New Annotation Of The Lolium Perenne Genome Described By Bryne Et Al, (2015)

Annotation of the Lolium perenne genome described by Bryne <em>et al,</em> (2015, DOI: 10.1111/tpj.13037). To identify genic regions RNA sequencing data were aligned to the genome using Tophat (Tophat version: V2.0.11; Bowtie2 version: 2.1.0). Isoforms, of genes, were identified using Cufflinks (Version: 2.2.0). Open reading frames (ORF), were found using using program ORFpredictor (version: 3.0). Frame selection was assisted by BLASTX searching the proteomes of <em>Arabidopsis thaliana</em> (TAIR, version: 10), <em>Oryza sativa</em> (Ensembl)<em>, Gycine max </em>(Ensembl)<em>, Populus trichocarpa </em>(Ensembl)<em> and Manihot esculenta </em>(cassava, v4.1). The predicted CDS was back translated to annotate the GFF file created by Cufflinks for CDS using scripts kindly provided by Palmieri<em> et al.,</em> 2012 (doi: 10.1371/journal.pone.0046415). These results are included in the file LG_V2_full.gtf. Functional annoatation was using three sources. First, protein sequences were search against the <em>A. thaliana</em> proteome using BLASTP. Second, the proteins were search against the Swiss-Prot non-redundant protein database (http://www.uniprot.org/downloads downloaded 14/03/2016, UniProt Consortium, 2014), again using BLASTP. In the third step, the protein sequences were scanned against InterPro's signatures using InterProScan (Version: 5.16-55). These data are included in the file ALLXLOC.txt.本数据集为Bryne等人（2015年，DOI: 10.1111/tpj.13037）所报道的多年生黑麦草（Lolium perenne）基因组注释信息。 为鉴定基因区域，研究人员使用Tophat工具（Tophat版本：V2.0.11；Bowtie2版本：2.1.0）将RNA测序数据比对至该参考基因组。利用Cufflinks工具（版本：2.2.0）鉴定基因的可变剪接异构体。通过ORFpredictor工具（版本：3.0）预测开放阅读框（Open Reading Frame, ORF）。开放阅读框的框选工作借助BLASTX完成，分别比对拟南芥（Arabidopsis thaliana，TAIR数据库版本10）、水稻（Oryza sativa，Ensembl数据库）、大豆（Glycine max，Ensembl数据库）、毛果杨（Populus trichocarpa，Ensembl数据库）以及木薯（Manihot esculenta，木薯参考基因组版本v4.1）的蛋白质组。研究人员将预测得到的编码序列（Coding Sequence, CDS）进行反向翻译，借助Palmieri等人2012年（DOI: 10.1371/journal.pone.0046415）提供的脚本，对Cufflinks生成的编码序列GFF文件进行注释。上述注释结果已整合至文件LG_V2_full.gtf中。 功能注释采用三类数据源完成：其一，通过BLASTP工具将蛋白质序列比对至拟南芥蛋白质组；其二，再次利用BLASTP工具将蛋白质序列比对至Swiss-Prot非冗余蛋白质数据库（下载地址：http://www.uniprot.org/downloads，下载时间：2016年3月14日，数据来源：UniProt联盟，2014年）；其三，使用InterProScan工具（版本：5.16-55）扫描蛋白质序列，匹配InterPro的特征签名。上述分析数据已存储至文件ALLXLOC.txt中。