catfish RNA-Seq for SNP identification
Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array
Transcriptome sequencing was conducted for channel catfish and blue catfish. Illumina sequencing was used to generate the short reads of expressed sequences. cDNAs were made from pooled RNA samples prepared from 11 tissues of 47 channel catfish and 19 blue catfish. The cDNAs were sequenced with one lane each using Illumina GA-II and Illumina HiSeq 2000 for each species, respectively. Paired-end sequence were generated with 36 bp and 100 bp read length on Illumina Genome Analyzer-II and Illumina HiSeq 2000.
Transcriptome sequencing was conducted for channel catfish and blue catfish using Illumina sequencing technology.  Approximately 220 million reads (15.6 Gb) for channel catfish and 280 million reads (19.5 Gb) for blue catfish were obtained by sequencing gene transcripts derived from various tissues of multiple individuals from a diverse genetic background. A total over 35 billion base pairs of expressed short read sequences were generated.  Over two million putative SNPs were identified from channel catfish and almost 2.5 million putative SNPs were identified from blue catfish.  Of these putative SNPs, a set of filtered SNPs were identified including 446,169 intra-specific SNPs for channel catfish, 555,175 intra-specific SNPs for blue catfish, and  322,006 inter-specific SNPs between channel catfish and blue catfish.  These filtered SNPs are distributed with 17,806 uniques genes in channel catfish and 18,887 unique genes in blue catfish.