Chromosome-Level Clam Genome Helps Elucidate the Molecular Basis of Adaptation to a Buried Lifestyle

Abstract

Bivalve mollusks are economically important invertebrates that exhibit marked diversity in benthic lifestyle and provide valuable resources for understanding the molecular basis of adaptation to benthic life. In this report, we present a high-quality, chromosome-anchored reference genome of the Venus clam, Cyclina sinensis. The chromosome-level genome was assembled by Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 103 Genomics, and high-throughput chromosome conformation capture technologies. The final genome assembly of C. sinensis is 903.2 Mb in size, with a contig N50 size of 2.6 Mb and a scaffold N50 size of 46.5 Mb. Enrichment analyses of significantly expanded and positively selected genes suggested evolutionary adaptation of this clam to buried life. In addition, a change in shell color represents another mechanism of adaptation to burial in sediment. The high-quality genome generated in this work provides a valuable resource for investigating the molecular mechanisms of adaptation to buried lifestyle.

Cloning and characterization of microphthalmia‐associated transcription factor‐like gene provide insights intoCyclina sinensisclam shell melanin deposition

“…This black colour fades to white or brownish yellow after a few days. The degree of fading in the black shell is directly related to the length of time after excavation from the mud (Wei et al, 2020). The darker the colour of the clam shell is, the shorter the time it has been out of the mud.…”

“…Interestingly, the black colour change in the shell of clams in and out of muddy sediment is reversible, probably due to melanin changes in the shell (Wei et al, 2020). The redox activity of melanin suggests that it can be repeatedly switched between oxidized and reduced states based on the different reducing powers of different environmental conditions (Kim et al, 2014).…”

“…Clams with black shells were collected from mud sediment, and the clams with white or brownish yellow shells were collected from seawater without sediment. The two‐way red arrow represents the reversible colour changes in the clam shell (Wei et al, 2020). (b) Schematic diagram of the internal organization structure of C. sinensis…”

“…cDNA was synthesized using the PrimerScript RT reagent Kit (Takara), and cDNA used as the template for RACE PCR was synthesized using the SMART™ RACE cDNA Amplification Kit (Takara) in accordance with the manufacturer's instructions. The primers for 5′‐ and 3′‐RACE were designed on the basis of the predicted mitf ‐ like sequence obtained from the whole‐genome sequence data of C. sinensis (Wei et al, 2020). The sequences of all the primers used in this study are displayed in Table 1.…”

“…However, the nonhereditary shell colour trait of bivalves, especially in the black shell of C. sinensis , has rarely been studied. Previous research showed that melanin is mainly found in the nacre layer and periostracum of the C. sinensis shells, and the shell colour changes from black to white or brownish yellow are reversible under different environmental conditions (within and outside of mud), probably due to changes in melanin redox activity (switching between oxidized and reduced states) in the shell (Wei et al, 2020).…”