Phylogenetic analysis of wild populations of Exopalaemon carinicauda in three regions of Zhejiang Province based on COI and 16S rRNA genes

Abstract

Phylogenetic analysis is an important technique in molecular systematics, which is often applied to the analysis of evolutionary relationships between organisms. At present, phylogenetic analysis is applied to many branches of biology, such as describing the phylogenetic relationship of different taxa by constructing phylogenetic trees, and analyzing and applying them in terms of their genetic relationship, describing homologous gene relationships, and exploring the historical changes of populations. Exopalaemon carinicauda, belonging to the family Palaemonidae and Exopalaemon, is one of the important economic shrimp species in China. It is mainly distributed in the shallow low-salt waters along the eastern coast of China and the west coast of the Korean Peninsula. It has the characteristics of fast growth, strong adaptability, large individual size and strong reproductive ability. In recent years, as an emerging aquaculture species, the aquaculture industry of white shrimp has developed rapidly, and the coastal area of Zhejiang is one of the important aquaculture production areas of white shrimp. In addition, Zhejiang is located in the central coastal region of China, where the north and south converge, and is a transition zone between the subtropical zone and the warm temperate zone, with a superior geographical location. The natural resources of the spinetail white shrimp along the coast of Zhejiang are very rich. This paper explores the phylogenetic differentiation of wild populations of P. spiniculus in coastal Zhejiang, and provides a theoretical basis for the protection and rational development and utilization of P. spp. resources. The COI and 16S rRNA gene fragments of the mitochondrial DNA (mtDNA) of three populations of S. spine-tailed P. japonica (JX) in northern Zhejiang, Sanmen Sanmen in central Zhejiang (TZ) and Pingyang (WZ) in Wenzhou in southern Zhejiang were amplified and determined, and the phylogenetic differentiation and genetic relationship among S. spinosa populations were studied. The total DNA of the muscle tissue of the spine-tailed white shrimp samples was extracted using the animal tissue genomic DNA extraction kit (Shanghai Sangon Bioengineering Co., Ltd.) from Shanghai Shenggong. After PCR amplification, it was sent to Beijing Qingke Biotechnology Co., Ltd. for sequencing.The obtained sequences were used for further analysis, and the genetic distance between species was calculated based on the Kimura two-parameter model. The phylogenetic phylogenetic tree was constructed by Bayesian Inference (BI) and Maximum Likelihood (ML) method. After comparison, the consistent sequence of COI gene of 529 bp and the consistent sequence of 16S rRNA of 434 bp were obtained, and the combined sequence of 963 bp was obtained. The average contents of T, C, A and G were 34.43%, 20.67%, 27.3% and 17.6%, respectively, the contents of A+T were 61.73%, and the contents of G+C were 38.27%. Among the 21 variable sites, the transition/reversal ratio (R) is 1.74. The average intraspecific genetic distance of the three populations was 0.015. The phylogenetic phylogenetic tree showed that the two groups of JX and WZ were relatively distant, and the TZ and WZ were relatively close. It is speculated that the genetic relationship of S. spiniculus is related to geographical distance, which also indicates that the genetic variation of S. spinosa mainly comes from within the population. The divergence time indicates that the time of the appearance of the spinetail white shrimp along the coast of Zhejiang is about the Cretaceous. The JX population was first differentiated at about 99.39 Ma (95%HDP: 95.03 Ma-130.95 Ma), and then the TZ and WZ populations were differentiated. It is speculated that the differentiation of white shrimp in Zhejiang Province is from north to south. This study clarified the phylogenetic relationship of P. lanceolata along the coast of Zhejiang, and provided a basis for future research on the faunal diversity and resource conservation of this taxon.