title: Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout.
abstract: Efforts to obtain a comprehensive genome sequence for rainbow trout are ongoing and will be complemented by transcriptome information that will enhance genome assembly and annotation. Previously, transcriptome reference sequences were reported using data from different sources. Although the previous work added a great wealth of sequences, a complete and well-annotated transcriptome is still needed. In addition, gene expression in different tissues was not completely addressed in the previous studies. In this study, non-normalized cDNA libraries were sequenced from 13 different tissues of a single doubled haploid rainbow trout from the same source used for the rainbow trout genome sequence. A total of ~1.167 billion paired-end reads were de novo assembled using the Trinity RNA-Seq assembler yielding 474,524 contigs > 500 base-pairs. Of them, 287,593 had homologies to the NCBI non-redundant protein database. The longest contig of each cluster was selected as a reference, yielding 44,990 representative contigs. A total of 4,146 contigs (9.2%), including 710 full-length sequences, did not match any mRNA sequences in the current rainbow trout genome reference. Mapping reads to the reference genome identified an additional 11,843 transcripts not annotated in the genome. A digital gene expression atlas revealed 7,678 housekeeping and 4,021 tissue-specific genes. Expression of about 16,000-32,000 genes (35-71% of the identified genes) accounted for basic and specialized functions of each tissue. White muscle and stomach had the least complex transcriptomes, with high percentages of their total mRNA contributed by a small number of genes. Brain, testis and intestine, in contrast, had complex transcriptomes, with a large numbers of genes involved in their expression patterns. This study provides comprehensive de novo transcriptome information that is suitable for functional and comparative genomics studies in rainbow trout, including annotation of the genome.
authors: Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, 37132, United States of America.
authors: Mohamed
authors: M
authors: Salem
authors: Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, 37132, United States of America.
authors: Bam
authors: B
authors: Paneru
authors: Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, 37132, United States of America.
authors: Rafet
authors: R
authors: Al-Tobasei
authors: Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, 37132, United States of America.
authors: Fatima
authors: F
authors: Abdouni
authors: School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington 99164, United States of America.
authors: Gary H
authors: GH
authors: Thorgaard
authors: The National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Leetown, West Virginia 25430, United States of America.
authors: Caird E
authors: CE
authors: Rexroad
authors: Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, West Virginia, 26506, United States of America.
authors: Jianbo
authors: J
authors: Yao
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D023681:Cichlids / Q000235:genetics; D020451:Contig Mapping; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling; D015723:Gene Library; D063990:Gene Ontology; D020043:Genes, Essential; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D017686:Oncorhynchus mykiss / Q000145:classification / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger