大管鞭虾线粒体全基因组测定及对虾总科的系统发育

Mitochondrial genome sequencing of Solenocera melantho and phylogenetic analysis of Penaeoidea

摘要:

目的 拓展管鞭虾科虾类的分子鉴定技术、种质资源评价以及系统进化等研究。方法 通过二代高通量测序技术得到大管鞭虾线粒体全基因组，对线粒体基因进行注释并对其序列结构进行分析。结果 大管鞭虾线粒体全基因组序列全长为15 940 bp，碱基组成为A (35.66%)、T (32%)、G (11.14%)、C (21.20%)；A+T含量为67.66%，表现出明显的AT偏向性。大管鞭虾线粒体共编码37个基因，包括13个蛋白质编码基因(PCGs)，22个tRNA和2个rRNA；其中14个基因位于负链，23个基因位于正链，与其他管鞭虾线粒体基因组相似。从对虾总科下的5科中选取10个物种为代表进行选择压力分析，发现在进化过程中对虾总科所有蛋白质编码基因都受到纯化选择作用。另外通过结合对虾总科下5科共32个物种的线粒体全基因组的13个蛋白质编码基因构建了系统发育树，结果支持管鞭虾科的单系性，以及大管鞭虾与中华管鞭虾亲缘关系最近。结论 研究结果弥补了大管鞭虾分子生物学领域的空白，明确了大管鞭虾的系统进化地位，通过比较物种之间的基因重排特点和构建系统发育树来探讨对虾总科种间进化规律，为对虾总科系统发育的研究提供了更多参考。

Abstract:

To expand research on molecular identification techniques, germplasm resource evaluation, and systematic evolution in Solenoceridae shrimp, we utilized second-generation high-throughput sequencing technology to obtain the complete mitochondrial genome of Solenocera melantho. The mitochondrial genes were annotated, and their sequence structure was analyzed. The total length of the S. melantho mitogenome was 15 940 bp, with a base composition of A (35.66%), T (32.00%), G (11.14%), and C (21.20%); the A+T content was 67.66%, indicating a pronounced AT bias. The S. melantho mitogenome encodes a total of 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs. Of these, 14 genes were located on the negative strand, while 23 genes were located on the positive strand, showing similarity to other Solenoceridae mitogenomes. Most PCGs initiated with typical codons ATG and ATT, but ACG for cox1, ATC for atp8, and ATA for nad5. The termination codons for cox1, cox2, cox3, nad3, and nad5 were incomplete, all being T--, while cob terminated with TAG, and all other PCGs used TAA as the termination codon. trnS1 lacked the DHU arm, and trnY lacked the acceptor stem, whileas the remaining 20 tRNAs exhibited the typical cloverleaf structure. Leu and Ser were the most commonly used amino acids, and GGA, UUA, and CGA were the three most frequently used codons. For selection pressure analysis, 10 representative species were selected from 5 families under Penaeoidea, revealing that all PCGs in Penaeoidea experienced purifying selection during evolution. Additionally, a phylogenetic tree was constructed using the 13 PCGs from the complete mitogenomes of 32 species from the 5 families under Penaeoidea. The results supported the monophyly of Solenoceridae and indicated that S. melantho was most closely related to S. crassicornis. This study filled the gap in the molecular biology of S. melantho, clarified its systematic evolutionary position, explored gene rearrangement characteristics among species, and provided more references for studying interspecific evolution in Penaeoidea through phylogenetic analysis.