Journal of Genomics最新文献_第9页

Identification of Sex-associated SNPs of Greater Amberjack (Seriola dumerili). 大琥珀属植物性别相关snp的鉴定。

Journal of Genomics Pub Date : 2018-05-19 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.24788

Junya Kawase, Jun-Ya Aoki, Kazuhisa Hamada, Akiyuki Ozaki, Kazuo Araki

{"title":"Identification of Sex-associated SNPs of Greater Amberjack (Seriola dumerili).","authors":"Junya Kawase, Jun-Ya Aoki, Kazuhisa Hamada, Akiyuki Ozaki, Kazuo Araki","doi":"10.7150/jgen.24788","DOIUrl":"https://doi.org/10.7150/jgen.24788","url":null,"abstract":"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.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"53-62"},"PeriodicalIF":0.0,"publicationDate":"2018-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.24788","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36189484","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: 8

In-silico Designing and Testing of Primers for Sanger Genome Sequencing of Dengue Virus Types of Asian Origin. 登革病毒亚洲源型Sanger基因组测序引物的芯片设计与测试

Journal of Genomics Pub Date : 2018-04-10 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.22460

Ajay Prakash Joshi, Annette Angel, Bennet Angel, Rajendra Kumar Baharia, Suman Rathore, Neha Sharma, Karuna Yadav, Sharad Thanvi, Indu Thanvi, Vinod Joshi

{"title":"In-silico Designing and Testing of Primers for Sanger Genome Sequencing of Dengue Virus Types of Asian Origin.","authors":"Ajay Prakash Joshi, Annette Angel, Bennet Angel, Rajendra Kumar Baharia, Suman Rathore, Neha Sharma, Karuna Yadav, Sharad Thanvi, Indu Thanvi, Vinod Joshi","doi":"10.7150/jgen.22460","DOIUrl":"https://doi.org/10.7150/jgen.22460","url":null,"abstract":"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.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"34-40"},"PeriodicalIF":0.0,"publicationDate":"2018-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.22460","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36054052","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: 1

De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts. 埋甲虫(鞘翅目:Silphidae)发育阶段转录组的重新组装和关键免疫转录物的鉴定。

Journal of Genomics Pub Date : 2018-04-10 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.24228

Harim I Won, Thomas T Schulze, Emalie J Clement, Gabrielle F Watson, Sean M Watson, Rosalie C Warner, Elizabeth A M Ramler, Elias J Witte, Mark A Schoenbeck, Claudia M Rauter, Paul H Davis

{"title":"De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts.","authors":"Harim I Won, Thomas T Schulze, Emalie J Clement, Gabrielle F Watson, Sean M Watson, Rosalie C Warner, Elizabeth A M Ramler, Elias J Witte, Mark A Schoenbeck, Claudia M Rauter, Paul H Davis","doi":"10.7150/jgen.24228","DOIUrl":"10.7150/jgen.24228","url":null,"abstract":"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.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"41-52"},"PeriodicalIF":0.0,"publicationDate":"2018-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.24228","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36054053","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: 12

Complete Genome Sequence of Microcystis aeruginosa NIES-2481 and Common Genomic Features of Group G M. aeruginosa. 铜绿微囊藻NIES-2481全基因组序列及G组铜绿微囊藻基因组特征。

Journal of Genomics Pub Date : 2018-03-19 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.24935

Haruyo Yamaguchi, Shigekatsu Suzuki, Yasunori Osana, Masanobu Kawachi

引用次数: 9

Genomic Analysis of Propane Metabolism in Methyl Tert-Butyl Ether-Degrading Mycobacterium Sp. Strain ENV421. 甲基叔丁基醚降解分枝杆菌ENV421株丙烷代谢的基因组分析

Journal of Genomics Pub Date : 2018-03-02 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.24929

Peter Robert Tupa, Hisako Masuda

引用次数: 7

High Quality Draft Genomes of the Type Strains Geobacillus thermocatenulatus DSM 730^T, G. uzenensis DSM 23175^T And Parageobacillus galactosidasius DSM 18751^T. 热链地杆菌DSM 730T、乌兹纳格氏杆菌DSM 23175T和半乳糖sidasiparageobacillus DSM 18751T型菌株的高质量基因组草图

Journal of Genomics Pub Date : 2018-02-03 eCollection Date: 2018-01-01 DOI: 10.7150/jgen.22986

Winnie Thabisa Ramaloko, Nadine Koen, Shamara Polliack, Habibu Aliyu, Pedro Humberto Lebre, Teresa Mohr, Florian Oswald, Michaela Zwick, Daniel Ray Zeigler, Anke Neumann, Christoph Syldatk, Don Arthur Cowan, Pieter De Maayer

{"title":"High Quality Draft Genomes of the Type Strains Geobacillus thermocatenulatus DSM 730T, G. uzenensis DSM 23175T And Parageobacillus galactosidasius DSM 18751T.","authors":"Winnie Thabisa Ramaloko, Nadine Koen, Shamara Polliack, Habibu Aliyu, Pedro Humberto Lebre, Teresa Mohr, Florian Oswald, Michaela Zwick, Daniel Ray Zeigler, Anke Neumann, Christoph Syldatk, Don Arthur Cowan, Pieter De Maayer","doi":"10.7150/jgen.22986","DOIUrl":"https://doi.org/10.7150/jgen.22986","url":null,"abstract":"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 23175T), G. thermocatenulatus (DSM 730T) and Parageobacillus galactosidasius (DSM 18751T). Phylogenomic analyses revealed that DSM 18751T and DSM 23175T represent later heterotypic synonyms of P. toebii and G. subterraneus, respectively, while DSM 730T 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'.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"20-23"},"PeriodicalIF":0.0,"publicationDate":"2018-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.22986","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35865824","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: 1

Genetic variation in N- and C-terminal regions of bovine DNAJA1 heat shock protein gene in African, Asian and American cattle. 非洲牛、亚洲牛和美洲牛 DNAJA1 热休克蛋白基因 N 端和 C 端区域的遗传变异。

Journal of Genomics Pub Date : 2018-01-01 DOI: 10.7150/jgen.23248

Oyeyemi O Ajayi, Sunday O Peters, Marcos De Donato, F Denis Mujibi, Waqas A Khan, Tanveer Hussain, Masroor E Babar, Ikhide G Imumorin, Bolaji N Thomas

{"title":"Genetic variation in N- and C-terminal regions of bovine DNAJA1 heat shock protein gene in African, Asian and American cattle.","authors":"Oyeyemi O Ajayi, Sunday O Peters, Marcos De Donato, F Denis Mujibi, Waqas A Khan, Tanveer Hussain, Masroor E Babar, Ikhide G Imumorin, Bolaji N Thomas","doi":"10.7150/jgen.23248","DOIUrl":"10.7150/jgen.23248","url":null,"abstract":"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.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/76/cf/jgenv06p0001.PMC5744232.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35699451","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: 0

Constructing a 'Chromonome' of Yellowtail (Seriola quinqueradiata) for Comparative Analysis of Chromosomal Rearrangements. 构建黄尾鱼染色体重排的比较分析。

Journal of Genomics Pub Date : 2018-01-01 DOI: 10.7150/jgen.23222

Junya Kawase, Jun-Ya Aoki, Kazuo Araki

{"title":"Constructing a 'Chromonome' of Yellowtail (Seriola quinqueradiata) for Comparative Analysis of Chromosomal Rearrangements.","authors":"Junya Kawase, Jun-Ya Aoki, Kazuo Araki","doi":"10.7150/jgen.23222","DOIUrl":"https://doi.org/10.7150/jgen.23222","url":null,"abstract":"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.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"6 ","pages":"9-19"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.23222","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35698929","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

Exploring Effects of Sex and Diet on Drosophila melanogaster Head Gene Expression. 性别和饮食对黑腹果蝇头部基因表达的影响

Journal of Genomics Pub Date : 2017-10-29 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.22393

Maria D L A Jaime, Juan Hurtado, Mariana Ramirez Loustalot-Laclette, Brian Oliver, Therese Markow

引用次数: 1

Draft genome sequence of a biosurfactant producing, Bacillus aquimaris strain SAMM MCC 3014 isolated from Indian Arabian coastline sea water. 产生物表面活性剂的水生芽孢杆菌SAMM MCC 3014从印度阿拉伯海岸线海水中分离的基因组序列草图。

Journal of Genomics Pub Date : 2017-10-08 eCollection Date: 2017-01-01 DOI: 10.7150/jgen.21724

Samadhan Waghmode, Laxmikant Dama, Tejashri Hingamire, Nidhi Bharti, Swapnil Doijad, Mangesh Suryavanshi

引用次数: 6