Chinese river crab is a favorite aquatic product species of the Chinese people, and its industrial scale is very large. In the process of breeding, the Chinese river crab is easy to “break hands and feet” when stimulated by the outside world, which has a great impact on its economic value.
Recently, the team of Professor Wang Chenghui of the School of Fisheries and Life Sciences of Shanghai Ocean University and partners have made new progress in the research field of chinese river crab genome and amputated limb regeneration. The study has been published in Science Advances.
Genome characteristics at the chromosome level of Chinese river crab Courtesy of the interviewee
Complete whole genome sequencing and assembly
The Chinese river crab is the most common crab species on the table of the Chinese people, and it is also a highly economically valuable aquatic crustacean. There are 28 provinces and municipalities in the country that cultivate Chinese river crabs, and its industry scale is huge. However, due to its large number of chromosomes (2n) and high genome repeat sequence, it has long faced the problem of difficulty in genome assembly.
In order to solve the above problems, Wang Chenghui’s team and Li Chenhong, professor of the School of Fisheries and Life Sciences of Shanghai Ocean University, Michael Hofreiter, professor of the University of Potsdam in Germany, and Lu Guoqing, professor of the University of Nebraska-Omaha, used the third-generation sequencing technology and combined with bioNano optical map and Hi-C high-throughput chromosome conformation capture technology to sequence and assemble the whole genome of chinese river crab in the Yangtze River system to obtain a fine genome map at the chromosome level.
The assembled Chinese river crab genome size was 1.67 Gb, covering 94.4% (1.77 Gb) of its genome size, of which Scaffold N50 was 16.98Mb and Contig N50 was 717.3 kb, and a total of 20286 protein-coding genes were identified.
Demystify the vitality of the awakening gene
The word “regeneration” sounds sci-fi, but in fact people’s bodies are also “regenerating” all the time, such as wound repair, liver regeneration, growing new hair and nails…
Compared with mammals, the “regeneration” ability of Chinese river crab is more magical, when the river crab is stimulated by the outside world, the muscles attached to the base node and the bottom node will contract strongly, the broken section will be disconnected, and after “breaking the hand and foot”, it can be regenerated after a period of time. The “regeneration” ability of Chinese river crab is very strong, so it is more common to break limbs in production and breeding, while most of the adult crabs with severed limbs enter the ordinary market at low prices, which has a great impact on the application and economic value of the entire industry.
Therefore, the exploration of the unique amputated limb regeneration phenomenon of Chinese river crab has both basic research and industrial application value.
“Based on the acquisition of the chromosomal-level genome of the Chinese river crab, we conducted a comparative genomics analysis to identify genes and gene families unique to arthropods.” Wang Chenghui told China Science Daily, “Through the comparative transcriptome and gene co-expression analysis of different developmental periods of broken limb regeneration, it was found that the Innexin gene family played an important molecular signaling role in the early stage of severed limb regeneration of Chinese river crab. For the first time, we found that the Innexin2 gene was specifically upregulated within 1 day after the dismemberment, and that the amputated limb regeneration process of the Chinese river crab was mediated by regulating the signaling pathway and immune response. ”
Interpreting the “compression package” of cell differentiation
The study also found that the early regeneration of the broken limbs of the Chinese river crab is regulated by epigenetics, in which the SMYDA gene family exists only in arthropods, and the expression is downregulated in the early stage of the Chinese river crab severed limbs, and the expression returns to the level of the unbroken limb during the growth of the limb buds.
Further analysis found that the gene family also expressed the overall differential expression in the metamorphosis process of Chinese river crab from big-eyed larvae to baby crabs, indicating that the arthropod-specific SMYDA gene family played an important epimodel role in the biological process of Chinese river crab involving obvious morphogenesis, such as metamorphosis and regeneration.
Wang Chenghui explained: “The SMYDA gene family is like a ‘compression package’ administrator who masters cell differentiation and proliferation, and the ‘compression package’ contains important documents for cell differentiation and proliferation, and the regulation of this gene family can make the ‘compression package’ unsealed, exposing the gene loci and causing the expression of subsequent related genes.” ”
The team also conducted a comparative analysis of the transcriptome of limb segmentation bass on P. vannamei, Giant river pea rota and Giant river prawn of Japan, and found that the related genes of the Innexin and SMYDA gene families had expression patterns that were basically the same as those of Chinese river crab after amputation, and speculated that crustaceans had a common mechanism with different molecular response mechanisms for the early molecular response of broken limb regeneration in vertebrates.
This study provides an important genomic resource and platform for the molecular breeding of Chinese river crab, and provides useful guidance for improving the level of aquaculture production and management. (Source: China Science Daily, Zhang Shuanghu, Huang Xin)
Related paper information:https://doi.org/10.1126/sciadv.abl4642