Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)

Abstract

The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea)

“…173 samples (> 500,000 reads per sample) were retained for downstream analyses. Reads were mapped to the 18 major linkage groups in the chromosome-level C. fluminea genome assembly ( Zhang et al, 2021 ) using BWA-mem v ( Li and Durbin, 2009 ). Alignments were sorted with samtools v1.10 ( Li et al, 2009 ), and duplicate reads were removed with picard v2.18.9 MarkDuplicates 5 .…”

Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family

“…The heterozygosity rate of P. generosa (1.37%) fell within the range of the heterozygosity rates of bivalves whose genomes have been sequenced and assembled, which vary broadly from 0.11% in Margaritifera margaritifera [ 22 ] to 3.20% in Crassostrea gigas [ 23 ]. The heterozygosity rate of P. generosa (1.37%) was close to that of another burrowing bivalve, Sinonovacula constricta (1.55%), and a deep-sea mussel, Bathymodiolus platifrons (1.03–1.24%) [ 13 , 24 ] ( Supplementary Table S4 ).…”

A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease

“…To explore the possibility that the INT-INT structure is derived from the excision of an LTDR or a monomer, we focused on two nonautonomous families, KolobokP-4N1_CorFlu and KolobokP-7N2_CorFlu . The two families are from the genome of Asian clam Corbicula fluminea , the assembly of which seems close to being complete [ 17 ]. They are relatively young based on their average family sequence diversities (2.3% or 1.3%, Table 3 ).…”