Chromosome‐level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)

Abstract

Bivalves, a highly diverse and the most evolutionarily successful class of invertebrates native to aquatic habitats, provide valuable molecular resources for understanding the evolutionary adaptation and aquatic ecology. Here, we reported a high‐quality chromosome‐level genome assembly of the razor clam Sinonovacula constricta using Pacific Bioscience single‐molecule real‐time sequencing, Illumina paired‐end sequencing, 10X Genomics linked‐reads and Hi‐C reads. The genome size was 1,220.85 Mb, containing scaffold N50 of 65.93 Mb and contig N50 of 976.94 Kb. A total of 899 complete (91.92%) and seven partial (0.72%) matches of the 978 metazoa Benchmarking Universal Single‐Copy Orthologs were determined in this genome assembly. And Hi‐C scaffolding of the genome resulted in 19 pseudochromosomes. A total of 28,594 protein‐coding genes were predicted in the S. constricta genome, of which 25,413 genes (88.88%) were functionally annotated. In addition, 39.79% of the assembled genome was composed of repetitive sequences, and 4,372 noncoding RNAs were identified. The enrichment analyses of the significantly expanded and contracted genes suggested an evolutionary adaptation of S. constricta to highly stressful living environments. In summary, the genomic resources generated in this work not only provide a valuable reference genome for investigating the molecular mechanisms of S. constricta biological functions and evolutionary adaptation, but also facilitate its genetic improvement and disease treatment. Meanwhile, the obtained genome greatly improves our understanding of the genetics of molluscs and their comparative evolution.

The Chromosome-Level Genome Assembly and Comprehensive Transcriptomes of the Razor Clam (Sinonovacula constricta)

“…In total, 386.2 Gb clean data were used for assembling the genome of S. constricta , including 129.73 Gb Illumina reads, 101.79 Gb Pacbio reads, and 154.68 Gb Hi-C reads ( Table 1 ). The genome size was estimated to be 1,244.27 Mb, with a heterozygous ratio of 1.53% and a repeat rate of 53.12%, which was consistent with the results of a previous study (Ran et al, 2019 ). By using the WTDBG pipeline, the resulting 1,331.97 Mb assembly was obtained with a contig N50 of 678,857 bp ( Table 1 ).…”

“…Therefore, it is an ideal model with which to investigate the adaptive mechanisms of a deep-burrowing lifestyle. Despite that increased genomic sequences (Dong et al, 2019 ; Ran et al, 2019 ) and transcriptomic data (Niu et al, 2013 ) have been generated, full-spectrum spatial-temporal transcriptomes are still insufficient for exploring its unique biology and adaptive evolution.…”

The evo‐devo of molluscs: Insights from a genomic perspective

“…A combination of fosmid pooling and hierarchical assembly applied in oyster assisted the first highly polymorphic molluscan genome decoded (Zhang et al, 2012). PacBio or Nanopore long reads have significantly improved the quality of genome assembly with increased contig N50 and reduced scaffold number (Bai et al, 2019; Dong et al, 2019; Guo et al, 2019; Liu et al, 2018; Ran et al, 2019; Sun et al, 2019). The emergence of high‐resolution chromosome conformation capture (Hi‐C) technology assisted the genome assembly at a chromosome level.…”

Transcriptional regulation mechanism of sterol regulatory element binding proteins on Δ6 fatty acyl desaturase in razor clamSinonovacula constricta

“…Cloning and potential regulatory sites of Sinonovacula constricta Δ6 fatty acyl desaturase promoter S. constricta genomic DNA was extracted from fresh foot muscle using a Marine Animal DNA Kit (CWBIO) and used as a template for Δ6 Fad promoter cloning. The 2000 bp upstream of Δ6 Fad translation initiation codon (ATG) was obtained from the genomic sequencing data of S. constricta (32) by querying Δ6 Fad cDNA (GenBank accession number MH220406). To further verify this promoter sequence, PCR was carried out by Mighty Amp TM DNA Polymerase version 3 (TaKaRa) using specific primers (Δ6 Fad promoter-V-F and -R in Table 1).…”