赵玉薇, 黄成, 唐驰鹏, 朱鹏, 张虹, 杨家林, 许尤厚, 李万就, 刘芳星. 2024: 基于转录组测序挖掘疣吻沙蚕性腺发育相关基因. 南方农业学报, 55(3): 623-637. DOI: 10.3969/j.issn.2095-1191.2024.03.004
引用本文: 赵玉薇, 黄成, 唐驰鹏, 朱鹏, 张虹, 杨家林, 许尤厚, 李万就, 刘芳星. 2024: 基于转录组测序挖掘疣吻沙蚕性腺发育相关基因. 南方农业学报, 55(3): 623-637. DOI: 10.3969/j.issn.2095-1191.2024.03.004
ZHAO Yu-wei, HUANG Cheng, TANG Chi-peng, ZHU Peng, ZHANG Hong, YANG Jia-lin, XU You-hou, LI Wan-jiu, LIU Fang-xing. 2024: Transcriptome sequencing for mining gonadal developmentrelated genes in Tylorrhynchus heterochaetus. Journal of Southern Agriculture, 55(3): 623-637. DOI: 10.3969/j.issn.2095-1191.2024.03.004
Citation: ZHAO Yu-wei, HUANG Cheng, TANG Chi-peng, ZHU Peng, ZHANG Hong, YANG Jia-lin, XU You-hou, LI Wan-jiu, LIU Fang-xing. 2024: Transcriptome sequencing for mining gonadal developmentrelated genes in Tylorrhynchus heterochaetus. Journal of Southern Agriculture, 55(3): 623-637. DOI: 10.3969/j.issn.2095-1191.2024.03.004

基于转录组测序挖掘疣吻沙蚕性腺发育相关基因

Transcriptome sequencing for mining gonadal developmentrelated genes in Tylorrhynchus heterochaetus

  • 摘要: 【目的】鉴定筛选出与疣吻沙蚕性腺发育相关的候选基因及信号通路,揭示其性别分化及变态的分子调控机制,为疣吻沙蚕大规模人工繁育技术的突破提供理论依据。【方法】以成熟雄性(M)、成熟雌性(F)和未变态疣吻沙蚕(R)为研究对象,通过Illumina NovaSeq 6000平台完成高通量转录组测序,经过滤、质量控制及拼接组装后,依据Fold Change≥2且错误发现率(FDR)<0.01的筛选标准,通过DESeq2筛选出差异表达基因(DEGs),然后进行GO功能注释分析和KEGG信号通路富集分析,并以实时荧光定量PCR对转录组测序结果进行验证。【结果】经转录组测序从9个疣吻沙蚕样品中获得46891条Unigenes,在COG、GO、KEGG、KOG、Pfam、Swiss-Prot、TrEMBL、eggNOG和Nr等9个主要功能数据库中有27878条Unigenes得到注释。依据筛选标准,共筛选出1798个DEGs,其中,M vs F组有349个DEGs,R vs F组有1090个DEGs,R vs M组有359个DEGs。GO功能注释分析发现,DEGs主要注释到细胞、细胞部分、结合、细胞过程、单生物过程等GO功能条目;KEGG信号通路富集分析结果表明,DEGs主要富集在氧化磷酸化、花生四烯酸代谢、视黄醇代谢、甘氨酸/丝氨酸/苏氨酸代谢等信号通路上。综合DEGs的KEGG信号通路富集分析及Nr数据库BLASTx比对分析,最终筛选出DMRT1、SOX7、HSP90、CALM等14个与疣吻沙蚕性腺发育相关的DEGs。实时荧光定量PCR检测的目的基因表达趋势与转录组测序分析结果基本一致,进一步证实转录组测序结果的准确性。【结论】疣吻沙蚕的性腺发育和成熟机制与多基因发挥功能及多个信号通路相关,包括雄性个体偏向MT-CYB、HSP60DNAH5等基因,雌性个体偏向HSP90、SOX7和COL1A1等基因,以及氧化磷酸化、花生四烯酸代谢、视黄醇代谢、甘氨酸/丝氨酸/苏氨酸代谢等与性腺发育相关的信号通路。

     

    Abstract: 【Objective】To identify candidate genes and signaling pathways associated with gonadal development in Tylorrhynchus heterochaetus, aiming to elucidate the molecular mechanisms underlying sexual maturation, which provided a theoretical foundation for advancing large-scale artificial breeding techniques for T. heterochaetus. 【Method】The study involved the examination of mature male (M), mature female (F), and undifferentiated T. heterochaetus (R) specimens. High-throughput transcriptome sequencing was conducted using the Illumina NovaSeq 6000 platform. Following data filtration, quality control, and splicing assembly, differentially expressed genes (DEGs) were identified using DESeq with criteria of Fold Change ≥2 and false discovery rate(FDR) <0.01. DEGs were further analyzed through GO functional annotation and KEGG pathway enrichment. The sequencing results were validated using real-time fluorescence quantitative PCR. 【Result】Transcriptome sequencing analysis yielded 46891 unigenes from 9 T. heterochaetus samples, and 27878 unigenes were annotated in 9 major functional databases such as COG, GO, KEGG, KOG, Pfam, Swiss-Prot, TrEMBL, eggNOG and Nr. According to the screening criteria, a total of 1798 DEGs were identified, including 349 DEGs in M vs F group, 1090 DEGs in R vs F group, and 359 DEGs in R vs M group. GO functional annotation indicated that DEGs were primarily associated with cell, cell parts, binding, cellular processes, and single biological processes. KEGG pathway enrichment analysis revealed that DEGs enriched in pathways such as oxidative phosphorylation, arachidonic acid metabolism, retinol metabolism, and glycine/serine/threonine metabolism. Fourteen DEGs related to gonadal development including DMRT1, SOX7, HSP90 and CALM were identified through KEGG pathway enrichment and BLASTx analysis of the Nr database. The expression trend of the target gene detected by real-time fluorescence quantitative PCR was basically consistent with the results of transcriptome sequencing analysis, which further confirmed the accuracy of transcriptome sequencing results. 【Conclusion】The mechanism underlying gonadal development and maturation involves the interplay of multiple genes and signaling pathways. This includes male-biased genes such as MT-CYB, HSP60 and DNAH5, and female-biased genes like HSP90, SOX7 and COL1A1, as well as oxidative phosphorylation, arachidonic acid metabolism, retinol metabolism, glycine / serine / threonine metabolism pathways related to gonadal development.

     

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