A comprehensive transcriptome of early development in yellowtail kingfish (Seriola lalandi)

Abstract

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.

Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus

“…Although the percentage of unigenes of L. albus with a BLAST-hit may appear to be a relatively small number, we found that this value does not differ from other de novo transcriptome studies with non-model echinoderms14153437. In this sense, the lack of homology with known proteins could be explained by biological reasons such as: i) the lack of annotated protein sequences of phylogenetically close species; ii) sequences from untranslated regions (UTR) of mRNA; iii) long noncoding RNA; and iv) orphan proteins38. These results are congruent to those reported for the transcriptome of the sea urchin S. intermedius 39, the sea star Acanthaster planci 14 and the brittle star Amphiura filiformis 40.…”

Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili

“…Insights into molecular mechanisms may lead to a better understanding of physiological traits such as growth and sex. To date, genetic resources for Seriola species have been developed mainly for yellowtail kingfish and the Japanese yellowtail, including genetic linkage maps [ 9 , 10 ] and a radiation hybrid (RH) map [ 9 ], as well as the production of transcriptome data [ 11 ]. For the greater amberjack, very few molecular resources have been published, but they do include a cytogenetic characterization, which revealed in total 24 mainly acrocentric chromosomes (2n) and, similar to other Carangidae species, no morphologically differentiated sex chromosome [ 12 ].…”

First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi

“…Despite the economic importance of Yellowtail kingfish (YTK) Seriola lalandi world-wide (e.g., with a current annual production of about 4,000 tons, valuing 56 million dollars in Australia), there has been very limited published information regarding genetic and genomic architecture for quantitative complex traits in this species. Recent studies generated initial genomic resources to examine genetic diversity of YTK populations ( Premachandra et al, 2017a ; Sepulveda and Gonzalez, 2017 ) or assessing predictive power of statistical models used for genomic selection ( Nguyen et al, 2018 ), as well using transcriptome information to identify genes related to fish immunity ( Jacobson et al, 2017 ) and those involved with skeletal deformity during early growth phase in this species ( Patel et al, 2016 ). To date, only a low-density genetic linkage map was developed for S. lalandi , involving a handful of 217 microsatellites markers ( Ohara et al, 2005 ).…”