Genomics Data最新文献_第2页

Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12 单核模型褐腐菌Postia (Rhodonia)胎盘SB12基因组序列草图

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.08.003

Jill Gaskell , Phil Kersten , Luis F. Larrondo , Paulo Canessa , Diego Martinez , David Hibbett , Monika Schmoll , Christian P. Kubicek , Angel T. Martinez , Jagjit Yadav , Emma Master , Jon Karl Magnuson , Debbie Yaver , Randy Berka , Kathleen Lail , Cindy Chen , Kurt LaButti , Matt Nolan , Anna Lipzen , Andrea Aerts , Dan Cullen

引用次数: 15

Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s. 针叶树病原菌杂交菌(Heterobasidion annosum s.s)基因组序列的比较分析。

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.10.003

Jaeyoung Choi , Gir-Won Lee , Ki-Tae Kim , Jongbum Jeon , Nicolas Détry , Hsiao-Che Kuo , Hui Sun , Fred O. Asiegbu , Yong-Hwan Lee

{"title":"Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s.","authors":"Jaeyoung Choi , Gir-Won Lee , Ki-Tae Kim , Jongbum Jeon , Nicolas Détry , Hsiao-Che Kuo , Hui Sun , Fred O. Asiegbu , Yong-Hwan Lee","doi":"10.1016/j.gdata.2017.10.003","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.10.003","url":null,"abstract":"<div>The causal agent of root and butt rot of conifer trees, Heterobasidion annosum, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of H. annosum sensu stricto (isolate 03012) was sequenced and analyzed with the genome sequences of 23 white-rot and 13 brown-rot fungi. The draft genome assembly of H. annosum has a size of 31.01Mb, containing 11,453 predicted genes. Whole genome alignment showed that 84.38% of H. annosum genome sequences were aligned with those of previously sequenced H. irregulare TC 32-1 counterparts. The result is further supported by the protein sequence clustering analysis which revealed that the two genomes share 6719 out of 8647 clusters. When sequencing reads of H. annosum were aligned against the genome sequences of H. irregulare, six single nucleotide polymorphisms were found in every 1kb, on average. In addition, 98.68% of SNPs were found to be homo-variants, suggesting that the two species have long evolved from different niches. Gene family analysis revealed that most of the white-rot fungi investigated had more gene families involved in lignin degradation or modification, including laccases and peroxidase. Comparative analysis of the two Heterobasidion spp. as well as white-/brown-rot fungi would provide new insights for understanding the pathobiology of the conifer tree pathogen.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 106-113"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.10.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90002091","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

Genome-wide analysis of mouse cortical neurons lacking miR-27b 缺乏miR-27b的小鼠皮质神经元的全基因组分析

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2015.11.021

M. Gu, V.Y. Poon

引用次数: 0

RNA-seq data comparisons of wild soybean genotypes in response to soybean cyst nematode (Heterodera glycines) 野生大豆基因型对大豆囊线虫(Heterodera glycines)响应的RNA-seq数据比较

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.08.001

Hengyou Zhang, Bao-Hua Song

{"title":"RNA-seq data comparisons of wild soybean genotypes in response to soybean cyst nematode (Heterodera glycines)","authors":"Hengyou Zhang, Bao-Hua Song","doi":"10.1016/j.gdata.2017.08.001","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.08.001","url":null,"abstract":"<div>Soybean [Glycine max (L.) Merr.] is an important crop rich in vegetable protein and oil, and is a staple food for human and animals worldwide. However, soybean plants have been challenged by soybean cyst nematode (SCN, Heterodera glycines), one of the most damaging pests found in soybean fields. Applying SCN-resistant cultivars is the most efficient and environmentally friendly strategy to manage SCN. Currently, soybean breeding and further improvement in soybean agriculture are hindered by severely limited genetic diversity in cultivated soybeans. G. soja is a soybean wild progenitor with much higher levels of genetic diversity compared to cultivated soybeans. In this study, transcriptomes of the resistant and susceptible genotypes of the wild soybean, Glycine soja Sieb & Zucc, were sequenced to examine the genetic basis of SCN resistance. Seedling roots were treated with infective second-stage juveniles (J2s) of the soybean cyst nematode (HG type 2.5.7) for 3, 5, 8days and pooled for library construction and RNA sequencing. The transcriptome sequencing generated approximately 245 million (M) high quality (Q>30) raw sequence reads (125bp in length) for twelve libraries. The raw sequence reads were deposited in NCBI sequence read archive (SRA) database, with the accession numbers SRR5227314-25. Further analysis of this data would be helpful to improve our understanding of the molecular mechanisms of soybean-SCN interaction and facilitate the development of diverse SCN resistance cultivars.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 36-39"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90015405","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: 20

Whole genome of Klebsiella aerogenes PX01 isolated from San Jacinto River sediment west of Baytown, Texas reveals the presence of multiple antibiotic resistance determinants and mobile genetic elements 从德克萨斯州贝镇西部圣哈辛托河沉积物中分离到的产气克雷伯氏菌PX01全基因组显示存在多种抗生素耐药性决定因素和可移动遗传因子

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.07.012

Rupa Iyer , Brian Iken , Ashish Damania

引用次数: 6

Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants 来自圣哈辛托河污水坑下游二恶英污染沉积物的硝化假单胞菌DF05基因组揭示了广泛的芳香降解基因决定因素

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.07.011

Rupa Iyer , Brian Iken , Ashish Damania

引用次数: 8

Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16® application in lettuce 比较宏基因组学揭示了氮肥和氨基16®对生菜土壤细菌群落的影响

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.07.013

Apostolos Kalivas , Ioannis Ganopoulos , Fotis Psomopoulos , Ioannis Grigoriadis , Aliki Xanthopoulou , Evangelos Hatzigiannakis , Maslin Osathanunkul , Athanasios Tsaftaris , Panagiotis Madesis

{"title":"Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16® application in lettuce","authors":"Apostolos Kalivas , Ioannis Ganopoulos , Fotis Psomopoulos , Ioannis Grigoriadis , Aliki Xanthopoulou , Evangelos Hatzigiannakis , Maslin Osathanunkul , Athanasios Tsaftaris , Panagiotis Madesis","doi":"10.1016/j.gdata.2017.07.013","DOIUrl":"10.1016/j.gdata.2017.07.013","url":null,"abstract":"<div>Nutrients in the form of fertilizers and/or other additives such as amino acids, dramatically influence plant development and growth, plant nutrient composition and the level of soil pollution. Moreover, the treatment of soil microbiota is emerging as a new strategy in plant breeding to achieve desirable traits. Thus, integrated study of fertilizer application and soil microbiota might lead to a better understanding of soil-plant interactions and inform the design of novel ways to fertilize plants. Herein we report metagenomics data for soil microbiota in lettuce (Lactuca sativa) treated with fertilizer, amino acids or their combinations as follows: N-fertilizer+Amino16®, Amino16®, N-fertilizer and no treatment control. Data have been deposited in the NCBI Sequence Read Archive (SRA) (accession number: PRJNA388765).</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 14-17"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.07.013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35311415","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 new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3) 新版本的葡萄参考基因组汇编(12X.v2)及其注释(VCost.v3)

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.09.002

A. Canaguier , J. Grimplet , G. Di Gaspero , S. Scalabrin , E. Duchêne , N. Choisne , N. Mohellibi , C. Guichard , S. Rombauts , I. Le Clainche , A. Bérard , A. Chauveau , R. Bounon , C. Rustenholz , M. Morgante , M.-C. Le Paslier , D. Brunel , A.-F. Adam-Blondon

引用次数: 189

Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarian Schmidtea mediterranea 小RNA组测序描绘了地中海施米德虫(Schmidtea mediterranea)多能成体干细胞的小RNA图谱

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.10.004

Yue Li , An Zeng , Xiao-Shuan Han , Ge Li , Yong-Qin Li , Bairong Shen , Qing Jing

{"title":"Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarian Schmidtea mediterranea","authors":"Yue Li , An Zeng , Xiao-Shuan Han , Ge Li , Yong-Qin Li , Bairong Shen , Qing Jing","doi":"10.1016/j.gdata.2017.10.004","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.10.004","url":null,"abstract":"<div>Small noncoding RNAs play a pivotal role in the regulation of gene expression, and are key regulators of animal development. Freshwater planarian exhibits an extraordinary ability to regenerate any missing body parts, representing an emerging model for studying mechanism underlying stem cell regulation and tissue regeneration.Here, we utilized next-generation sequencing (NGS) to identify small RNAs that are expressed in planarian adult stem cells, and are implicated in tissue regeneration. We profiled microRNAs (miRNAs), piwi-interacting RNA (piRNAs), small rDNA-derived RNAs (srRNAs) and endogenous interfering RNAs (endo-siRNAs) population from size 18–30nt, measured the expression of 244 conserved miRNAs, and identified 41 novel miRNAs and 64 novel endo-siRNAs. Expression profiling analyses revealed that most piRNAs and srRNAs are up-regulated during regeneration, and that the most abundantly expressed srRNAs are from 5.8s and 28s rRNA. Furthermore, a target prediction method was adopted to investigate the anti-correlation of small RNAs and mRNA expression. We built up a gene regulatory network based on the genes that are targeted by dynamically changed small RNAs.These results expand the known small RNA repertoire in planarian, and provide valuable insights and a rich resource for understanding the small RNAs landscape in stem cell-mediated regeneration.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 114-125"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.10.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91634586","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: 7

Transcriptome analysis of the Chinese giant salamander (Andrias davidianus) using RNA-sequencing 中国大鲵(Andrias davidianus)转录组测序分析

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.10.005

Yong Huang, Jian Li Xiong, Xiao Chan Gao, Xi Hong Sun

{"title":"Transcriptome analysis of the Chinese giant salamander (Andrias davidianus) using RNA-sequencing","authors":"Yong Huang, Jian Li Xiong, Xiao Chan Gao, Xi Hong Sun","doi":"10.1016/j.gdata.2017.10.005","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.10.005","url":null,"abstract":"<div>The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690bp and N50 of 1263bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 126-131"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.10.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91634585","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