New annotation of the Lolium perenne genome described by Bryne et al, (2015)

Annotation of the Lolium perenne genome described by Bryne et al, (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 Arabidopsis thaliana (TAIR, version: 10), Oryza sativa (Ensembl), Gycine max (Ensembl), Populus trichocarpa (Ensembl) and Manihot esculenta (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 et al., 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 A. thaliana 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.