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Auto Tag: Genome assembly

July 7, 2019

Complete genome sequence of the Vibrio vulnificus strain VV2014DJH, a human-pathogenic bacterium isolated from a death case in China.

Vibrio vulnificus, an opportunistic pathogen, is the causative agent of life-threatening septicemia and severe wound infections. However, the pathogenicity and virulence factors of V. vulnificus are not fully understood. Here we report the complete genome sequence of V. vulnificus VV2014DJH, which was isolated from a death case.The genome of the V. vulnificus VV2014DJH contains two circular chromosomes with a mean G+C content of 46.8%, but does not consists of any plasmids. The chromosome I and chromosome II consist of 3,303,590 and 1,770,972 bp, respectively. In addition, the genome consists of 4617 protein coding genes, 172 RNA genes and type I, II and III secretion systems were predicted.In this study, the genomic information of the V. vulnificus VV2014DJH has been described. The information would contribute to the increasing scope and depth of Vibrio genome database, and provide insights into the pathogenicity and virulence factors of V. vulnificus.

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July 7, 2019

Unlocking the biological potential of Euglena gracilis: evolution, cell biology and significance to parasitism

Photosynthetic euglenids are major components of aquatic ecosystems and relatives of trypanosomes. Euglena gracilis has considerable biotechnological potential and great adaptability, but exploitation remains hampered by the absence of a comprehensive gene catalogue. We address this by genome, RNA and protein sequencing: the E. gracilis genome is >2Gb, with 36,526 predicted proteins. Large lineage-specific paralog families are present, with evidence for flexibility in environmental monitoring, divergent mechanisms for metabolic control, and novel solutions for adaptation to extreme environments. Contributions from photosynthetic eukaryotes to the nuclear genome, consistent with the shopping bag model are found, together with transitions between kinetoplastid and canonical systems. Control of protein expression is almost exclusively post-transcriptional. These data are a major advance in understanding the nuclear genomes of euglenids and provide a platform for investigating the contributions of E. gracilis and its relatives to the biosphere.

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July 7, 2019

The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes.

Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture. Copyright © 2017 Elsevier Ltd. All rights reserved.

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July 7, 2019

Genomic clues to the parental origin of the wild flowering cherry Prunus yedoensis var. nudiflora (Rosaceae)

Prunus yedoensis Matsumura is one of the popular ornamental flowering cherry trees native to northeastern Asia, and its wild populations have only been found on Jeju Island, Korea. Previous studies suggested that wild P. yedoensis (P. yedoensis var. nudiflora) is a hybrid species; however, there is no solid evidence on its exact parental origin and genomic organization. In this study, we developed a total of 38 nuclear gene-based DNA markers that can be universally amplifiable in the Prunus species using 586 Prunus Conserved Orthologous Gene Set (Prunus COS). Using the Prunus COS markers, we investigated the genetic structure of wild P. yedoensis populations and evaluated the putative parental species of wild P. yedoensis. Population structure and phylogenetic analysis of 73 wild P. yedoensis accessions and 54 accessions of other Prunus species revealed that the wild P. yedoensis on Jeju Island is a natural homoploid hybrid. Sequence-level comparison of Prunus COS markers between species suggested that wild P. yedoensis might originate from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura. Moreover, approximately 81% of the wild P. yedoensis accessions examined were likely F1 hybrids, whereas the remaining 19% were backcross hybrids resulting from additional asymmetric introgression of parental genotypes. These findings suggest that complex hybridization of the Prunus species on Jeju Island can produce a range of variable hybrid offspring. Overall, this study makes a significant contribution to address issues of the origin, nomenclature, and genetic relationship of ornamental P. yedoensis.

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July 7, 2019

Mechanisms of adaptive divergence and speciation in Littorina saxatilis: Integrating knowledge from ecology and genetics with new data emerging from genomic studies

New opportunities to understand marine speciation and evolution of local adaptation come with genomic approaches and with the development of comprehensive model systems. The marine snail Littorina saxatilis is one example of a developing marine model for investigating genetic mechanisms of rapid divergence and evolution in natural systems. This species is strongly polymorphic and shows formation of local ecotypes throughout its distribution. Support is strong for primary (in situ) and parallel formation of reproductively semi-isolated ecotypes with contact zones between heterogeneous intertidal microhabitats. This makes this species an ideal organism for gaining new insights into the interplay of divergent selection, gene flow and genetic drift during local adaptation and speciation. A relatively well-resolved draft genome and a genetic map describing 17 linkage groups (“chromosomes”) are key tools for investigating the role of structural genomic variation, such as inversions, gene duplications and translocations. Whole genome re-sequencing of pools of individuals and the first comprehensive study of a contact zone contribute direct information on selection and barriers to gene flow present in specific regions of the genome. Linking selection at the phenotypic level to patterns obser ved in the genome is under way by quantitative trait loci mapping and annotation of candidate genes, while the role of single mutations on individual fitness will have to await development of gene manipulation tools. The features of the snail system facilitate the study of local adaptation and speciation and its genomic basis, but the underlying evolutionary processes are expected to be similar in other organisms, and hence this species is a useful model.

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July 7, 2019

The state of whole-genome sequencing

Over the last decade, a technological paradigm shift has slashed the cost of DNA sequencing by over five orders of magnitude. Today, the cost of sequencing a human genome is a few thousand dollars, and it continues to fall. Here, we review the most cost-effective platforms for whole-genome sequencing (WGS) as well as emerging technologies that may displace or complement these. We also discuss the practical challenges of generating and analyzing WGS data, and how WGS has unlocked new strategies for discovering genes and variants underlying both rare and common human diseases.

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July 7, 2019

Fragmentation of surface adsorbed and aligned DNA molecules using soft lithography for next-generation sequencing

In this study, the enzymatic in situ cutting of linearized DNA molecules at approximately 11 kbp intervals is demonstrated using a soft lithography technique. The ultimate goal is to provide a general ordered cutting method to greatly simplify the assembly process. DNA was stretched onto PMMA (Poly methyl methacrylate) coated silicon by withdrawing the substrate from a DNA solution (a process termed “combing”). The stretched lambda DNA could be linearly cut with a soft lithography stamp used to selectively apply DNase I. After cutting the DNA on the substrate, the DNA fragments are removed from the surface by incubating PMMA in the commercial NEBuffer 3.1 at 75°C. The recovered fragments desorbed into the buffer and were sequenced using the PacBio RS II sequencer without an amplification step. The mean coverage was 2870X for the approximately 11 kbp fragmented sample and 100% of the lambda genome was sequenced. Methods to extend of the technique to ordered fragmentation are discussed.

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July 7, 2019

Lactobacillus allii sp. nov. isolated from scallion kimchi.

A novel strain of lactic acid bacteria, WiKim39T, was isolated from a scallion kimchi sample consisting of fermented chili peppers and vegetables. The isolate was a Gram-positive, rod-shaped, non-motile, catalase-negative and facultatively anaerobic lactic acid bacterium. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain WiKim39T belonged to the genus Lactobacillus, and shared 97.1-98.2?%?pair-wise sequence similarities with related type strains, Lactobacillus nodensis, Lactobacillus insicii, Lactobacillus versmoldensis, Lactobacillus tucceti and Lactobacillus furfuricola. The G+C?content of the strain based on its genome sequence was 35.3?mol%. The ANI values between WiKim39T and the closest relatives were lower than 80?%. Based on the phenotypic, biochemical, and phylogenetic analyses, strain WiKim39T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus allii sp. nov. is proposed. The type strain is WiKim39T (=KCTC 21077T=JCM 31938T).

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July 7, 2019

Linear peptides are the major products of a biosynthetic pathway that encodes for cyclic depsipeptides.

Three new dentigerumycin analogues are produced by Streptomyces sp. M41, a bacterium isolated from a South African termite, Macrotermes natalensis. The structures of the complex nonribosomal peptide synthetase-polyketide synthase (NRPS/PKS) hybrid compounds were determined by 1D- and 2D-NMR spectroscopy, high-resolution mass spectrometry, and circular dichroism (CD) spectroscopy. Both cyclic and linear peptides are reported, and the genetic organization of the NRPS modules within the biosynthetic gene cluster accounts for the observed structural diversity.

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July 7, 2019

Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.

Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.© 2017 Prasad et al.; Published by Cold Spring Harbor Laboratory Press.

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July 7, 2019

Glaucophyta

The Glaucophyta is by far the least species-rich phylum of the Archaeplastida comprising only four described genera, Glaucocystis, Cyanophora, Gloeochaete, and Cyanoptyche, and 15 species. However, recent molecular and morphological analyses reveal that glaucophytes are not as species poor as hitherto assumed with many novel lineages existing in natural environments. Glaucophytes are freshwater phototrophs of moderate to low abundance and retain many ancestral plastid traits derived from the cyanobacterial donor of this organelle, including the remnant peptidoglycan wall in their envelope. These plastids were originally named “cyanelles,” which was later changed to “muroplasts” when their shared ancestry with other Archaeplastida was recognized. The model glaucophyte, Cyanophora paradoxa, is well studied with respect to biochemistry, proteomics, and the gene content of the nuclear and organelle genomes. Investigation of the biosynthesis of cytosolic starch led to a model for the transition from glycogen to starch storage during plastid endosymbiosis. The photosynthetic apparatus, including phycobilisome antennae, resembles that of cyanobacteria. However, the carbon-concentrating mechanism is algal in nature and based on pyrenoids. Studies on protein import into muroplasts revealed a primordial Toc/Tic translocon. The peptidoglycan wall was elucidated with respect to composition, biosynthesis, and involvement of nuclear genes. The muroplast genome is distinct, not due to the number of encoded genes but, rather, because of the presence of unique genes not present on other plastid genomes. The mosaic nature of the gene-rich (27,000) nuclear genome came as a surprise, considering the relatively small genomes of unicellular red algae.

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July 7, 2019

Microbial bioinformatics for food safety and production.

In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput ‘omics’ technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety. © The Author 2015. Published by Oxford University Press.

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July 7, 2019

Effects of genome structure variation, homeologous genes and repetitive DNA on polyploid crop research in the age of genomics.

Compared to diploid species, allopolyploid crop species possess more complex genomes, higher productivity, and greater adaptability to changing environments. Next generation sequencing techniques have produced high-density genetic maps, whole genome sequences, transcriptomes and epigenomes for important polyploid crops. However, several problems interfere with the full application of next generation sequencing techniques to these crops. Firstly, different types of genomic variation affect sequence assembly and QTL mapping. Secondly, duplicated or homoeologous genes can diverge in function and then lead to emergence of many minor QTL, which increases difficulties in fine mapping, cloning and marker assisted selection. Thirdly, repetitive DNA sequences arising in polyploid crop genomes also impact sequence assembly, and are increasingly being shown to produce small RNAs to regulate gene expression and hence phenotypic traits. We propose that these three key features should be considered together when analyzing polyploid crop genomes. It is apparent that dissection of genomic structural variation, elucidation of the function and mechanism of interaction of homoeologous genes, and investigation of the de novo roles of repeat sequences in agronomic traits are necessary for genomics-based crop breeding in polyploids. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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July 7, 2019

First Azospirillum genome from aquatic environments: Whole-genome sequence of Azospirillum thiophilum BV-S(T), a novel diazotroph harboring a capacity of sulfur-chemolithotrophy from a sulfide spring.

Azospirillum thiophilum BV-S(T), isolated from a sulfide spring, is a novel nitrogen-fixing bacterium harboring sulfur-lithotrophy. In order to identify genetic characteristics with habitat- and metabolic features contrasting to those from terrestrial Azospirillum species, we present here the genome sequence of a novel species A. thiophilum BV-S(T), with a significance of first genome report in the aquatic Azospirillum species. The genome of strain BV-S(T) is comprised of 7.6Mb chromosome with a GC content of 68.2%. This information will contribute to expand understandings of sulfur-oxidizer microbes that preserve inherencies as a diazotroph, and further it will provide insights into genome plasticity of the genus Azospirillum for niche specific adaptations. Copyright © 2015 Elsevier B.V. All rights reserved.

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