Chromosome‐level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs

Abstract

The blue king crab, Paralithodes platypus, which belongs to the family Lithodidae, is a commercially and ecologically important species. However, a high‐quality reference genome for the king crab has not yet been reported. Here, we assembled the first chromosome‐level blue king crab genome, which contains 104 chromosomes and an N50 length of 51.15 Mb. Furthermore, we determined that the large genome size can be attributed to the insertion of long interspersed nuclear elements and long tandem repeats. Genome assembly assessment showed that 96.54% of the assembled transcripts could be aligned to the assembled genome. Phylogenetic analysis showed the blue king crab to have a close relationship with the Eubrachyura crabs, from which it diverged 272.5 million years ago. Population history analyses indicated that the effective population of the blue king crab declined sharply and then gradually increased from the Cretaceous and Neogene periods, respectively. Furthermore, gene families related to developmental pathways, steroid and thyroid hormone synthesis, and inflammatory regulation were expanded in the genome, suggesting that these genes contributed substantially to the environmental adaptation and unique body plan evolution of the blue king crab. The high‐quality reference genome reported here provides a solid molecular basis for further study of the blue king crab's development and environmental adaptation.

Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation

“…High-quality published genomes of four decapods were chosen for comparative genomics: the Pacific white shrimp (Litopenaeus vannamei [47];), the marbled crayfish (Procambarus virginalis [48];), the swimming crab (Portunus trituberculatus [49];) and the blue king crab (Paralithodes platypus; GenBank: GCA_013283005.1). An updated version of the blue king crab genome was later published by Tang et al (2021) [50]. The isopod Armadillidium vulgare [51] and the amphipod Parhyale hawaiensis [52] were furthermore included as outgroups.…”

Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species

“…Although the assembly of PacBio sequencing data has higher continuity than that of SOAPdenovo assembly, it was still highly fragmented, as it was composed of more than 40,000 contigs, and the contig N50 lengths were significantly shorter than many recently published crustacean genomes, e.g., Eulimnadia texana (18.07 Mb) ( Baldwin-Brown et al, 2018 ), P. trituberculatus (4.12 Mb) ( Tang et al, 2020 ), and Paralithodes platypus (147.47 Kb) ( Tang et al, 2021 ). Thus, we next investigated the factors that caused the high fragmentation of these assemblies.…”

Recent advances in crustacean genomics and their potential application in aquaculture

“…Their genome expansion has been suggested to be the result of repeated proliferation rather than WGD. 30,31,[54][55][56] Even in closely related species, such as those in the genus Armadillidium, the recent proliferation of TEs can also lead to an increase in genome size. 57 As expected, branchiopods and copepods generally have smaller genomes and lower levels of TEs, whereas some isopods (e.g., B. jamesi) and decapods (e.g., P. platypus, P. carinicauda and Synalpheus snapping shrimp) have larger genomes and higher levels of TEs (Table 3).…”