A chromosome-level genome of Portunus trituberculatus provides insights
into its evolution, salinity adaptation, and sex determination
Abstract
Portunus trituberculatus (Crustacea: Decapoda: Brachyura), commonly
known as the swimming crab, is of major ecological importance, as well
as being important to the fisheries industry. P. trituberculatus is also
an important farmed species in China due to its rapid growth rate and
high economic value. Here, we report the genome sequence of the swimming
crab, which was assembled at the chromosome scale, covering
~1.2 Gb, with 79.99% of the scaffold sequences
assembled into 53 chromosomes. The contig and scaffold N50 values were
108.7 kb and 15.6 Mb, respectively, with 19,981 protein-coding genes and
a high proportion of simple sequence repeats (49.43%). Based on
comparative genomic analyses of crabs and shrimps, the C2H2 zinc finger
protein family was found to be the only gene family expanded in crab
genomes, and its members were mainly expressed in early embryonic
development and during the flea-like larval stage, suggested it was
closely related to the evolution of crabs. Combined with transcriptome
and Bulked Segregant Analysis (BSA) providing insights into the genetic
basis of salinity adaptation in P. trituberculatus, strong immunity and
rapid growth of the species were also observed. In addition, the
specific region of the Y chromosome was located for the first time in
the genome of P. trituberculatus, and Dmrt1 was identified as a key sex
determination gene in this region. Decoding the swimming crab genome not
only provides a valuable genomic resource for further biological and
evolutionary studies, but is also useful for molecular breeding of
swimming crabs.