Total RNA was isolated from the skin tissues of channel catfish and common carp using the RNeasy Plus Universal Kit (Qiagen, CA) according to the manufacturer's instructions. Raw sequencing reads were filtered for base quality ≥15 and read length ≥30 bp. The de novo assembly was produced using Trinity (version r2012-06-08)68 (link). The assembled contigs for each species were used as queries against the NCBI Non-Redundant protein database using BLASTX with maximum e-value of 1e−5, and only the best match was annotated for each contig.
Interspecific comparative skin transcriptome analyses between common carp (scaled) and channel catfish (scaleless) were conducted using TBLASTX with a E-value cutoff of 1e−5 with the following steps: (1) The carp skin transcriptome and the channel catfish skin transcriptome were de novo assembled, separately; (2) The carp skin transcriptome was annotated by BLASTX analysis against the non-redundant database; (3) A list of unique protein-coding transcripts from the common carp skin transcriptome were compiled and queried against the channel catfish skin transcriptome; (4) For carp contigs with no matches to the channel catfish transcriptome assembly but with matches to the non-redundant database, the sequences of each best match were retrieved from the non-redundant database and used to query the channel catfish skin transcriptome assembly. Those carp transcripts that remained unidentified were annotated as genes that were expressed in the carp skin but not expressed in the channel catfish skin.
Interspecific comparative skin transcriptome analyses between common carp (scaled) and channel catfish (scaleless) were conducted using TBLASTX with a E-value cutoff of 1e−5 with the following steps: (1) The carp skin transcriptome and the channel catfish skin transcriptome were de novo assembled, separately; (2) The carp skin transcriptome was annotated by BLASTX analysis against the non-redundant database; (3) A list of unique protein-coding transcripts from the common carp skin transcriptome were compiled and queried against the channel catfish skin transcriptome; (4) For carp contigs with no matches to the channel catfish transcriptome assembly but with matches to the non-redundant database, the sequences of each best match were retrieved from the non-redundant database and used to query the channel catfish skin transcriptome assembly. Those carp transcripts that remained unidentified were annotated as genes that were expressed in the carp skin but not expressed in the channel catfish skin.
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