Differentially-Expressed Genes Associated with Faster Growth of the Pacific Abalone, Haliotis discus hannai

Abstract

The Pacific abalone Haliotis discus hannai is used for commercial aquaculture in Korea. We examined the transcriptome of Pacific abalone Haliotis discus hannai siblings using NGS technology to identify genes associated with high growth rates. Pacific abalones grown for 200 days post-fertilization were divided into small-, medium-, and large-size groups with mean weights of 0.26 ± 0.09 g, 1.43 ± 0.405 g, and 5.24 ± 1.09 g, respectively. RNA isolated from the soft tissues of each group was subjected to RNA sequencing. Approximately 1%–3% of the transcripts were differentially expressed in abalones, depending on the growth rate. RT-PCR was carried out on thirty four genes selected to confirm the relative differences in expression detected by RNA sequencing. Six differentially-expressed genes were identified as associated with faster growth of the Pacific abalone. These include five up-regulated genes (including one specific to females) encoding transcripts homologous to incilarin A, perlucin, transforming growth factor-beta-induced protein immunoglobulin-heavy chain 3 (ig-h3), vitelline envelope zona pellucida domain 4, and defensin, and one down-regulated gene encoding tomoregulin in large abalones. Most of the transcripts were expressed predominantly in the hepatopancreas. The genes identified in this study will lead to development of markers for identification of high-growth-rate abalones and female abalones.

A Microarray Study of Carpet-Shell Clam (Ruditapes decussatus) Shows Common and Organ-Specific Growth-Related Gene Expression Differences in Gills and Digestive Gland

“…Growth is generally associated to an increase of protein synthesis (Fraser and Rogers, 2007 ). In other studies in mollusks growth rate was also positively associated with the expression of proteins implicated in protein synthesis, including many ribosomal proteins (Meyer and Manahan, 2010 ; van der Merwe et al, 2011 ; Choi et al, 2015 ). In our microarray, 380 probes were identified as genes related to this important function, but only 3 in the digestive gland showed differential expression between F and S clams.…”

“…One potential partial explanation for this paradox is that the annotation of mollusk genes is difficult due to their evolutionary distance to vertebrates, which are the main source of genetic functional information for GO analyses in animals. In fact, most transcriptomic studies of growth in mollusks report a low rate of transcript annotation, and the percent of identified proteins among DEGs is usually below 40% (Meyer and Manahan, 2010 ; Choi et al, 2015 ; Valenzuela-Miranda et al, 2015 ). The low rate of identified and annotated genes can have the consequence of lowering the power of enrichment tests for GO categories and KEGG pathways, resulting in the misidentification of functionally relevant sets of genes.…”

“…In another study, Shi and He ( 2014 ) performed RNA-Seq on large and small farmed pearl oysters and confirmed differential expression associated to faster growth for 19 genes using qPCR. Among other mollusk taxa, only abalones, which are gastropods, have been the subject of transcriptomic studies of growth (van der Merwe et al, 2011 ; Choi et al, 2015 ; Valenzuela-Miranda et al, 2015 ). All together these studies indicate that differential expression associated to differential growth appears at a great variety of genes with very different functions.…”

“…Therefore, the use of whole-animal samples in transcriptomic studies of growth limits importantly the data and conclusions that can be drawn from those studies. While in some of the studies reported above the expression of a small set of selected genes was further analyzed in specific organs by quantitative PCR (van der Merwe et al, 2011 ; Shi and He, 2014 ; Choi et al, 2015 ), they represent a tiny fraction of the whole set of differentially expressed genes (DEGs) discovered, and therefore they offer only limited information on the molecular basis of organ-specific functions related to differential growth. The analysis of transcriptomic profiles of separate organs is clearly necessary.…”

Genome Sequences of a Novel Picorna-Like Virus from Pacific Abalone ( Haliotis discus hannai ) in South Korea

“…However, the aquaculture production rate of abalone has been decreasing recently, possibly due to several reasons, such as deterioration of aquaculture environments, genetic degradation, and diseases (2). A variety of marine viruses cause significant economic losses in an aquaculture species (3, 4).…”