The chromosomal-level genome assembly and comprehensive transcriptomes of Chinese razor clam (Sinonovacula constricta) with deep-burrowing life style and broad-range salinity adaptation

Abstract

60 Background: The Chinese razor clam, Sinonovacula constricta, is one of the 61 commercially important marine bivalves with deep-burrowing lifestyle and 62 remarkable adaptability of broad-range salinity. Despite its economic impact and 63 representative of the less-understood deep-burrowing bivalve lifestyle, there are few 64 genomic resources for exploring its unique biology and adaptive evolution. Herein, 65 we reported a high-quality chromosomal-level reference genome of S. constricta, the 66 first genome of the family Solenidae, along with a large amount of 67 short-read/full-length transcriptomic data of whole-ontogeny developmental stages, 68 all major adult tissues, and gill tissues under salinity challenge . 69 Findings: A total of 101.79 Gb and 129.73 Gb sequencing data were obtained with 70 the PacBio and Illumina platforms, which represented approximately 186.63X 71 genome coverage. In addition, a total of 160.90 Gb and 24.55 Gb clean data were also 72 obtained with the Illumina and PacBio platforms for transcriptomic investigation. A 73 de novo genome assembly of 1,340.13 Mb was generated, with a contig N50 of 74 689.18 kb. Hi-C scaffolding resulted in 19 chromosomes with a scaffold N50 of 57.99 75 Mb. The repeat sequences account for 50.71% of the assembled genome. A total of 76 26,273 protein-coding genes were predicted and 99.5% of them were annotated. 77 Phylogenetic analysis revealed that S. constricta diverged from the lineage of 78 Pteriomorphia at approximately 494 million years ago. Notably, cytoskeletal protein 79 tubulin and motor protein dynein gene families are rapidly expanded in the S. 80 constricta genome and are highly expressed in the mantle and gill, implicating 81 potential genomic bases for the well-developed ciliary system in the S. constricta. 82 Conclusions: The high-quality genome assembly and comprehensive transcriptomes 83 generated in this work not only provides highly valuable genomic resources for future 84 studies of S. constricta, but also lays a solid foundation for further investigation into 85 the adaptive mechanisms of benthic burrowing mollusks. 86 system 88 89 109 exploring its unique biology and adaptive evolution. Here, we generated the 110 high-quality chromosomal-level genome assembly and comprehensive transcriptomes 111 of S. constricta and investigated the transcriptomic changes under different 112 environmental stresses. These genomic resources will lay a prime foundation for 113 future studies of its lifestyle-related adaptive evolution and genetic improvement in 114 commercial breeding programs.

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

“…A striking finding came from the macrosynteny analysis of chromosome-anchored genome assemblies of the scallop Patinopecten yessoensis and other animals (Wang et al, 2017), which revealed a near-perfect correspondence between the 19 scallop chromosomes and the 17 bilaterian ALGs, a level of chromosome preservation that far exceeds other bilaterians with chromosome-level assemblies (ALG conservation index: 0.81 for scallop, whereas 0-0.42 for other bilaterians). Follow-up studies confirmed the conservation of ancient bilaterian karyotype in other bivalve and gastropod molluscs (Dong et al, 2019;Sun et al, 2019), suggesting that molluscan ancestor may have a karyotype highly similar to that of the bilaterian ancestor. Several interesting chromosomal rearrangement events were identified, including partial translocation of ALG2 and the fusion of ALG5 and ALG16 in three bivalves (Wang et al, 2017) and translocation of ALG6 and fusion of ALG4, ALG14, and ALG16 in the gastropod Pomacea canaliculata (Sun et al, 2019), providing insights into chromosomal evolution in different molluscan lineages.…”

“…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.…”

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

“…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.…”