Journal of GenomicsPub Date : 2020-04-07eCollection Date: 2020-01-01DOI: 10.7150/jgen.39147
Tomasz Szmatoła, Artur Gurgul, Igor Jasielczuk, Weiwei Fu, Katarzyna Ropka-Molik
{"title":"A detailed characteristics of bias associated with long runs of homozygosity identification based on medium density SNP microarrays.","authors":"Tomasz Szmatoła, Artur Gurgul, Igor Jasielczuk, Weiwei Fu, Katarzyna Ropka-Molik","doi":"10.7150/jgen.39147","DOIUrl":"https://doi.org/10.7150/jgen.39147","url":null,"abstract":"<p><p>In the present study, runs of homozygosity (ROH) detected with the use of a standard bovine 54k single nucleotide polymorphism (SNP) genotyping assay and two different ROH detection approaches, based on 50 (M1) or 15 (M2) consecutive SNPs, were compared with results of whole genome sequencing. Both microarray-based methods accurately recognised medium-sized ROH, however, it was found that M2 method seemed to better than M1 identify short ROH, but highly overestimated their number, leading to numerous false positive calls. Moreover, long ROH identified with microarray data tended to break into shorter segments in sequencing data because of the presence of regions with high heterozygosity within the ROH sequences. This may indicate, that these long ROH are formed by closely positioned shorter homozygous segments that may be of older origin or may be created by two similar but not identical haplotypes, showing minor internal recombination signs. Such finding also suggests that at least some of the results of previous studies in regard to long ROH may be biased leading to inaccurate estimations of genomes autozygosity via ROH classification into length categories.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"43-48"},"PeriodicalIF":0.0,"publicationDate":"2020-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.39147","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37867345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Draft Genome Sequences of <i>Bifidobacterium animalis</i> Consecutively Isolated from Healthy Japanese Individuals.","authors":"Tomoya Tsukimi, Tsubasa Watabe, Kazuki Tanaka, Mitsuhiko P Sato, Haruo Suzuki, Masaru Tomita, Shinji Fukuda","doi":"10.7150/jgen.38516","DOIUrl":"https://doi.org/10.7150/jgen.38516","url":null,"abstract":"<p><p><i>Bifidobacterium</i> species are well recognized as probiotics and colonized in various parts of the human body. Here, we report the draft genome sequences of <i>Bifidobacterium animalis</i> isolated from two healthy Japanese volunteers, one of which was sampled twice before and after a 10-year interval. A core genome phylogeny analysis indicated that the strains isolated from the same volunteer were closely related. This paper is the first report of multiple draft genome sequences of <i>B. animalis</i> independently isolated from the same individual and provides insight into the probiotic potential of a member of this species.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"37-42"},"PeriodicalIF":0.0,"publicationDate":"2020-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.38516","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37867406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of GenomicsPub Date : 2020-03-01eCollection Date: 2020-01-01DOI: 10.7150/jgen.43928
Aditi Kulkarni, Wanqin Yu, Alex S Moon, Ashmita Pandey, Kathryn A Hanley, Jiannong Xu
{"title":"Programmable CRISPR interference for gene silencing using Cas13a in mosquitoes.","authors":"Aditi Kulkarni, Wanqin Yu, Alex S Moon, Ashmita Pandey, Kathryn A Hanley, Jiannong Xu","doi":"10.7150/jgen.43928","DOIUrl":"https://doi.org/10.7150/jgen.43928","url":null,"abstract":"<p><p>In the CRISPR-Cas systems, Cas13a is an RNA-guided RNA nuclease specifically targeting single strand RNA. We developed a Cas13a mediated CRISPR interference tool to target mRNA for gene silencing in mosquitoes. A <i>Cas13a</i> expressing plasmid was delivered to mosquitoes by intrathoracic injection, and <i>Cas13a</i> transcripts were detectable at least 10 days post-delivery. The target specific crRNA was synthesized <i>in vitro</i> using T7 RNA polymerase. The Cas13a plasmid and target crRNA can be delivered by intrathoracic injection together, or the Cas13a construct can be provided first, and then target crRNA can be given later when appropriate. The machinery was tested in two mosquito species. In <i>Anopheles gambiae</i>, <i>vitellogenin</i> gene was silenced by Cas13a/<i>Vg-</i>crRNA, which was accompanied by a significant reduction in egg production. In <i>Aedes aegypti</i>, the α- and δ-subunits of <i>COPI</i> genes were silenced by Cas13a/crRNA, which resulted in mortality and fragile midguts, reproducing a phenotype reported previously. Co-silencing genes simultaneously is achievable when a cocktail of target crRNAs is given. No detectable collateral cleavages of non-target transcripts were observed in the study. In addition to dsRNA or siRNA mediated RNA interference, the programmable CRISPR interference method offers an alternative to knock down genes in mosquitoes.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"30-36"},"PeriodicalIF":0.0,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.43928","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37753233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of GenomicsPub Date : 2020-02-21eCollection Date: 2020-01-01DOI: 10.7150/jgen.43162
David A Coil, Guillaume Jospin, Jonathan A Eisen
{"title":"Draft Genome Analysis of <i>Christensenella minuta</i> DSM 22607, exhibiting an unusual expansion of transporter homologs of unknown function.","authors":"David A Coil, Guillaume Jospin, Jonathan A Eisen","doi":"10.7150/jgen.43162","DOIUrl":"https://doi.org/10.7150/jgen.43162","url":null,"abstract":"<p><p><i>Christensenella minuta</i> was first formally described in 2012 as a member of a novel species, genus, and proposed family of Christensenellaceae. <i>C. minuta</i> was later shown in one study to be part of the most heritable taxonomic group in the human gut microbiome and to be enriched in people with low body mass index (BMI). Mouse work demonstrated that injection of cultured <i>C. minuta</i> into germ-free mice prevented the onset of obesity after a fecal transplant to the mice from high BMI individuals. Here we describe the genome sequence of <i>C. minuta</i> DSM 22607. Examination and analysis of the annotation revealed an unusually high number of genes predicted to be involved in carbohydrate metabolism, many of which were multiple homologs of RbsA, RbsB and RbsC, which together make up the Ribose ABC Transport System. These genes may be also involved in quorum sensing which could potentially relate to the importance of <i>C. minuta</i> in the gut microbiome.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"25-29"},"PeriodicalIF":0.0,"publicationDate":"2020-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.43162","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37753232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Draft genome sequence of <i>Deinococcus</i> sp<i>.</i> KR-1, a potential strain for palladium-leaching.","authors":"Hironaga Akita, Yuya Itoiri, Akio Kumagai, Noriyo Takeda, Akinori Matsushika, Mamoru Oshiki, Zen-Ichiro Kimura","doi":"10.7150/jgen.42020","DOIUrl":"https://doi.org/10.7150/jgen.42020","url":null,"abstract":"<p><p>Strain KR-1 was isolated from pond water collected in Japan. Because this strain was capable of adsorbing palladium particles in sterilized water, strain KR-1 will be a useful biocatalyst for palladium-leaching from metal waste. Here we present a draft genome sequence of <i>Deinococcus</i> sp. KR-1, which consists of a total of 7 contigs containing 4,556,772 bp with a GC content of 70.0% and comprises 4,450 predicted coding sequences. Based on the 16S rRNA gene sequence analysis, strain KR-1 was identified as <i>Deinococcus</i> sp. KR-1.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"21-24"},"PeriodicalIF":0.0,"publicationDate":"2020-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.42020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37647661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of GenomicsPub Date : 2020-01-25eCollection Date: 2020-01-01DOI: 10.7150/jgen.42095
Jocelyn Gatz-Schrupp, Peter Deckard, Benjamin Hufford, Steven Ly, Peter Tupa, Hisako Masuda
{"title":"Isolation and genomic analysis of 11-aminoundecanoic acid-degrading bacterium <i>Pseudomonas</i> sp. JG-B from nylon 11 enrichment culture.","authors":"Jocelyn Gatz-Schrupp, Peter Deckard, Benjamin Hufford, Steven Ly, Peter Tupa, Hisako Masuda","doi":"10.7150/jgen.42095","DOIUrl":"https://doi.org/10.7150/jgen.42095","url":null,"abstract":"<p><p>Nylon 11 is a polymer synthesized from 11-aminoundecanoic acid, and widely used in commercial manufacturing. In this study, we describe the isolation of the first organism capable of metabolizing 11-aminoundecanoic acid from nylon 11 enrichment culture. The strain shows rapid growth on 11-aminoundecanoic acid as a sole source of carbon, nitrogen, and energy. Furthermore, the genome sequence of strain JG-B was deciphered and shown to belong to genus <i>Pseudomonas</i>. Many genes encoding putative extracellular hydrolases, as well as homologues of nylon 6 hydrolases (NylB and NylA) were identified, suggesting the metabolic versatility and possibility that this organism could also depolymerase nylon 11 polymers.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"16-20"},"PeriodicalIF":0.0,"publicationDate":"2020-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.42095","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37647660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of GenomicsPub Date : 2020-01-19eCollection Date: 2020-01-01DOI: 10.7150/jgen.38461
Kathia Belaid, Erik Swanson, Alyssa Carré-Mlouka, Valérie Hocher, Sergio Svistoonoff, Djamel Gully, Stephen Simpson, Krystalynne Morris, W Kelley Thomas, Said Amrani, Louis S Tisa, Hassen Gherbi
{"title":"Draft Genome Sequence of the Symbiotic <i>Frankia</i> sp. strain B2 isolated from root nodules of <i>Casuarina cunninghamiana</i> found in Algeria.","authors":"Kathia Belaid, Erik Swanson, Alyssa Carré-Mlouka, Valérie Hocher, Sergio Svistoonoff, Djamel Gully, Stephen Simpson, Krystalynne Morris, W Kelley Thomas, Said Amrani, Louis S Tisa, Hassen Gherbi","doi":"10.7150/jgen.38461","DOIUrl":"https://doi.org/10.7150/jgen.38461","url":null,"abstract":"<p><p><i>Frankia</i> sp. strain B2 was isolated from <i>Casuarina cunninghamiana</i> nodules<i>.</i> Here, we report the 5.3-Mbp draft genome sequence of <i>Frankia</i> sp. strain B2 with a G+C content of 70.1 % and 4,663 candidate protein-encoding genes. Analysis of the genome revealed the presence of high numbers of secondary metabolic biosynthetic gene clusters.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"11-15"},"PeriodicalIF":0.0,"publicationDate":"2020-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.38461","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37647659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Draft genome sequences of <i>Salmonella</i> Oslo isolated from seafood and its laboratory generated auxotrophic mutant.","authors":"Kadeeja Jazeela, Anirban Chakraborty, Praveen Rai, Ballamoole Krishna Kumar, Shabarinath Srikumar, Scot van Nguyen, Daniel Hurley, Seamus Fanning, Indrani Karunasagar, Vijaya Kumar Deekshit","doi":"10.7150/jgen.40059","DOIUrl":"https://doi.org/10.7150/jgen.40059","url":null,"abstract":"<p><p>In recent years, the concept of bacteria-mediated cancer therapy has gained significant attention as an alternative to conventional therapy. The focus has been on non-typhoidal <i>Salmonella</i> (NTS), particularly <i>S.</i> Typhimurium, for its anti-cancer properties, however, other NTS serovars such as <i>Salmonella</i> Oslo, which are associated with foodborne illnesses could potentially be effective anti-cancer agents. Here, we report the draft genome sequence of <i>Salmonella</i> Oslo isolated from seafood and its laboratory generated auxotrophic mutant.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"7-10"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.40059","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37504958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genomic Characteristics of the Toxic Bloom-Forming Cyanobacterium <i>Microcystis aeruginosa</i> NIES-102.","authors":"Haruyo Yamaguchi, Shigekatsu Suzuki, Yasunori Osana, Masanobu Kawachi","doi":"10.7150/jgen.40978","DOIUrl":"https://doi.org/10.7150/jgen.40978","url":null,"abstract":"<p><p><i>Microcystis aeruginosa</i>, a bloom-forming cyanobacterium distributed mainly in freshwater environments, can be divided into at least 12 groups (A-K and X) based on multi-locus phylogenetic analyses. In this study, we characterized the genome of microcystin-producing <i>M. aeruginosa</i> NIES-102, assigned to group A, isolated from Lake Kasumigaura, Japan. The complete genome sequence of <i>M. aeruginosa</i> NIES-102 comprised a 5.87-Mbp circular chromosome containing 5,330 coding sequences. The genome was the largest among all sequenced genomes for the species. In a comparison with the genome of <i>M. aeruginosa</i> NIES-843, which belongs to the same group, the microcystin biosynthetic gene cluster and CRISPR-Cas locus were highly similar. A synteny analysis revealed small-scale rearrangements between the two genomes. Genes encoding transposases were more abundant in these two genomes than in other <i>Microcystis</i> genomes. Our results improve our understanding of structural genomic changes and adaptation to a changing environment in the species.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"8 ","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.40978","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37504957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genomic characterization of a pectinolytic isolate of <i>Serratia oryzae</i> isolated from lake water.","authors":"Nicole Hugouvieux-Cotte-Pattat, Cécile Jacot-des-Combes, Jérôme Briolay","doi":"10.7150/jgen.38365","DOIUrl":"10.7150/jgen.38365","url":null,"abstract":"<p><p>Only one isolate of <i>Serratia oryzae</i>, the type strain J11-6<sup>T</sup> has been characterized up to now. This strain was found in the endophytic bacterial flora of rice. As part of an ongoing investigation into pectinolytic bacteria present in lake water in France, a few <i>Serratia</i> strains were isolated, including S32 and J9 identified as new strains of <i>S. oryzae</i>. The genome of strain S32 consists of a circular chromosome of 4,810,389 bp that contains 4,584 protein-coding genes. The genome of S32, as well as those of the type strain J11-6<sup>T</sup>, contains several genes involved in pectin degradation and in the intracellular assimilation of pectin oligomers. The specific detection of enzyme activities confirmed that strain S32 secretes functional pectinases and that it also produces extracellular cellulase and protease activities. The ability to produce plant cell wall degrading enzymes shows that <i>S. oryzae</i> shares characteristics of plant associated bacteria, including phytopathogens.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 1","pages":"64-72"},"PeriodicalIF":0.0,"publicationDate":"2019-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6831795/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47874838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}