Fig. 1

Characterization and phylogenetic analysis of the hard clam genome. a Genomic landscape of the hard clam. From outer to inner circles: a, the 19 chromosomes at the Mb scale; b, IAP gene number on each chromosome; c, chromosomal distribution of 159 IAPs, with outer and inner lines indicating sense and antisense strands, respectively. Each hyphen on circle margin represents an IAP gene copy; d~h, DNA transposons density, TE density, repeat density, gene density, and GC density across the genome, respectively, drawn in 1 Mb non-overlapping windows. b Time-calibrated phylogenetic tree of the hard clam within metazoans. Numbers on the branches indicate the number of genes gained (+, green) and lost (−, red). Pfu, Pinctada fucata; Cvi, Crassostrea virginica; Mph, Modiolus philippinarum; Afa, Azumapecten farreri; Mme, Mercenaria mercenaria; Rph, Ruditapes philippinarum; Csq, Chrysomallon squamiferum; Lgi, Lottia gigantea; Bgl, Biomphalaria glabrata; Aca, Aplysia californica; Adu, Architeuthis dux; Obi, Octopus bimaculoides; Cte, Capitella teleta; Hro, Helobdella robusta; Ame, Apis mellifera; Dme, Drosophila melanogaster; Hsa, Homo sapiens; Bfl, Branchiostoma floridae; Nve, Nematostella vectensis. c The top 10 expanded and top three contracted pathways that were enriched in the hard clam