The Gene-Rich Genome of the ScallopPecten maximus

Abstract

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>The King Scallop, <jats:italic>Pecten maximus</jats:italic>, 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.</jats:p></jats:sec><jats:sec><jats:title>Findings</jats:title><jats:p>Here 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.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>The genome assembly of <jats:italic>Pecten maximus</jats:italic> 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 <jats:italic>Nav1</jats:italic>, known as a gene conferring resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.</jats:p></jats:sec>

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

“…This genome shared some typical features of other bivalves, such as a low GC content (32%) and a widespread presence of repeats (43% of the assembly), but it was particularly rich in both protein-coding (60,338) and non-coding (75,973) genes. While these figures largely exceed those observed in most sequenced bivalve species [12,14], they closely matched the numbers recently reported in the king scallop [17] and in the zebra mussel [41] (Additional file 1: Data Note 3). The reconstruction of the evolutionary relationships among M. galloprovincialis and 15 selected lophotrochozoan species [42][43][44][45], followed by an analysis of gene family trees [46], revealed that this large gene repertoire is the result of multiple lineage-specific duplication events that took place after the split between Mytilus and the rest of Mytilida (Fig.…”

“…Although M. galloprovincialis displays a morphologically conserved karyotype compared with other mussels and has not undergone known whole-genome duplication or allopolyploidization events [11], it shares with other bivalves a relatively large and complex genome, characterized by high heterozygosity and numerous mobile elements [12][13][14][15][16][17]. These factors posed a serious challenge to previous assembly efforts, which resulted in extremely fragmented genome sequences for this species [18,19] which, unlike the congeneric Mytilus coruscus [20] and a few other mussel species [15], still lacks a highly contiguous reference genome assembly.…”

Independent adoptions of a set of proteins found in the matrix of the mineralized shell-like eggcase of Argonaut octopuses

“…A combination of transcriptome and proteome analysis has been used to identify these proteins (e.g., Miyamoto et al 2013;Arivalagan et al 2017;Zhao et al 2018;Setiamarga et al 2020), with some data validated at the genomic level because of the availability of draft genomes (Mann et al 2012;Zhang et al 2012;Takeuchi et al 2016;Kenny et al 2020). Many of these proteins are present in trace amounts inside the shell and are therefore referred to as SMPs.…”

Transcriptional Response in the Digestive Gland of the King Scallop (Pecten maximus) After the Injection of Domoic Acid

“…This gene codes for the enzyme pyrroline-5-carboxylate reductase 2 that catalyzes the conversion of pyrroline-5-carboxylate to proline, and proline has a protective effect against oxidative stress [ 65 ]. Kenny et al [ 66 ] suggested that mutations in the sodium channel gene, Neuron Navigator 1 ( Nav1 ), could protect against the effects of domoic acid in P. maximus . We have not found transcripts of the Nav1 gene in the digestive gland of P. maximus , therefore the sodium channel is likely expressed in nervous tissue but not in the digestive gland.…”

“…OmicsBox—Version 1.4.11.) [ 83 , 84 ], using local Blastx 2.10.0+ [ 88 ], (E-value threshold of 10 −3 ) against a database of Pecten maximus [ 66 ], Mizuhopecten yessoensis [ 89 ], Crassostrea gigas [ 70 ] and SwissProt proteins obtained from NCBI and UNIPROT:…”