DOI: 10.5061/dryad.sv31k
title: Data from: A comprehensive transcriptome of early development in yellowtail kingfish (Seriola lalandi)

description: Seriola lalandi is an ecologically and economically important species that
 is globally distributed in temperate and subtropical marine waters. The
 aim of this study was to identify large numbers of genic single nucleotide
 polymorphisms (SNPs) and differential gene expression (DGE) related to the
 early development of normal and deformed S. lalandi larvae using
 high-throughput RNA-seq data. A de novo assembly of reads generated 40 066
 genes ranging from 300 bases to 64 799 bases with an N90 of 788 bases.
 Homology search and protein signature recognition assigned gene ontology
 (GO) terms to a total of 15 744 (39.34%) genes. A search against the Kyoto
 Encyclopedia of Genes and Genomes Pathway database (KEGG) retrieved 6808
 KEGG orthology (KO) identifiers for 10 520 genes (26.25%), and mapping of
 KO identifiers generated 337 KEGG pathways. Comparisons of annotated genes
 revealed that 1262 genes were downregulated and 1047 genes were
 upregulated in the deformed larvae group compared to the normal group of
 larvae. Additionally, we identified 6989 high-quality SNPs from the
 assembled transcriptome. These putative SNPs contain 4415 transitions and
 2574 transversions, which will be useful for further ecological studies of
 S. lalandi. This is the first study to use a global transcriptomic
 approach in S. lalandi, and the resources generated can be used further
 for investigation of gene expression of marine teleosts to investigate
 larval developmental biology. The results of the GO enrichment analysis
 highlight the crucial role of the extracellular matrix in normal skeleton
 development, which could be important for future studies of skeletal
 deformities in S. lalandi and other marine species.
description: Sequences of S. lalandi
 transcriptome (fasta file)Transcriptome contigs
 assembled from filtered paired end sequencing reads on Illumina HiSeq™
 2000 platform using Trinity. Only non-redundant (cluster in CAP3), more
 than 300bp contigs with open reading frame were keptS.lalandi_final_transcriptome.fastaBLAST results, Annotation information, Gene Ontology (.dat file for Blast2GO)Standard input file for BLAST2GO. This file can be loaded directly into .jnlp executable file downloaded from BLAST2GO website. Includes BLASTX results against NCBI’s non-redundant protein database, InterProScan search result for functional signature of protein domain. Gene Ontology information based on best hit gene matches and KEGG resultsblast2go_final-S.lalandi.datInformation on SNPs identified from transcriptome data (vcf file)The details of SNPs calling are described in Materials and methodsSeriola_lalandi_variant_file.vcfThe mapping count tableThis count table was used as an input for differential gene expression analysis in edgeRCount_table_S_lalandi.csvTable containing differential expressed genes (result of edgeR)This table contains data of list of genes that were &lt; 0.01 FDR value and differed in their expression value at least 2 fold between two groupsFinal_Results_edgeR.csvGO term reduction tableGene Ontology terms were summarized and redundant GO terms were removed by semantic similarity-based approach employed in REViGO .REVIGO_Results.csvPathways-K_numbers_contigs-IDThis is a text file containing all the pathways reconstructed in KEGG automatic annotation server from this RNA-seq study. All the pathways and the K-numbers (each K number represents an ortholog group of genes, and it is directly linked to an object in the KEGG pathway map or the BRITE functional hierarchy) along with contigs-id associated with corresponding K-number are presented in one file. One can search specific pathways of interest and can note the K numbers and contigs-id therein. There after, these contigs-id can be interrogated in blast2go.dat file to obtain fasta sequences of gene/set of genes from the pathway of interest (in order to design primers or other purpose).