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ARS Home » Southeast Area » Stoneville, Mississippi » Warmwater Aquaculture Research Unit » Research » Publications at this Location » Publication #279988

Research Project: Genetics, Physiology, and Health Research to Improve Catfish Production

Location: Warmwater Aquaculture Research Unit

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

item Liu, Shikai
item Zhang, Yu
item Zhou, Zunchun
item Waldbieser, Geoffrey - Geoff
item Sun, Fanyue
item Lu, Jianguo
item Zhang, Jiaren
item Jiang, Yanliang
item Zhang, Hao
item Wang, Xiuli
item Rajendran, K
item Khoo, Lester
item Kucuktas, Huseyin
item Peatman, Eric
item Liu, Zhanjiang

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2012
Publication Date: 1/16/2012
Citation: Liu, S., Zhang, Y., Zhou, Z., Waldbieser, G.C., Sun, F., Lu, J., Zhang, J., Jiang, Y., Zhang, H., Wang, X., Rajendran, K.V., Khoo, L., Kucuktas, H., Peatman, E., Liu, Z. 2012. Efficient assembly and annotation of the transcriptome of catfish by RNA-seq analysis of a doubled haploid homozygote. Biomed Central (BMC) Genomics. 13:595.

Interpretive Summary: Efficient annotation of the channel catfish whole genome sequence assembly requires the comprehensive identification of all the portions of the genome that are transcribed into RNA. A cooperative project between scientists at Auburn University and the USDA, ARS, Catfish Genetics Research Unit used next-generation high-throughput DNA sequencing of RNA prepared from tissues of a unique, homozygous catfish to produce more than 300 million complementary DNA sequences. Bioinformatic analyses assembled these sequences into more than 25,000 unique protein-encoding genes. This research helped define the channel catfish transcriptome and provided a valuable resource to help assist in the assembly and annotation of the channel catfish genome.

Technical Abstract: Upon the completion of whole genome sequencing, thorough genome annotation that associates genome sequences with biological meanings is essential. Genome annotation depends on the availability of transcript information as well as orthology information. In teleost fish, genome annotation is seriously hindered by genome duplication. Because of gene duplications, one cannot establish orthologies simply by homology comparisons. Rather intense phylogenetic analysis or structural analysis of orthologies is required for the identification of genes. To conduct phylogenetic analysis and orthology analysis, full-length transcripts are essential. Generation of large numbers of full-length transcripts using traditional transcript sequencing is very difficult and extremely costly. In this work, we took advantage of a doubled haploid catfish, which has two sets of identical chromosomes and in theory there should be no allelic variations. As such, transcript sequences generated from next-generation sequencing can be favorably assembled into full-length transcripts. Deep sequencing of the doubled haploid channel catfish transcriptome was performed using Illumina HiSeq 2000 platform, yielding over 300 million high-quality trimmed reads totaling 27 Gbp. Assembly of these reads generated 374,975 non-redundant transcript-derived contigs. Functional annotation of the assembly allowed identification of 25,144 unique protein-encoding genes. A total of 2,659 unique genes were identified as putative duplicated genes in the catfish genome because the assembly of the corresponding transcripts harbored PSVs or MSVs (in the form of pseudo-SNPs in the assembly). Of the 25,144 contigs with unique protein hits, around 20,000 contigs matched 50% length of reference proteins, and over 14,000 transcripts were identified as full-length with complete open reading frames. The characterization of consensus sequences surrounding start codon and the stop codon confirmed the correct assembly of the full-length transcripts. The large set of transcripts assembled in this study is the most comprehensive set of genome resources ever developed from catfish, which will provide the much needed resources for functional genome research in catfish, serving as a reference transcriptome for genome annotation, analysis of gene duplication, gene family structures, and digital gene expression analysis. The putative set of duplicated genes provide a starting point for genome scale analysis of gene duplication in the catfish genome, and should be a valuable resource for comparative genome analysis, genome evolution, and genome function studies.