards Probiotics and have given an impetus to their use as dietary supplements for the improvement of general health and as adjuvant therapies for certain diseases. The increased demand for probiotic products in the recent times has provided the thrust for probiotic research applied to several areas of human biology. The advances in genomic technologies have further facilitated the sequencing of the genomes of such probiotic bacteria and their genomic analyses to identify the genes that endow the beneficial effects they are known to exert. This work reviews the application of genomic strategies on probiotic bacteria, while providing the details about the probiotic strains whose genome sequences are available. It also consolidates the Genomic tools used for the sequencing, assembly and annotation of the probiotic genes and how it has helped in comparative genomic analyses.

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July 7, 2019

Darwin: A genomics co-processor provides up to 15,000 X acceleration on long read assembly

of life in fundamental ways. Genomics data, however, is far outpacing Moore’s Law. Third-generation sequencing tech- nologies produce 100× longer reads than second generation technologies and reveal a much broader mutation spectrum of disease and evolution. However, these technologies incur prohibitively high computational costs. Over 1,300 CPU hours are required for reference-guided assembly of the human genome (using [47]), and over 15,600 CPU hours are required for de novo assembly [57]. This paper describes “Darwin” — a co-processor for genomic sequence alignment that, without sacrificing sensitivity, provides up to 15,000× speedup over the state-of-the-art software for reference-guided assembly of third-generation reads. Darwin achieves this speedup through hardware/algorithm co-design, trading more easily accelerated alignment for less memory-intensive filtering, and by optimizing the memory system for filtering. Darwin combines a hardware-accelerated version of D-SOFT, a novel filtering algorithm, with a hardware-accelerated version of GACT, a novel alignment algorithm. GACT generates near-optimal alignments of arbitrarily long genomic sequences using constant memory for the compute-intensive step. Dar- win is adaptable, with tunable speed and sensitivity to match emerging sequencing technologies and to meet the requirements of genomic applications beyond read assembly.

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July 7, 2019

Emerging mechanisms of antimicrobial resistance in bacteria and fungi: advances in the era of genomics.

Bacteria and fungi continue to develop new ways to adapt and survive the lethal or biostatic effects of antimicrobials through myriad mechanisms. Novel antibiotic resistance genes such as lsa(C), erm(44), VCC-1, mcr-1, mcr-2, mcr-3, mcr-4, bla KLUC-3 and bla KLUC-4 were discovered through comparative genomics and further functional studies. As well, mutations in genes that hitherto were unknown to confer resistance to antimicrobials, such as trm, PP2C, rpsJ, HSC82, FKS2 and Rv2887, were shown by genomics and transcomplementation assays to mediate antimicrobial resistance in Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecium, Saccharomyces cerevisae, Candida glabrata and Mycobacterium tuberculosis, respectively. Thus, genomics, transcriptomics and metagenomics, coupled with functional studies are the future of antimicrobial resistance research and novel drug discovery or design.

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July 7, 2019

Genome sequence resources for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)

Puccinia striiformis f. sp. tritici causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei causes stripe rust on barley. Several P. striiformis f. sp. tritici genomes are available, but no P. striiformis f. sp. hordei genome is available. More genomes of P. striiformis f. sp. tritici and P. striiformis f. sp. hordei are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced P. striiformis f. sp. tritici isolate 93-210 and P. striiformis f. sp. hordei isolate 93TX-2, using PacBio and Illumina technologies and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interactions.

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July 7, 2019

Isolation and identification of an anthracimycin analogue from Nocardiopsis kunsanensis, a halophile from a saltern, by genomic mining strategy.

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.

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July 7, 2019

The draft genome of the lichen-forming fungus Lasallia hispanica (Frey) Sancho & A. Crespo

Lasallia hispanica (Frey) Sancho & A. Crespo is one of three Lasallia species occurring in central-western Europe. It is an orophytic, photophilous Mediterranean endemic which is sympatric with the closely related, widely distributed, highly clonal sister taxon L. pustulata in the supra- and oro-Mediterranean belts. We sequenced the genome of L. hispanica from a multispore isolate. The total genome length is 41·2 Mb, including 8488 gene models. We present the annotation of a variety of genes that are involved in protein secretion, mating processes and secondary metabolism, and we report transposable elements. Additionally, we compared the genome of L. hispanica to the closely related, yet ecologically distant, L. pustulata and found high synteny in gene content and order. The newly assembled and annotated L. hispanica genome represents a useful resource for future investigations into niche differentiation, speciation and microevolution in L. hispanica and other members of the genus.

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