Gossypium raimondii (D5) genome JGI_v2_a2.1

Assembly Details

This release is a high quality version of the Cotton D genome from DNA provided by Andrew Paterson at Univ. GA. It was sequenced with a combination of Sanger based sequence (1.52x assembled coverage with 0.95x coverage from BAC end sequence and fosmids end sequence) Roche 454 pyrosequencing (14.95x linear and 3.1x non-redundant pairs assembled coverage), and Illumina based short reads (primarily to correct 454 insertion/deletion errors) and assembled the genome using our modified version of Arachne2.

V2.0 includes the removal of small repetitive contigs within scaffolds and a new detailed map integration with the recently available tetraploid map that was used to correct several scaffold orientation issues. The combination of:

was used to identify misjoins in the assembly. Misjoins were characterized by a combination of an abrupt change in the linkage group (or synteny) within a region of low BAC/Fosmid support. A total of 13 misjoins were identified and subsequently broken.

Scaffolds were oriented, ordered, and joined together using the aforementioned resources. A total of 51 joins were assembled to form a final assembly containing 13 chromosomes. This release is of suitably high quality to match our previous fully Sanger sequenced plant genomes.


Gene Predictions

85,746 transcript assemblies were made from about 1B pairs of D5 paired-end Illumina RNAseq reads, 55,294 transcript assemblies about 0.25B D5 single end Illumina RNAseq reads, 62,526 transcript assemblies from 0.15B TET single end Illumina RNAseq reads. All these transcript assemblies from RNAseq reads were made using PERTRAN (Shu et. al., manuscript in preparation). 120,929 transcript assemblies were constructed using PASA (Haas, 2003) from 56,638 D5 Sanger ESTs, 2.5M D5 454 RNAseq reads and all RNAseq transcript assemblies above. 133,073 transcript assemblies were constructed using PASA from 296,214 TET Sanger ESTs and about 2.9M TET 454 reads. The larger number of transcript asssemblies from fewer TET sequences is due to fragment nature of the assemblies. Loci were determined by transcript assembly alignments and/or EXONERATE alignments of proteins from arabi (Arabidopsis thaliana), cacao, rice, soybean, grape and poplar proteins to repeat-soft-masked G. raimnondaii genome using RepeatMasker (Smit, 1996-2012) with up to 2K BP extension on both ends unless extending into another locus on the same strand.

Gene models were predicted by homology-based predictors, FGENESH+ (Salamov, 2000), FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), and GenomeScan (Yeh, 2001). The best scored predictions for each locus are selected using multiple positive factors including EST and protein support, and one negative factor: overlap with repeats. The selected gene predictions were improved by PASA. Improvement includes adding UTRs, splicing correction, and adding alternative transcripts. PASA-improved gene model proteins were subject to protein homology analysis to above mentioned proteomes to obtain Cscore and protein coverage. Cscore is a protein BLASTP score ratio to MBH (mutual best hit) BLASTP score and protein coverage is highest percentage of protein aligned to the best of homologs. PASA-improved transcripts were selected based on Cscore, protein coverage, EST coverage, and its CDS overlapping with repeats. The transcripts were selected if its Cscore is larger than or equal to 0.5 and protein coverage larger than or equal to 0.5, or it has EST coverage, but its CDS overlapping with repeats is less than 20%. For gene models whose CDS overlaps with repeats for more that 20%, its Cscore must be at least 0.9 and homology coverage at least 70% to be selected. The selected gene models were subject to Pfam analysis and gene models whose protein is more than 30% in Pfam TE domains were removed. Final gene set has 37,505 protein coding genes and 77,267 protein coding transcripts.

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