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. 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, suggesting it was closely related to the evolution of crabs. The combination of transcriptome and bulked segregant analysis provided insights into the genetic basis of salinity adaptation and rapid growth in P. trituberculatus. In addition, the specific region of the Y chromosome was located for the first time in the genome of P. trituberculatus, and three genes were preliminarily identified as candidate genes for sex determination 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.

Identification and Evolution Analysis of the Complete Methyl Farnesoate Biosynthesis and Related Pathway Genes in the Mud Crab, Scylla paramamosain

“…To date, it is still hypothesized that MO is the exclusive site for MF synthesis in crustaceans, and that MF is the only JH found in crustacean species. With the development of sequencing technology, several genome assemblies of crustacean species have been reported [ 31 , 32 , 33 , 34 , 35 , 36 ], providing valuable data for gene identification, species adaption, and evolution studies. For example, a comprehensive analysis of genes involved in sesquiterpenoid biosynthesis provided new insights into the spread of sesquiterpenoid hormones in the animal kingdom [ 37 ].…”

Identification of Neuropeptides Using Long-Read RNA-Seq in the Swimming Crab Portunus trituberculatus, and Their Expression Profile Under Acute Ammonia Stress

“…Comparison of clean reads with the reference genome resulted in a mapped rate of 73.81%. The mapped reads were clustered to obtain consensus sequences, and the consensus sequences were aligned to reference genome of P. trituberculatus to eliminate redundant reads ( Lv et al, 2021 ). After removing redundant reads, 25,054 non-redundant sequences were generated.…”

“…The full-length transcripts were identified using the method of Pinfish pipeline, detected using Pychopper, and aligned to reference genome of P. trituberculatus with minimap2 v2.16 ( Deamer et al, 2016 ). At present, there are two chromosome-level reference genome for P. trituberculatus, which are publicly available ( Tang et al, 2020 ; Lv et al, 2021 ). In order to find more neuropeptide-encoding genes, we used the recent version with higher number of annotated genes ( Lv et al, 2021 ).…”

“…At present, there are two chromosome-level reference genome for P. trituberculatus, which are publicly available ( Tang et al, 2020 ; Lv et al, 2021 ). In order to find more neuropeptide-encoding genes, we used the recent version with higher number of annotated genes ( Lv et al, 2021 ). The consensus sequence was obtained by clustering according to the results of comparison, and known and novel transcripts were identified using Gffcompare v0.11.2.…”

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

“…Therefore, practical and effective measures are expected to be taken to reinforce the identification and protection of genetic diversity and prevent degeneration of P. trituberculatus germplasm. For example, developing high-quality markers such as SNPs using a chromosome-level genome of P. trituberculatus ( Tang et al, 2020 ; Lv et al, 2021 ), and carrying out a large-scale investigation to fully elucidate the genetic diversity and population structure of P. trituberculatus in the Bohai Sea. Additionally, increasing the scale of swimming crab aquaculture, extending the fishing moratorium, and performing long-term genetic monitoring is also helpful for the conservation and utilization of germplasm resources in P. trituberculatus .…”