Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae

Abstract

Background: Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [1]. Abalone is an economically important fishery and aquaculture animal that is considered a highly prized seafood delicacy. The total global supply of abalone has increased 5-fold since the 1970s and farm production increased explosively from 50 mt to 103 464 mt in the past 40 years. Additionally, researchers have recently focused on abalone given their reported tumor suppression effect. However, despite the valuable features of this marine animal, no genomic information is available for the Haliotidae family and related research is still limited. To construct the H. discus hannai genome, a total of 580-G base pairs using Illumina and Pacbio platforms were generated with 322-fold coverage based on the 1.8-Gb estimated genome size of H. discus hannai using flow cytometry. The final genome assembly consisted of 1.86 Gb with 35 450 scaffolds (>2 kb). GC content level was 40.51%, and the N50 length of assembled scaffolds was 211 kb. We identified 29 449 genes using Evidence Modeler based on the gene information from ab initio prediction, protein homology with known genes, and transcriptome evidence of RNA-seq. Here we present the first Haliotidae genome, H. discus hannai, with sequencing data, assembly, and gene annotation information. This will be helpful for resolving the lack of genomic information in the Haliotidae family as well as providing more opportunities for understanding gastropod evolution.

The Scaly-foot Snail genome and implications for the origins of biomineralised armour

“…Among the expanded genes on Chr11 (262 genes), one that controls protein binding to proteoglycan (for instance, chitin) known as DMBT1 24 with scavenger receptor cysteine-rich (SRCR) domains was found to be highly expressed in both the scalesecreting epithelium and shell-secreting mantle ( Fig. 4a) with up to 65 tandemly duplicated paralogues compared with one or two copies in other molluscs 25 . Proteins with SRCR domains are commonly detected in shell matrix proteins 18 .…”

The evolution of molluscs

“…Alongside the emerging patterns of molluscan phenotypic evolution based on morphogenetic and palaeontological data, significant insights have been gained concerning the molecular mechanisms that govern their development (Wanninger & Wollesen, ). Thereby, the release of the genomes of various gastropods including the Pacific abalone Haliotis discus hannai (Nam et al, ), the freshwater snail Biomphalaria glabrata (Adema et al, ), and the basally branching owl limpet Lottia gigantea (Simakov et al, ) together with several bivalves [e.g. Crassostrea gigas (Thunberg, 1793) (Zhang et al, ), Patinopecten yessoensis (Jay, 1857) (Wang et al, ), and other scallop, oyster, and mussel species (Takeuchi et al, ; Du et al, ; Li et al, , ; Sun et al, )] and the California two‐spot octopus Octopus bimaculoides Pickford & McConnaughey, 1949 (Albertin et al, ) provided an important framework for studies into key developmental regulators such as Hox and ParaHox genes as well as signalling molecules involved in dorso‐ventral axis patterning (bone morphogenetic protein (BMP)/decapentaplegic (Dpp) pathway) and left/right determination (Nodal pathway).…”

Expression of Heat Shock Proteins in Thermally Challenged Pacific Abalone Haliotis discus hannai

“…Based on this principle, most studies in abalone randomly selected HSP70 as a molecular marker to assess the thermal condition. However, the release of the draft genome [15] facilitated the analysis of transcriptome-wide expression profiles in a short time span.…”

“…First, low quality sequences (PHRED score; Q ≤ 20) and adapter contamination were eliminated using Trimmomatic v.0.36 [23]. The cleaned sequences were mapped to the draft version of the reference genome [15] using the STAR mapper, along with the RNA-Seq by the Expectation Maximization (RSEM) method to obtain the expression value for each gene/transcript in the genome [24]. The read counts estimated by RSEM were subjected to edgeR v.3.22.5 to obtain differential expression scores and determine statistical significance [25].…”

“…To mitigate temperature-related problems, in-depth knowledge of abalone genetics is required. In particular, for H. discus hannai, few de novo transcriptome profiling studies have been conducted to capture transcript expression patterns under various stresses [12][13][14] since the release of the draft genome [15]. In most studies of Pacific abalone and other abalones, heat shock family proteins were randomly selected as molecular quantification markers for thermally challenged abalones [16][17][18].…”