An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species

Abstract

Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2. This assembly approach resulted in 8,371 scaffolds and total length of 1.498 Gb; the N50 was 1.895 Mb, and the longest scaffold was 13.2 Mb. Gene models were predicted, using MAKER2, from RNA-Seq data and all related expressed sequence tags and proteins from NCBI; this resulted in 57,785 genes with an average length of 8,255 bp. In addition, single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone. Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms. Among the six abalone species examined, the endangered white abalone appears to harbor the lowest levels of heterozygosity. This draft genome assembly and the sequencing data provide a foundation for genome-enabled aquaculture improvement for red abalone, and for genome-guided conservation efforts for the other five species and, in particular, for the endangered white and black abalone.

Best Foot Forward: Nanopore Long Reads, Hybrid Meta-Assembly, and Haplotig Purging Optimizes the First Genome Assembly for the Southern Hemisphere Blacklip Abalone (Haliotis rubra)

“…Using the k-mer approach based on 291.7 Gb of Illumina short read data, the H. rubra haploid genome size was predicted to be between 1.24 to 1.31 Gb with moderate-high heterozygosity of 1.27 to 1.44% ( Supplemental Table 2 ). Additional processing of the Illumina reads followed by another GenomeScope analysis with the max kmer coverage filter disabled resulted in a predicted haploid genome size of 1.56 Gb, a value closer to the 1.65 Gb haploid size estimated for a different haliotid species based on k-mer distributions (Nam et al, 2017; Masonbrink et al, 2019). Nanopore sequencing generated a total of 28 Gb (0.5-3.1 Gb per flowcell, more than 10 kb median read length) and 25 Gb data (6.8-11 Gb per flowcell, 1-2 kb median read length) for the DU_JTF1 and DU_PF1 libraries, respectively ( Supplemental Table 1 ).…”

“…For example, hybrid assembly of the clownfish genome with 11× Nanopore and 54× Illumina reads generated 94% fewer scaffolds and 18-fold longer N 50 length compared to the Illumina-only assembly (Tan et al, 2018). To date, two abalone genomes are publicly available and were both assembled using PacBio and Illumina reads (Nam et al, 2017; Masonbrink et al, 2019). The first abalone genome belonging to the species Haliotis discus hannai was reported 2 years ago with a scaffold N 50 of 211 kb (Nam et al, 2017).…”

“…The first abalone genome belonging to the species Haliotis discus hannai was reported 2 years ago with a scaffold N 50 of 211 kb (Nam et al, 2017). Two years later, the second abalone genome ( H. rufescens ) was published with a substantially improved contiguity (pre- and post-HiRise2 scaffold N 50 of 588 kb and 1.895 Mb, respectively) presumably due the availability of higher PacBio data coverage and the use of a dedicated MaSuRCA hybrid assembler (Zimin et al, 2017; Masonbrink et al, 2019).…”

Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

“…As expected for mostly non-model species, the present study highlights a general paucity of published mitochondrial and nuclear genome assemblies, population-scale data, as well as geographical metadata submitted to barcode databases (BOLD, GenBank), with some mollusk populations better described at the population genomic level, i.e., Crassostrea sp., Mytilus sp., Haliotis sp., and Pecten sp. (Zbawicka et al, 2014a(Zbawicka et al, , 2018Fraïsse et al, 2016;Mathiesen et al, 2016;Wenne et al, 2016;Gutierrez et al, 2017;Harney et al, 2018;Wilson et al, 2018;El Ayari et al, 2019;Masonbrink et al, 2019;Paterno et al, 2019;Vendrami et al, 2019a,b). It is worth noting that the phylogenetically robust data reported here significantly increases the number of released complete mitochondrial genome sequences by 6-fold for R. decussatus, five-fold for R. philippinarum, three-fold for A. islandica, and D. polymorpha, and finally two-fold for H. rufescens, H. tuberculata, and P. maximus.…”

An Evolutionary Perspective of Dopachrome Tautomerase Enzymes in Metazoans

“…To increase the representativeness of poorly supported lophotrochozoan clades, we retrieved the gene models of two gastropods ( Biomphalaria glabrata and Haliotis spp.) [39], one brachiopod ( Lingula anatina ) [40], one nemertean ( Notospermus geniculatus ), one phoronid ( Phoronis australis ) [40] and 10 bivalve species ( Bathymodiolus platifrons , Modiolus philippinarum [41], Crassostrea gigas [42], C. virginica, Pinctada fucata [43], Ruditapes philippinarum [44], S accostrea glomerata [45], Mizuhopecten yessoensis [46] Limnoperna fortunei [47] and Scapharca broughtonii [48]. We also analyzed the only genome available for copepods (i.e., Tigriopus kingsejongensis ) [49] and one platyhelminth ( Schmidtea mediterranea ) [50].…”