Exploring the Molecular Regulatory Mechanisms of Planktonic Larvae Development in Mytilus coruscus Using Weighted Gene Co-expression Network Analysis and Time-series Differential Analysis
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摘要: 厚壳贻贝（Mytilus coruscus）味道鲜美，富含多种营养物质，是我国沿海重要的经济贝类之一。厚壳贻贝育苗的关键时期在其幼虫变态发育阶段，而幼虫发育是一个动态且复杂的过程，有大量基因的参与以及各种复杂生物学过程共同作用。本研究基于高通量测序技术，对厚壳贻贝幼虫发育的5个关键时期（担轮期、D形期、壳顶期、眼点期、稚贝期）样本进行高通量转录组测序，共筛选出20 894个差异基因。对差异基因进行加权基因共表达网络以及时序差异分析，筛选出6个符合特定时序发育模式的关键子模块，共鉴定出2 395个基因。分别对各子模块内基因进行GO富集分析和蛋白网络互作分析，筛选出30个与厚壳贻贝生长发育过程相关的枢纽基因，包括Fen1、Ndufab1b、Ndufs8a、Pcan、Rnaseh2a；Cdh1、Cacng4b、Cav1、Blm、Ryr1a；Mars1、Cdc42、Aasdh、Apoba、Cav1；Kif11、Cdc20、Ubc、Kif23、Cdc6；Ubc、Rps16、Rpl23、Rpsa、Rps27a；Cdc20、Setd2、Ssrp1a、Cav1、Rab8a。这些基因在厚壳贻贝幼虫发育过程的主要参与调控DNA复制和细胞分裂、线粒体与核糖体功能、蛋白质合成等。本研究在转录组水平上探索了厚壳贻贝浮游幼虫发育过程调控的分子机理，对研究厚壳贻贝功能基因，以及后续培育更优表型性状厚壳贻贝新品种具有重要的理论指导意义。Abstract: Mytilus coruscus is renowned for its delicious taste and rich nutritional content, making it one of the significant economic shellfish along the coast of China. The critical period for M. coruscus seedling cultivation lies in its larval metamorphosis stage. However, the larval development of M. coruscus is a dynamic and complex process, involving the participation of numerous genes and various intricate biological processes. In this study, we based on high-throughput transcriptome sequencing technology, conducted transcriptome sequencing on larval samples of M. coruscus at five key developmental stages (Trocophore, D-veliger, Umbo, Pediveliger, and Post-larvae), identifying a total of 20 894 differentially expressed genes. Weighted gene co-expression network analysis and time-course difference analysis were performed on the differentially expressed genes, followed by joint analysis. Six key submodules conforming to specific temporal developmental patterns were selected, identifying a total of 2 395 genes. Gene Ontology enrichment analysis and protein network interaction analysis were conducted on genes within each submodule. Thirty hub genes related to the growth and development process of M. coruscus were identified, such as Fen1、Ndufab1b、Ndufs8a、Pcan、Rnaseh2a; Cdh1、Cacng4b、Cav1、Blm、Ryr1a; Mars1、Cdc42、Aasdh、Apoba、Cav1; Kif11、Cdc20、Ubc、Kif23、Cdc6; Ubc、Rps16、Rpl23、Rpsa、Rps27a; Cdc20、Setd2、Ssrp1a、Cav1、Rab8a. They playing major regulatory roles in larval development, including regulation of DNA replication and cell division processes, mitochondrial and ribosomal functions, and protein synthesis processes. This study explores the molecular mechanisms underlying the regulation of M. coruscus larval development at the transcriptome level, providing important theoretical guidance for studying functional genes in M. coruscus and subsequent molecular breeding practices aimed at cultivating new varieties with superior phenotypic traits.
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图 2 厚壳贻贝5个发育时期幼虫样本的PCA分析
每一点代表一个样品。
Fig. 2 PCA of five developmental stages larvae samples in M. coruscus.
Each point represents one biological repetition.
图 3 厚壳贻贝幼虫测序样本间的相关系数热图
Fig. 3 Thermogram of correlation coefficient between samples of M. coruscus larvae
图 4 厚壳贻贝5个发育时期幼虫的表达基因数统计
Fig. 4 Statistics on the number of expressed genes in five developmental stages larvae in M. coruscus
图 5 厚壳贻贝5个发育时期幼虫的表达基因数量韦恩图
Fig. 5 Venn diagram of the number of genes expressed in larvae of M. coruscus at five developmental stages
图 6 厚壳贻贝幼虫5个时期差异基因聚类热图
Fig. 6 Heatmap of differentially expressed genes across five developmental stages of M. coruscus
图 7 厚壳贻贝幼虫5个发育时期的差异基因比较统计
Fig. 7 Comparative statistics of differential genes in the larvae of M. coruscus at five developmental stages
图 8 厚壳贻贝5个发育时期幼虫优势表达基因的共表达网络构建
Fig. 8 Construction of co-expression network of the dominantly expressed genes in larvae of M. coruscus at five developmental stages
图 10 共表达模块中模块与性状的关系
Fig. 10 Relationships of consensus module-trait in co-expression modules
图 11 厚壳贻贝5个发育时期幼虫的基因表达时序图
Fig. 11 Sequence diagram of expression of genes at five developmental stages in M. coruscus
图 12 加权基因共表达网络与时序聚类的基因重叠性分析
Fig. 12 Gene overlap analysis between WGCNA and time-course cluster
图 13 6个子模块中基因的GO富集分析
a为Cluster1-MEpink，b为Cluster2-MEblack，c为Cluster4-MEgreen，d为Cluster5-MEtan，e为Cluster8-MEbrown，f为Cluster9-MEgreenyellow.
Fig. 13 GO enrichment analysis of genes in six submodules
a is Cluster1-MEpink, b is Cluster2-MEblack, c is Cluster4-MEgreen, d is Cluster5-MEtan, e is Cluster8-MEbrown, f is Cluster9-MEgreenyellow.
图 14 6个子模块中的基因的蛋白互作网络图
Fig. 14 The protein interaction network diagrams for the genes in the six submodules
表 1 转录组数据质控结果统计
Tab. 1 Statistics of transcriptome data quality control results
样本
Sample原始读长度Raw Reads (M) 高质量读
长度Clean Reads (M)碱基正确率在99%的占比Q20 (%) 碱基正确率在99.9%的占比Q30 (%) 能定位到基因组上的
高质量读长
数目占比Mapped Ratio (%)A1 43.82 42.16 96.53 91.37 96.21 A2 43.82 42.28 96.73 91.85 96.49 A3 45.57 42.42 97.01 92.51 93.08 B1 45.57 43.37 96.74 91.90 95.16 B2 43.82 41.99 96.78 91.91 95.82 B3 43.82 42.16 96.84 92.09 96.22 C1 43.82 42.10 96.72 91.82 96.08 C2 43.82 42.02 96.83 92.09 95.88 C3 43.82 42.23 96.69 91.73 96.37 D1 43.82 42.29 96.54 91.35 96.50 D2 43.82 42.41 97.48 93.32 96.78 D3 43.82 42.30 97.54 93.44 96.53 E1 43.82 42.19 97.24 92.81 96.28 E2 43.82 42.10 97.21 92.71 96.07 E3 43.82 42.03 97.19 92.7 95.91 平均值 44.05 42.27 96.94 92.24 95.96 注：A1−A3为担轮期、B1−B3为D形期、C1−C3为壳顶期、D1−D3为眼点期、E1−E3为稚贝期；M即Million，代表每百万条。 Notes: A1-A3 is Trocophore, B1-B3 is D-veliger, C1-C3 is Umbo, D1-D3 is Pediveliger, E1-E3 is Post-larvae; M is Million. 
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表 2 GO条目富集统计表
Tab. 2 Statistics of enrichment GO terms
模块 Moudle 显著富集GO条目 分子功能（MF） 细胞组分（CC） 生物过程（BP） Cluster1-MEpink 214 51 54 109 Cluster2-MEblack 50 26 16 8 Cluster4-MEgreen 37 10 1 26 Cluster5-MEtan 47 11 10 26 Cluster8-MEbrown 201 46 41 114 Cluster9-MEgreenyellow 50 24 13 13
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表 3 表达基因中的转录因子分布情况统计
Tab. 3 Statistics on the distribution of transcription factors among expressed genes
基因家族
TF familyCluster1-
MEpinkCluster2-
MEblackCluster4-
MEgreenCluster5-
MEtanCluster8-
MEbrownCluster9-
MEgreenyellowARID 0 2 1 1 4 0 ETS 0 0 0 1 0 1 Fork 0 0 0 1 1 0 HMG 1 0 2 1 1 0 Homeobox 1 8 7 1 7 4 MBD 1 0 0 0 0 1 PAX 1 0 0 0 0 0 T-box 0 2 1 1 1 1 THAP 0 0 1 0 1 0 ZBTB 0 1 0 4 0 0 注：第2−7列代表每个子模块中该转录因子表达基因的个数。 Notes: columns 2-7 in the table represent the number of genes expressed by this transcription factor in each sub-module.
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