Genomics Data最新文献_第4页

Draft genome sequence of Massilia sp. KIM isolated from South African grassland biome soils 南非草原生物群系土壤中分离的麻孢菌(Massilia sp. KIM)基因组序列草图

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.06.002

Surendra Vikram , Nerissa Govender , Mubanga Helen Kabwe , Oliver Bezuidt , Thulani P. Makhalanyane

引用次数: 4

Draft genome sequence of Bradyrhizobium paxllaeri LMTR 21T isolated from Lima bean (Phaseolus lunatus) in Peru 秘鲁利马豆(Phaseolus lunatus)缓生根瘤菌LMTR 21T基因组序列草图

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.06.008

Ernesto Ormeño-Orrillo , Luis Rey , David Durán , Carlos A. Canchaya , Marco A. Rogel , Doris Zúñiga-Dávila , Juan Imperial , Tomás Ruiz-Argüeso , Esperanza Martínez-Romero

引用次数: 4

Profiling and characterization of a longissimus dorsi muscle microRNA dataset from an F2 Duroc × Pietrain pig resource population 来自F2 Duroc × Pietrain猪资源群体背最长肌microRNA数据集的分析和表征

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.07.006

Kaitlyn R. Daza , Juan P. Steibel , Deborah Velez-Irizarry , Nancy E. Raney , Ronald O. Bates , Catherine W. Ernst

{"title":"Profiling and characterization of a longissimus dorsi muscle microRNA dataset from an F2 Duroc × Pietrain pig resource population","authors":"Kaitlyn R. Daza , Juan P. Steibel , Deborah Velez-Irizarry , Nancy E. Raney , Ronald O. Bates , Catherine W. Ernst","doi":"10.1016/j.gdata.2017.07.006","DOIUrl":"10.1016/j.gdata.2017.07.006","url":null,"abstract":"<div>To elucidate the effects of microRNA (miRNA) regulation in skeletal muscle of adult pigs, miRNA expression profiling was performed with RNA extracted from longissimus dorsi (LD) muscle samples from 174 F2 pigs (~5.5months of age) from a Duroc×Pietrain resource population. Total RNA was extracted from LD samples, and libraries were sequenced on an Illumina HiSeq 2500 platform in 1×50bp format. After processing, 232,826,977 total reads were aligned to the Sus scrofa reference genome (v10.2.79), with 74.8% of total reads mapping successfully. The miRDeep2 software package was utilized to quantify annotated Sus scrofa mature miRNAs from miRBase (Release 21) and to predict candidate novel miRNA precursors. Among the retained 295 normalized mature miRNA expression profiles sscmiR1, sscmiR133a3p, sscmiR378, sscmiR206, and sscmiR10b were the most abundant, all of which have previously been shown to be expressed in pig skeletal muscle. Additionally, 27 unique candidate novel miRNA precursors were identified exhibiting homologous sequence to annotated human miRNAs. The composition of classes of small RNA present in this dataset was also characterized; while the majority of unique expressed sequence tags were not annotated in any of the queried databases, the most abundantly expressed class of small RNA in this dataset was miRNAs. This data provides a resource to evaluate miRNA regulation of gene expression and effects on complex trait phenotypes in adult pig skeletal muscle. The raw sequencing data were deposited in the Sequence Read Archive, BioProject PRJNA363073.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 50-53"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.07.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35192132","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: 4

A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts 不同植物寄主上sojina Cercospora sojina与Mycosphaerella病原菌属其他成员的基因组比较分析

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.07.007

Fanchang Zeng , Xin Lian , Guirong Zhang , Xiaoman Yu , Carl A. Bradley , Ray Ming

{"title":"A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts","authors":"Fanchang Zeng , Xin Lian , Guirong Zhang , Xiaoman Yu , Carl A. Bradley , Ray Ming","doi":"10.1016/j.gdata.2017.07.007","DOIUrl":"10.1016/j.gdata.2017.07.007","url":null,"abstract":"<div>Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. Here, we report the genome sequence of C. sojina, and comparative genome analysis with plant pathogen members of the genus Mycosphaerella (Zymoseptoria. tritici (synonyms M. graminicola), M. pini, M. populorum and M. fijiensis - pathogens of wheat, pine, poplar and banana, respectively). Synteny or collinearity was limited between genomes of major Mycosphaerella pathogens. Comparative analysis with these related pathogen genomes indicated distinct genome-wide repeat organization features. It suggests repetitive elements might be responsible for considerable evolutionary genomic changes. These results reveal the background of genomic differences and similarities between Dothideomycete species. Wide diversity as well as conservation on genome features forms the potential genomic basis of the pathogen specialization, such as pathogenicity to woody vs. herbaceous hosts. Through comparative genome analysis among five Dothideomycete species, our results have shed light on the genome features of these related fungi species. It provides insight for understanding the genomic basis of fungal pathogenicity and disease resistance in the crop hosts.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 54-63"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.07.007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35192133","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

Genome assembly of Chryseobacterium sp. strain IHBB 10212 from glacier top-surface soil in the Indian trans-Himalayas with potential for hydrolytic enzymes 印度跨喜马拉雅山脉冰川顶表土中黄杆菌菌株IHBB 10212的基因组组装及其水解酶潜力

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.06.003

Mohinder Pal , Mohit Kumar Swarnkar , Hena Dhar , Sanjay Chhibber , Arvind Gulati

{"title":"Genome assembly of Chryseobacterium sp. strain IHBB 10212 from glacier top-surface soil in the Indian trans-Himalayas with potential for hydrolytic enzymes","authors":"Mohinder Pal , Mohit Kumar Swarnkar , Hena Dhar , Sanjay Chhibber , Arvind Gulati","doi":"10.1016/j.gdata.2017.06.003","DOIUrl":"10.1016/j.gdata.2017.06.003","url":null,"abstract":"<div>The cold-active esterases are gaining importance due to their catalytic activities finding applications in chemical industry, food processes and detergent industry as additives, and organic synthesis of unstable compounds as catalysts. In the present study, the complete genome sequence of 4,843,645bp with an average 34.08% G+C content and 4260 protein-coding genes are reported for the low temperature-active esterase-producing novel strain of Chrysobacterium isolated from the top-surface soil of a glacier in the cold deserts of the Indian trans-Himalayas. The genome contained two plasmids of 16,553 and 11,450bp with 40.54 and 40.37% G+C contents, respectively. Several genes encoding the hydrolysis of ester linkages of triglycerides into fatty acids and glycerol were predicted in the genome. The annotation also predicted the genes encoding proteases, lipases, amylases, β-glucosidases, endoglucanases and xylanases involved in biotechnological processes. The complete genome sequence of Chryseobacterium sp. strain IHBB 10212 and two plasmids have been deposited vide accession numbers CP015199, CP015200 and CP015201 at DDBJ/EMBL/GenBank.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 46-49"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.06.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35183372","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

Erratum to “RNA-seq detects pharmacological inhibition of Epstein-Barr virus late transcription during spontaneous reactivation” [Genomics Data 13 (2017) 5–6] “RNA-seq检测爱泼斯坦-巴尔病毒在自发再激活过程中的晚期转录的药理抑制”的勘误[基因组学数据13 (2017)5-6]

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.07.001

An T. Phan , Delsy M. Martinez , JJ L. Miranda

引用次数: 0

De novo transcriptome assembly for the lung of the ornamented pygmy frog (Microhyla fissipes) 装饰侏儒蛙肺的从头转录组组装

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.07.002

Lusha Liu , Shouhong Wang , Lanying Zhao , Jianping Jiang

{"title":"De novo transcriptome assembly for the lung of the ornamented pygmy frog (Microhyla fissipes)","authors":"Lusha Liu , Shouhong Wang , Lanying Zhao , Jianping Jiang","doi":"10.1016/j.gdata.2017.07.002","DOIUrl":"10.1016/j.gdata.2017.07.002","url":null,"abstract":"<div>Microhyla fissipes, belonging to Neobatrachia, is a new model organism to study developmental biology, adaptive mechanisms from aquatic to terrestrial life, environmental toxicology, and human disease. M. fissipes use of lungs soon after hatching makes it extremely valuable for the study of lung function and development mechanisms. However, our knowledge of genes and pathways associated with lung development in M. fissipes is very limited. In this study, we conducted de novo transcriptome assembly for the lung of M. fissipes using the Illumina HiSeq4000 platform. We obtained approximately 9.0GB clean data from the lung of the stage 28 tadpole with lung inflation (NCBI accession numbers: SRP107055). De novo transcriptome assembly identified 209,358 transcripts and 93,813 unigenes. In addition, BLASTX against NR, NT, KO, SwissProt, PFAM, GO and KOG databases were used to annotate all the 93,813 unigenes. This study provides the transcriptome and functional annotation of genes in M. fissipes lung development, which will be useful for comparative transcriptome analyses and promote research into mechanism of lung development in anuran.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 44-45"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.07.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35183371","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: 2

Transcriptome analysis of reproductive tissue differentiation in Jatropha curcas Linn. 麻疯树生殖组织分化的转录组分析。

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.05.008

Nisha Govender , Siju Senan , Zeti-Azura Mohamed-Hussein , Wickneswari Ratnam

引用次数: 4

De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean 哥伦比亚加勒比海地区红海龟巢的从头转录组组装

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.06.005

Javier Hernández-Fernández , Andrés Pinzón , Leonardo Mariño-Ramírez

引用次数: 6

Genome sequence of the type strain CLIB 1764T (= CBS 14374T) of the yeast species Kazachstania saulgeensis isolated from French organic sourdough 从法国有机酵母中分离的萨克斯坦酵母CLIB 1764T (= CBS 14374T)型菌株的基因组序列

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.07.003

Véronique Sarilar , Lieven Sterck , Saki Matsumoto , Noémie Jacques , Cécile Neuvéglise , Colin R. Tinsley , Delphine Sicard , Serge Casaregola

引用次数: 16