Chromosome-level genome assembly of the deep-sea solemyid bivalve Acharax haimaensis

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Abstract
Solemyidae, an ancient lineage of protobranch bivalves, are characterized by unique morphology and obligate symbiosis with sulfur-oxidizing bacteria, enabling survival in sulfide-rich sediments. However, limited genomic resources have hindered understanding of their evolutionary history, symbiotic interactions, and environmental adaptation. Here, we report a chromosome-level reference genome of Acharax haimaensis, assembled using PacBio, Illumina, and Hi-C sequencing. The 4.27 Gb genome, with a scaffold N50 of 195.52 Mb, was anchored to 22 chromosomes and achieved high completeness (98.2%) based on BUSCO. Transposable elements occupy 50.17% of the assembly, dominated by long interspersed nuclear elements (14.20%). We predicted 38,343 protein-coding genes, of which 87.25% were functionally annotated. Macrosynteny analysis revealed each chromosome comprises two to four segments of ancestral linkage groups, indicating extensive chromosomal breakage and fusion in early bivalve evolution. Phylogenetic inference suggested A. haimaensis diverged from the common ancestor of Autobranchia ~550 Mya. This first deep-sea protobranch genome provides an essential resource for exploring bivalve evolution and the genetic basis of symbiosis and adaptation to extreme environments.
Funding Information
  • National Natural Science Foundation of China (42376058)
  • National Natural Science Foundation of China (42221005 to WMX)
  • Ministry of Science and Technology of the People's Republic of China (2024YFC2816000)

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