Chromosome-level genome assembly of sea scallop Placopecten magellanicus provides insights into the genetic characteristics and adaptive evolution of large scallops.

Placopecten magellanicus (Gmelin, 1791), a deep-sea Atlantic scallop, holds significant commercial value as a benthic marine bivalve along the northwest Atlantic coast. Recognizing its economic importance, the need to reconstruct its genome assembly becomes apparent, fostering insights into natural resources and generic breeding potential. This study reports a high-quality chromosome-level genome of P. magellanicus, achieved through the integration of Illumina short read sequencing, PacBio HiFi sequencing, and Hi-C sequencing techniques. The resulting assembly spans 1778 Mb with a scaffold N50 of 86.71 Mb. An intriguing observation arises - the genome size of P. magellanicus surpasses that of its Pectinidae family peers by 1.80 to 2.46 times. Within this genome, 28,111 protein-coding genes were identified. Comparative genomic analysis involving five scallop species unveils the critical determinant of this expanded genome: the proliferation of repetitive sequences recently inserted, contributing to its enlarged size. The landscape of whole genome collinearity sheds light on the relationships among scallop species, enhancing our broader understanding of their genomic framework. This genome provides genomic resources for future molecular biology research on scallops and serves as a guide for the exploration of longevity-related genes in scallops.

A high-quality chromosome-level genome assembly of the bivalve mollusk Mactra veneriformis.

Mactra veneriformis (Bivalvia: Mactridae) is a bivalve mollusk of major economic importance in China. Decreased natural yields of M. veneriformis have led to an urgent need for genomic resources. To address this problem and the currently limited knowledge of molecular evolution in this genus, we here report a high-quality chromosome-level genome assembly of M. veneriformis. Our approach yielded a 939.32 Mb assembled genome with an N50 contig length of 7,977.84 kb. Hi-C scaffolding of the genome resulted in assembly of 19 pseudochromosomes. Repetitive elements made up ∼51.79% of the genome assembly. A total of 29,315 protein-coding genes (PCGs) were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and Ruditapes philippinarum diverged around 231 million years ago (MYA). Inter-species comparisons revealed that 493 gene families have undergone expansion and 449 have undergone contraction in the M. veneriformis genome. Chromosome-based macrosynteny analysis revealed a high degree of synteny between the 19 chromosomes of M. veneriformis and those of Patinopecten yessoensis. These results suggested that M. veneriformis has a similar karyotype to that of P. yessoensis, and that a highly conserved 19-chromosome karyotype was formed in the early differentiation stages of bivalves. In summary, the genomic resources generated in this work serve as a valuable reference for investigating the molecular mechanisms underlying biological functions in M. veneriformis and will facilitate future genetic improvement and disease treatment in this economically important species. Furthermore, the assembled genome greatly improves our understanding of early genomic evolution of the Bivalvia.

Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shells.

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we report a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50 = 2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the haemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.

Characterization of the complete mitochondrial genome of Alectryonella plicatula (Bivalvia: Ostreidae).

In this study, we sequenced and analyzed the complete mitochondrial genome of Alectryonella plicatula (Gmelin 1791), the newly determined mitochondrial genome is 18225 bp in length, it is a circular molecule and consists of 12 protein-coding genes (atp8 is absent), 24 transfer RNA (with two copies of trnP and trnQ), and 2 ribosomal RNA genes (splitting of the rrnL gene and duplication of the rrnS gene were identified). Phylogenetic analysis based on 12 protein coding genes showed that Alectryonella plicatula is closely related to Crassostrea gigas.

Identification and characterisation of pathogenic Vibrio splendidus from Yesso scallop (Patinopecten yessoensis) cultured in a low temperature environment.

A fatal disease with apparent lesions on the adductor muscles of Yesso scallop Patinopecten yessoensis has occurred for three consecutive years from 2009 to 2011 in the northeastern China. This disease has been suspected to be closely associated with bacterial infections. In the present study, 96 bacteria were isolated from the lesions of moribund scallops. They were grouped into Vibrio (88 strains), Moritella (5 strains), Pseudomonas (2 strains) and Shewanella (1 strain) by 16S rDNA sequencing. In the Vibrio group, Vibrio splendidus was the predominant species, consisting of 43 strains. A strain of V. splendidus, named JZ6, was identified as a potential pathogen because it possessed two important virulence factors, Vsm and OmpU. Stain JZ6 was cold-adapted, and could surviveand exhibit haemolytic activity from 4°C to 32°C, with the highest activity observed at 10°C. The pathogenicity of JZ6 was further confirmed by injection and immersion challenges to scallops at 10°C. The cumulative mortality rates in the two experiments were 80% and 45%, respectively, which were significantly higher (P<0.05) than those of control and blank groups. The disorganisation of muscle fibres in challenged scallops was observed to be histopathologically identical to that in moribund Yesso scallop collected from the same farm. The results indicate that V. splendidus is the predominantly culturable bacteria from the lesions of diseased Yesso scallop, and JZ6 probably is the pathogenic agent to Yesso scallop in this low temperature environment.