Comparative Transcriptomic Analysis for Identification of Environmental-Responsive Genes in Seven Species of Threadfin Breams (Nemipterus)
文献类型： 外文期刊
作者： Dang, Zhaoke 1 ; Wu, Qiaer 2 ; Zhou, Yanbo 2 ; Wang, Liangming 2 ; Liu, Yan 2 ; Yang, Changping 2 ; Liu, Manting 2 ; Xie, Qijian 2 ; Chen, Cheng 2 ; Ma, Shengwei 2 ; Shan, Binbin 2 ;
作者机构： 1.Shanghai Ocean Univ, Coll Marine Living Resource Sci & Management, Shanghai 201306, Peoples R China
2.Chinese Acad Fisheries Sci, South China Sea Fisheries Res Inst, Guangzhou 510300, Peoples R China
3.Minist Agr & Rural Affairs, Key Lab Offshore Fisheries Dev, Guangzhou 510300, Peoples R China
4.Minist Agr Rural Affairs, Key Lab Marine Ranching, Guangzhou 510300, Peoples R China
关键词：
期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：4.9； 五年影响因子：5.7 ）
ISSN： 1661-6596
年卷期： 2025 年 26 卷 15 期
页码：
收录情况： SCI
摘要： Members of the genus Nemipterus are economically important fish species distributed in the tropical and subtropical Indo-West Pacific region. The majority of species in this genus inhabit waters with sandy-muddy substrates on the continental shelf, although different species are found at slightly varying water depths. In this study, we sequenced seven species within the genus Nemipterus after identifying the specimens using complementary morphological analysis and DNA barcoding. Each species yielded over 40,000,000 clean reads, totaling over 300,000,000 clean reads across the seven species. A total of 276,389 unigenes were obtained after de novo assembly and a total of 168,010 (60.79%) unigenes were annotated in the protein database. The comprehensive functional annotation based on the KOG, GO, and KEGG databases revealed that these unigenes are mainly associated with numerous physiological, metabolic, and molecular processes, and that the seven species exhibit similarity in these aspects. By constructing a phylogenetic tree and conducting divergence time analysis, we found that N. bathybius and N. virgatus diverged most recently, approximately during the Neogene Period (14.9 Mya). Compared with other species, N. bathybius and N. virgatus are distributed in deeper water layers. Therefore, we conducted selection pressure analysis using these two species as the foreground branches and identified several environmental-responsive genes. The results indicate that genes such as aqp1, arrdc3, ISP2, Hip, ndufa1, ndufa3, pcyt1a, ctsk, col6a2, casp2 exhibit faster evolutionary rates during long-term adaptation to deep-water environments. Specifically, these genes are considered to be associated with adaptation to aquatic osmoregulation, temperature fluctuations, and skeletal development. This comprehensive analysis provides valuable insights into the evolutionary biology and environmental adaptability of threadfin breams, contributing to the conservation and sustainable management of these species.
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