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. A chromosome-level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation, and sex determination

Discovery of Sex-Determining Genes in Portunus trituberculatus: A Comparison of Male and Female Transcriptomes During Early Developmental Stages

“…In our previous study, we located the SD region on two contigs in P. trituberculatus (Lv et al, 2020b). Based on the genomic annotations, 41 genes were found in the SD (Supplementary Table 2), among which, eight genes were significantly differentially expressed between females and males.…”

How to become a crab: Phenotypic constraints on a recurring body plan

“…[98] It is only within the last year that high-quality genomic resources have become available for meiurans, though only for carcinized members. Two species of eubrachyuran, Portunus trituberculatus, [107,108] and Scylla paramamosain [109] (both members of the same family), and one species of king crab, Paralithodes platypus [110] now have published chromosome-level genome assemblies. The eubrachyuran Eriocheir japonica sinensis also has a recently updated genome assembly.…”

“…Loci of interest could be identified by comparing transcriptomes across the metamorphic transition from megalopa larva to juvenile, when the pleon becomes folded in most crabs. One study [108] has implicated decreased expression in the P. trituberculatus transcriptome at exactly this stage for the Hox genes Ubx and abd-A (expression of the latter patterns the pleon in P. hawaiensis [116,117] ). More is known about the genomics of metamorphosis in lobsters [118] and shrimp [119] than in meiurans.…”

How to Become a Crab: Phenotypic Constraints on a Recurring Body Plan

“…It is only within the last year that high-quality genomic resources have become available for meiurans, though only for carcinized members. One species of eubrachyuran, Portunus trituberculatus (Lv et al 2020;Tang et al 2020c) and one species of king crab, Paralithodes platypus (Tang et al 2020a) now have published chromosome-level genome assemblies. The eubrachyuran Eriocheir japonica sinensis has a recently updated genome assembly (Song et al 2016;Tang et al 2020b).…”

“…Loci of interest could be identified by comparing transcriptomes across the metamorphosis from megalopa larva to juvenile, when the pleon becomes folded in most crabs. One study (Lv et al 2020) has implicated decreased expression in the P. trituberculatus transcriptome at exactly this stage for the Hox genes Ubx and abd-A (expression of the latter patterns the pleon in P. hawaiensis: Martin et al 2016;Serano et al 2016). More is known about the genomics of metamorphosis in lobsters (Ventura et al 2018) and shrimp (Zhang et al 2019) than in meiurans.…”