A chromosome‐level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean

Abstract

Mud crabs, found throughout the Indo‐Pacific region, are coastal species that are important fisheries resources in many tropical and subtropical Asian countries. Here, we present a chromosome‐level genome assembly of a mud crab (Scylla paramamosain). The genome is 1.55 Gb (contig N50 191 kb) in length and encodes 17,821 proteins. The heterozygosity of the assembled genome was estimated to be 0.47%. Effective population size analysis suggested that an initial large population size of this species was maintained until 200 thousand years ago. The contraction of cuticle protein and opsin genes compared with Litopenaeus vannamei is assumed to be correlated with shell hardness and light perception ability, respectively. Furthermore, the analysis of three chemoreceptor gene families, the odorant receptor (OR), gustatory receptor (GR) and ionotropic receptor (IR) families, suggested that the mud crab has no OR genes and shows a contraction of GR genes and expansion of IR genes. The numbers of the three gene families were similar to those in three other decapods but different from those in two nondecapods and insects. In addition, IRs were more diversified in decapods than in nondecapod crustaceans, and most of the expanded IRs in the mud crab genome were clustered with the antennal IR clades. These findings suggested that IRs might exhibit more diverse functions in decapods than in nondecapods, which may compensate for the smaller number of GR genes. Decoding the S. paramamosain genome not only provides insight into the genetic changes underpinning ecological traits but also provides valuable information for improving the breeding and aquaculture of this species.

Comparative Genomic and Transcriptomic Analyses of CHHs and Their Putative Receptors in Scylla paramamosain, Portunus trituberculatus, and Eriocheir sinensis

“…These features match the findings from the CHH1 genes of P. trituberculatus and E. sinensis in this study. However, we did not identify CHH1 genomic sequences in the S. paramamosain genome, which might be attributed to incomplete genomic assembly (Zhao et al, 2021). There are three indications suggesting that the Sp-CHH1 gene has four exons and generates two splice variants.…”

“…Recently, due to advances in sequencing technologies, several decapod genomes have been sequenced and assembled (Gutekunst et al, 2018;Zhang et al, 2019;Tan et al, 2020;Tang et al, 2020Tang et al, , 2021Van Quyen et al, 2020;Cui et al, 2021;Uengwetwanit et al, 2021;Zhao et al, 2021), providing an important basis for comprehensive understanding and differentiation of decapod CHHs and their putative receptors, as well as for further exploration of CHHs genomic structures and characteristics. In this study, CHHs and their putative GPCRs were identified and characterized in three species of economically important crabs: the mud crab, Scylla paramamosain, P. trituberculatus, and the Chinese mitten crab, Eriocheir sinensis.…”

Comparative Metabolomics and Lipidomics of Four Juvenoids Application to Scylla paramamosain Hepatopancreas: Implications of Lipid Metabolism During Ovarian Maturation

“…The selected genes were those encoding hepatocyte nuclear factor 4 (HNF4), carnitine palmitoyl transferase (CPT), very-long-chain acyl-CoA dehydrogenase (VLCAD), palmitoyl protein thioesterase (PPT) and 3-ketoacyl-CoA thiolase (KAT). Table 1 shows the primers used according to genome study ( 46 ). Three replicates were prepared for each sample.…”

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.…”