Whole Genome Assembly of the Snout Otter Clam, Lutraria rhynchaena, Using Nanopore and Illumina Data, Benchmarked Against Bivalve Genome Assemblies

Thai, Binh Thanh; Gan, Han Ming; Austin, Christopher M.; Croft, Laurence J.; Trieu, Tuan; Tan, Mun Hua

doi:10.3389/fgene.2019.01158

Cited by 21 publications

(13 citation statements)

References 51 publications

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“…Scallops have been the subject of genome sequencing projects in the past, with genomes published for three species, Azumapecten farreri (as Chlamys [17]) and Mizuhopecten yessoensis (as Patinopecten; [18]) from the subfamily Pedinae, and Argopecten purpuratus from the subfamily Pectininae [19]. Other sequenced genomes for more distantly related bivalves include those of the Sydney Rock Oyster Saccostrea glomerata [20], Eastern oyster Crassostrea virginica [unpublished, but see 21], the Snout Otter Clam Lutraria rhynchaena [22], Blood Clam Scapharca broughtonii [23] and Manila Clam Ruditapes philippinarum [24]. There are also extant resources for the mussel Mytillus galloprovincialis [25] and the freshwater mussels Venustaconcha ellipsiformis [26], Limnoperna fortunei [27], Dreissena rostriformis [28] and Dreissena polymorpha [unpublished, but see 29].…”

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confidence: 99%

The Gene-Rich Genome of the ScallopPecten maximus

Kenny

McCarthy

Dudchenko

et al. 2020

Preprint

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AbstractBackgroundThe King Scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and its ubiquity means that it plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies and fisheries management.FindingsHere we report the genome sequencing of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10x Chromium and Hi-C data, and its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb, and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species.ConclusionsThe genome assembly of Pecten maximus and its annotated gene set provide a high-quality platform for a wide range of investigations, including studies on such disparate topics as shell biomineralization, pigmentation, vision and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known as a gene conferring resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.

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confidence: 99%

The Gene-Rich Genome of the ScallopPecten maximus

Kenny

McCarthy

Dudchenko

et al. 2020

Preprint

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“…The A. granulata genome has a heterozygosity of 0.653%, making it one of the least heterozygous molluscan genomes sequenced to date (Supplementary Figure 4). High heterozygosity is often attributed to high rates of gene flow associated with broadcast spawning and far-dispersing larvae (Solé-Cava & Thorpe 1991), and it is frequently noted as an obstacle to genome assembly in molluscs (Zhang et al 2012; Wang et al 2017; Powell et al 2018; Thai et al 2019). We expected the genome of A. granulata to have high heterozygosity because this species is a broadcast spawner with a wide geographic range (Glynn 1970).…”

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confidence: 99%

The iron-responsive genome of the chitonAcanthopleura granulata

Varney

Speiser

McDougall

et al. 2020

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Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the teeth of their rasp-like radula with a coat of iron. Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome has features that may be specialized for iron biomineralization, including a high proportion of genes regulated directly by iron and two isoforms of ferritin, one iron-regulated and the other constitutively translated. The A. granulata genome also contains homologs of many biomineralization genes identified previously in conchiferan molluscs, suggesting the ancestral mollusc had a diverse genetic toolkit for biomineralization.

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“…De novo genome assembly of short and long reads was performed with the Maryland Super-Read Celera Assembler pipeline, MaSuRCA (Zimin et al, 2013; Zimin, Puiu, et al, 2017). This is one of the most common assemblers for performing short and long reads hybrid genome assemblies of eukaryotes, with consistently good results across studies (Jiang et al, 2019; Tan et al, 2018; Thai et al, 2019). In brief, MaSuRCA typically works as follows: Illumina paired-end short reads are first assembled into non-ambiguous super-reads, which are then mapped to Nanopore reads to further assemble them in long, high-quality pre-mega-reads.…”

Section: Methodsmentioning

confidence: 90%

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

Papa

Wellenreuther

Morrison

et al. 2022

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Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management attains its sustainability goals. Here we generated 55 Gb of short Illumina reads (92 coverage) and 73 Gb of long Nanopore reads (122) to produce the first genome assembly of the marine teleost tarakihi (Nemadactylus macropterus), a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq RNA reads were obtained from four tissue types of another specimen to assist in gene annotation. The final genome assembly was 568 Mb long and consisted of 1,214 scaffolds with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii BUSCOs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared to the same values reported for other fishes. Repetitive elements covered 30.45% of the genome and 20,169 protein-coding genes were annotated. Iso-Seq analysis recovered 91,313 unique transcripts (isoforms) from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly along with the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics, as well as comparative eco-evolutionary studies in other teleost and related organisms.

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Whole Genome Assembly of the Snout Otter Clam, Lutraria rhynchaena, Using Nanopore and Illumina Data, Benchmarked Against Bivalve Genome Assemblies

Cited by 21 publications

References 51 publications

The Gene-Rich Genome of the ScallopPecten maximus

The Gene-Rich Genome of the ScallopPecten maximus

The iron-responsive genome of the chitonAcanthopleura granulata

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

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