Journal of Genomics最新文献_第8页

Genomic Insights Into A Novel, Alkalitolerant Nitrogen Fixing Bacteria, Azonexus sp. Strain ZS02. 一种新型耐碱固氮细菌Azonexus sp.菌株ZS02的基因组研究。

Journal of Genomics Pub Date : 2019-01-01 DOI: 10.7150/jgen.28153

Zohier B Salah, Christopher J Charles, Paul N Humphreys, Andrew P Laws, Simon P Rout

{"title":"Genomic Insights Into A Novel, Alkalitolerant Nitrogen Fixing Bacteria, Azonexus sp. Strain ZS02.","authors":"Zohier B Salah, Christopher J Charles, Paul N Humphreys, Andrew P Laws, Simon P Rout","doi":"10.7150/jgen.28153","DOIUrl":"https://doi.org/10.7150/jgen.28153","url":null,"abstract":"Alkaline environments represent a significant challenge to the growth of micro-organisms. Despite this, there are a number of alkaline environments which contain active microbial communities. Here we describe the genome of a diazotrophic, alkalitolerant strain of Azonexus, which was isolated from a microcosm seeded with hyperalkaline soils resulting from lime depositions. The isolate has a genome size 3.60 Mb with 3431 protein coding genes. The proteome indicated the presence of genes associated with the cycling of nitrogen, in particular the fixation of atmospheric nitrogen. Although closely related to Azonexus hydrophilus strain d8-1 by both 16S (97.9%) and in silico gDNA (84.1%) relatedness, the isolate demonstrates a pH tolerance above that reported for this strain. The proteome contained genes for the complete Na+/H+ antiporter (subunits A to G) for cytoplasmic pH regulation; this may account for the phenotypic characteristics of this strain which exhibited optimal growth conditions of pH 9 and 30°C.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 ","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.28153","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36880958","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}

引用次数: 3

De novo male gonad transcriptome draft for the marine mussel Perumytilus purpuratus with a focus on its reproductive-related proteins. 紫贻贝(Perumytilus purpuratus)雄性生殖腺从头转录组草图，重点研究其生殖相关蛋白。

Journal of Genomics Pub Date : 2018-11-16 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.27864

Carolina Briones, José J Nuñez, Montse Pérez, Daniela Espinoza-Rojas, Cristian Molina-Quiroz, Ricardo Guiñez

{"title":"De novo male gonad transcriptome draft for the marine mussel Perumytilus purpuratus with a focus on its reproductive-related proteins.","authors":"Carolina Briones, José J Nuñez, Montse Pérez, Daniela Espinoza-Rojas, Cristian Molina-Quiroz, Ricardo Guiñez","doi":"10.7150/jgen.27864","DOIUrl":"https://doi.org/10.7150/jgen.27864","url":null,"abstract":"Perumytilus purpuratus is a marine mussel considered a bioengineer species with a broad distribution in the Pacific and Atlantic coast of South America. Studies have shown two geographically and genetically differentiated subpopulations at molecular level and in sperm morphological traits. To open avenues for molecular research on P. purpuratus, a global de novo transcriptome from gonadal tissue of mature males was sequenced using the Illumina platform. From a total of 126.38 million reads, 37,765 transcripts were successfully annotated. BUSCO analysis determined a level of 89% completeness for the assembled transcriptome. The functional gene ontology (GO) annotation indicated that, in terms of abundance, the transcripts related with molecular function were the most represented, followed by those related with biological process and cellular components. Additionally, a subset of GO annotations generated using the \"sperm\" term resulted in a total of 1,294 sequences where the biological process category was the more represented, with transcripts strongly associated to sperm-processes required for fertilization, and with processes where the sperm-egg interaction could be implicated. Our work will contribute to the evolutionary understanding of the molecular mechanisms related to tissue-specific functions. This work reports the first male gonad transcriptome for the mussel P. purpuratus, generating a useful transcriptomic resource for this species and other closely related mytilids.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"127-132"},"PeriodicalIF":0.0,"publicationDate":"2018-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.27864","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36793088","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}

引用次数: 11

Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan. 从日本千叶土壤中分离的一种溴酸还原菌红球菌Br-6的基因组分析

Journal of Genomics Pub Date : 2018-11-15 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.27741

Kohei Ito, Masafumi Harada, Nobuyoshi Nakajima, Shigeki Yamamura, Masaru Tomita, Haruo Suzuki, Seigo Amachi

引用次数: 0

Isolation and genomic characterization of six endophytic bacteria isolated from Saccharum sp (sugarcane): Insights into antibiotic, secondary metabolite and quorum sensing metabolism. 从甘蔗中分离的6种内生细菌的分离和基因组特征:抗生素、次生代谢物和群体感应代谢的见解。

Journal of Genomics Pub Date : 2018-10-02 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.28335

Anutthaman Parthasarathy, Han Ming Gan, Narayan H Wong, Michael A Savka, KayLee K Steiner, Kurtis R Henry, André O Hudson

引用次数: 7

Whole-Genome Sequence of the Novel Antarctobacter heliothermus Strain SMS3, Found in Association with the Marine Diatom Skeletonema marinoi. 与海洋藻骨藻相关的新型高温南极细菌SMS3的全基因组序列。

Journal of Genomics Pub Date : 2018-09-04 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.27637

Mats Töpel, Matthew I M Pinder, Oskar N Johansson, Olga Kourtchenko, Anna Godhe, Adrian K Clarke

引用次数: 2

Expression and network analysis of YBX1 interactors for identification of new drug targets in lung adenocarcinoma. YBX1相互作用因子的表达及网络分析用于肺腺癌新药靶点的鉴定。

Journal of Genomics Pub Date : 2018-06-26 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.20581

Suriya Narayanan Murugesan, Birendra Singh Yadav, Pramod Kumar Maurya, Amit Chaudhary, Swati Singh, Ashutosh Mani

{"title":"Expression and network analysis of YBX1 interactors for identification of new drug targets in lung adenocarcinoma.","authors":"Suriya Narayanan Murugesan, Birendra Singh Yadav, Pramod Kumar Maurya, Amit Chaudhary, Swati Singh, Ashutosh Mani","doi":"10.7150/jgen.20581","DOIUrl":"https://doi.org/10.7150/jgen.20581","url":null,"abstract":"Y-Box Binding protein 1 (YBX-1) is known to be involved in various types of cancers. It's interactors also play major role in various cellular functions. Present work aimed to study the expression profile of the YBX-1 interactors during lung adenocarcinoma (LUAD). The differential expression analysis involved 57 genes from 95 lung adenocarcinoma samples, construction of gene network and topology analysis. A Total of 43 genes were found to be differentially expressed from which 17 genes were found to be down regulated and 26 genes were up-regulated. We observed that Polyadenylate-binding protein 1 (PABPC1), a protein involved in YBX1 translation, is highly correlated with YBX1. The interaction network analysis for a differentially expressed non-coding RNA Growth Arrest Specific 5 (GAS5) suggests that two proteins namely, Growth Arrest Specific 2 (GAS2) and Peripheral myelin protein 22 (PMP22) are potentially involved in LUAD progression. The network analysis and differential expression suggests that Collagen type 1 alpha 2 (COL1A2) can be potential biomarker and target for LUAD.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"103-112"},"PeriodicalIF":0.0,"publicationDate":"2018-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.20581","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36285094","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}

引用次数: 9

Mitochondrial genomes of the South American frogs Eupsophus vertebralis and E. emiliopugini (Neobatrachia: Alsodidae) and their phylogenetic relationships. 南美蛙Eupsophus脊椎蛙和E.emiliopugini的线粒体基因组及其系统发育关系。

Journal of Genomics Pub Date : 2018-06-19 DOI: 10.7150/jgen.26122

Elkin Y Suárez-Villota, Camila A Quercia, José J Nuñez

{"title":"Mitochondrial genomes of the South American frogs Eupsophus vertebralis and E. emiliopugini (Neobatrachia: Alsodidae) and their phylogenetic relationships.","authors":"Elkin Y Suárez-Villota, Camila A Quercia, José J Nuñez","doi":"10.7150/jgen.26122","DOIUrl":"10.7150/jgen.26122","url":null,"abstract":"We report the sequencing and compare the mitochondrial genomes of the South American ground frogs Eupsophus vertebralis and E. emiliopugini and reconstruct phylogenetic relationships among Eupsophus species. These genomes consist of 16,156 and 16,711 bp in length, respectively and contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes (tRNA), and partial non-coding D-loop region. Both genomes share 94.5% identity with 879 variable sites. A phylogenetic analysis with other available mitogenomes recovered both species as the sister clade of Alsodes gargola. Sequences from D-loop, CO1, and Cyt b, amplified and sequenced with primers developed from the mitochondrial genomes, allowed us to reconstruct phylogenetic relationships among Eupsophus species. Since our report represents the first mitogenomes for the genus Eupsophus, we expect these data will be valuable for further studies on conservation genetics and on the evolution of Patagonian amphibians.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"98-102"},"PeriodicalIF":0.0,"publicationDate":"2018-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.26122","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36285092","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}

引用次数: 5

Genetic Diversity of Bovine Major Histocompatibility Complex Class II DRB3 locus in cattle breeds from Asia compared to those from Africa and America. 亚洲牛主要组织相容性复合体ⅱ类DRB3位点的遗传多样性与非洲和美洲牛的比较

Journal of Genomics Pub Date : 2018-06-12 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.26491

Sunday O Peters, Tanveer Hussain, Adeyemi S Adenaike, Matthew A Adeleke, Marcos De Donato, Jordan Hazzard, Masroor E Babar, Ikhide G Imumorin

{"title":"Genetic Diversity of Bovine Major Histocompatibility Complex Class II DRB3 locus in cattle breeds from Asia compared to those from Africa and America.","authors":"Sunday O Peters, Tanveer Hussain, Adeyemi S Adenaike, Matthew A Adeleke, Marcos De Donato, Jordan Hazzard, Masroor E Babar, Ikhide G Imumorin","doi":"10.7150/jgen.26491","DOIUrl":"https://doi.org/10.7150/jgen.26491","url":null,"abstract":"Genetic polymorphisms and diversity of BoLA-DRB3.2 are essential because of DRB3 gene's function in innate immunity and its association with infectious diseases resistance or tolerance in cattle. The present study was aimed at assessing the level of genetic diversity of DRB3 in the exon 2 (BoLA-DRB3.2) region in African, American and Asian cattle breeds. Amplification of exon 2 in 174 cattle revealed 15 haplotypes. The breeds with the highest number of haplotypes were Brangus (10), Sokoto Gudali (10) and Dajal (9), while the lowest number of haplotypes were found in Holstein and Sahiwal with 4 haplotypes each. Medium Joining network obtained from haplotypic data showed that all haplotypes condensed around a centric area and each sequence (except in H-3, H-51 and H-106) representing almost a specific haplotype. The BoLA-DRB3.2 sequence analyses revealed a non-significant higher rate of non-synonymous (dN) compared to synonymous substitutions (dS). The ratio of dN/dS substitution across the breeds were observed to be greater than one suggesting that variation at the antigen-binding sites is under positive selection; thus increasing the chances of these breeds to respond to wide array of pathogenic attacks. An analysis of molecular variance revealed that 94.01 and 5.99% of the genetic variation was attributable to differences within and among populations, respectively. Generally, results obtained suggest that within breed genetic variation across breeds is higher than between breeds. This genetic information will be important for investigating the relationship between BoLADRB3.2 and diseases in various cattle breeds studied with attendant implication on designing breeding programs that will aim at selecting individual cattle that carry resistant alleles.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"88-97"},"PeriodicalIF":0.0,"publicationDate":"2018-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.26491","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36245316","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}

引用次数: 13

Genome Wide Analysis Reveals the Extrinsic Cellulolytic and Biohydrogen Generating Abilities of Neocallimastigomycota Fungi. 全基因组分析揭示了Neocallimastigomycota真菌的外部纤维素分解和生物产氢能力。

Journal of Genomics Pub Date : 2018-06-10 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.25648

Ayyappa Kumar Sista Kameshwar, Wensheng Qin

{"title":"Genome Wide Analysis Reveals the Extrinsic Cellulolytic and Biohydrogen Generating Abilities of Neocallimastigomycota Fungi.","authors":"Ayyappa Kumar Sista Kameshwar, Wensheng Qin","doi":"10.7150/jgen.25648","DOIUrl":"https://doi.org/10.7150/jgen.25648","url":null,"abstract":"Ruminating animals, especially cattle lack the carbohydrate active enzyme encoding genes which are required for the degradation of the glycosidic linkages of plant cell wall carbohydrates (such as cellulose, hemicellulose, lignin and pectin). Thus, ruminating animals are completely dependent on the microorganisms (anaerobic bacteria and fungi, methanogenic archaea and protozoa) residing in their rumen (hindgut). In this study, we have retrieved and analyzed the complete genome wide annotations of the Neocallimastigomycota division fungi such as Anaeromyces robustus, Neocallismatix californiae, Orpinomyces sp, Piromyces finnis, Piromyces sp E2. We have retrieved the InterPro, CAZy, KOG, KEGG, SM Clusters and MEROPS genome level data of these anaerobic fungi from JGI-MycoCosm database. Results obtained in our study reveals that, the genomes of anaerobic fungi completely lack genes encoding for lignin degrading auxiliary activity enzymes. Contrastingly, these fungi outnumbered other fungi by having highest number of CAZyme encoding genes. The genes encoding for dockerins and carbohydrate binding modules exaggerated other CAZymes which are involved in the structure and functioning of cellulosomes. Presence of cellulosomes and higher number of carbohydrate transport and metabolism genes also endorses the plant cell wall carbohydrate degrading abilities of these fungi. We also reported the tentative total cellulolytic, hemicellulolytic and pectinolytic abilities. And we have explicitly reported the genes, enzymes and the mechanisms involved in structure and functioning of the cellulosomes and hydrogenosomes. Our present work reveals the genomic machinery underlying the extrinsic plant cell wall degrading abilities of the anaerobic fungi. Results obtained in our study can be significantly applied in improving the gut health of cattle and especially in the fields of biofuel, biorefining and bioremediation-based industries.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"74-87"},"PeriodicalIF":0.0,"publicationDate":"2018-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.25648","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36245315","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}

引用次数: 19

Isolation and Identification of an Anthracimycin Analogue from Nocardiopsis kunsanensis, a Halophile from a Saltern, by Genomic Mining Strategy. 利用基因组挖掘策略从盐碱地嗜盐菌kunsannocardiopsis ensis中分离和鉴定一种炭疽霉素类似物。

Journal of Genomics Pub Date : 2018-05-21 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.24368

Fernanda L Sirota, Falicia Goh, Kia-Ngee Low, Lay-Kien Yang, Sharon C Crasta, Birgit Eisenhaber, Frank Eisenhaber, Yoganathan Kanagasundaram, Siew Bee Ng

{"title":"Isolation and Identification of an Anthracimycin Analogue from Nocardiopsis kunsanensis, a Halophile from a Saltern, by Genomic Mining Strategy.","authors":"Fernanda L Sirota, Falicia Goh, Kia-Ngee Low, Lay-Kien Yang, Sharon C Crasta, Birgit Eisenhaber, Frank Eisenhaber, Yoganathan Kanagasundaram, Siew Bee Ng","doi":"10.7150/jgen.24368","DOIUrl":"https://doi.org/10.7150/jgen.24368","url":null,"abstract":"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.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"63-73"},"PeriodicalIF":0.0,"publicationDate":"2018-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.24368","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36135796","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}

引用次数: 9