Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

Table 5 Reciprocal BLAST comparison between catfish and five model fish with sequenced genome

Species	#Total proteins	#Protein coding genes	#Proteins have hits in catfish	#Genes have hits in catfish	#Unique protein hits by catfish	#Unique gene hits by catfish
zebrafish	40,585	26,152	39,250	25,330	24,281	20,014
fugu	47,841	18,523	47,583	18,336	26,230	15,834
medaka	24,661	19,686	23,311	18,465	18,200	16,007
stickleback	27,576	20,787	26,375	19,740	19,503	16,835
Tetraodon	23,118	19,602	22,648	19,208	17,636	15,996

First, protein sequences of five model fish in Ensembl database were searched against catfish contigs using TBLASTN to assess the extent of reference sequences that were observed in catfish; reciprocally, all catfish contigs were searched against protein sequences of five model fish using BLASTX to assess the number of genes represented by the catfish sequences when compared to those in each of the five species.

ISSN: 1471-2164