Transcriptome analysis of metamorphosis stage of Holothuria leucospilota
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摘要: 海参幼苗发育需要经历耳状幼体、樽形幼体、五触手幼体及幼苗阶段,而从浮游幼体变态发育至附着幼苗阶段的高死亡率是热带海参繁育中的共性问题,目前有关热带海参变态发育的调控机制仍不清楚。以玉足海参 (Holothuria leucospilota) 为研究对象,采集小耳幼体 (A)、中耳幼体 (B)、大耳幼体 (C) 和樽形幼体 (D) 4个时期样品进行高通量转录组测序分析,以探究其变态发育的分子机制。结果显示,共产生83.6 GB Raw reads,拼接获得93 528个Unigenes。对4个组测序文库的相邻组间 (A_vs_B, B_vs_C, C_vs_D) 进行两两比较,A_vs_B、B_vs_C和C_vs_D的差异表达基因数目分别为17 732、11 757和11 319 个。GO功能富集显示,差异基因主要富集于分子功能、催化活性等与细胞成长相关的GO功能。此外对KEGG通路进行了分析,结果显示差异基因显著富集于PI3K-Akt、细胞周期、癌症途径等与细胞分化增殖、凋亡相关的信号通路中,其中在幼体由浮游的大耳状幼体变态至附着的樽形幼体过程中,癌症途径的富集频率显著上升,表明其在幼体生长发育模式转换上发挥了关键作用。筛选的差异表达基因及预测的功能信息可为热带海参生长发育调控机制研究、人工繁育及分子改良应用提供参考。Abstract: Development of sea cucumber larvae needs to go through stages of auricularia, doliolaria, pentactula and juvenile. High mortality rate from metamorphosis and development of planktonic larvae to attachment stage of seedlings is a common problem in tropical sea cucumbers breeding. However, the gene regulation mechanism underlying the metamorphosis development of tropical sea cucumber is still unclear. In this study, we chose larval Holothuria leucospilota from four periods of early auricularia (A), mid auricularia (B), late auricularia (C) and doliolaria (D) as samples for high-throughput transcriptome sequencing to investigate the molecular mechanism underlying its metamorphosis development. The results show that a total of 83.6 GB Raw reads were generated, and 93 528 Unigenes were obtained by splicing. Pairwise comparisons between adjacent groups of the four sequencing libraries show that the number of genes with significant differential expression in A_vs_B, B_vs_C and C_vs_D were 17 732, 11 757 and 11 319, respectively. GO function enrichment shows that differential genes were mainly enriched in GO functions related to cell growth, such as molecular function and catalytic activity. In addition, KEGG pathways were analyzed, and the results show that the differential genes were significantly enriched in pathways related to cell differentiation, proliferation and apoptosis, such as PI3K-Akt, cell cycle and cancer pathways. Among them, the enrichment frequency of the pathway in cancer significantly increased during the metamorphosis process, which indicates a key role in the transformation of larval growth and development mode. The screened differentially expressed genes and predicted functional information can lay a foundation for the research on the regulatory mechanism of growth and development, artificial breeding and molecular improvement application of H. leucospilota.
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图 5 相邻组间差异表达基因火山图
注:A_vs_B. B期以A期为参照基准比较;B_vs_C. C期以B期为参照基准比较;C_vs_D. D期以C期为参照基准比较。后图同此。
Figure 5. Volcano map of differentially expressed genes between adjacent groups
Note: A_vs_B. Stage B was compared with Stage A; B_vs_C. Stage C was compared with Stage B; C_vs_D. Stage D was compared with Stage C. The same case in following figures.
表 1 引物信息
Table 1. Primer information
基因 ID
Gene ID正向引物
Forward primer反向引物
Reverse primerU_57660 CACTCACGCAGAAGATGT CCAGCAATTCCAAGTTCAAT U_166100 CCTCATCCTTGCTGCTATT GTCACTCCAACACCAACA U_10254 AGTCACAGAACAGAGGTAAT CGAACGGTCCACATATCA U_21303 ACACCGAACACAGGAATC CCGTTAAGGAGTAAGAGTCA U_27749 TCATTGTTCGGATTGATTGC AACTGCTGACATTGACCAT U_179808 GGATGGCAAGATGAATACTG CGTCGCTATTAAGATTAGGAG β-Actin GTCAGGTCATCACTATCGGCAAT AGAGGTCTTTACGGATGTCAACGT 表 2 转录本组装结果统计分析
Table 2. Statistics analysis of transcript assembly results
项目类型
Item type数量
Number总序列数 Total sequence number 93 528 碱基总数 Total base 287 791 031 最长转录本长度 Maximum transcript length 9 920 最短转录本长度 Minimum transcript length 133 转录本平均长度 Average transcript length 3 077.06 N50 长度 N50 length 3 608 E90N50 长度 E90N50 length 3 575 GC 百分比 GC percent 38.67% Mapped 率 Mapped percent 73.71% 表 3 相邻组间差异表达基因 GO 富集分析 (前 5)
Table 3. GO enrichment analysis of differentially expressed genes between adjacent groups (Top five)
相邻组间
IntergroupGO ID GO 分类
GO Term频率
FrequencyP 值
P value类型
TypeA _vs _B GO: 0071840 细胞成分组织或生物发生
Cellular component organization or biogenesis0.072 0.091 233 GO: 0016043 细胞成分组织
Cellular component organization0.068 0.303 803 GO: 0044281 小分子代谢过程
Small molecule metabolic process0.066 0.000 836 生物过程
Biological processGO: 0007017 基于微管的过程
Microtubule-based process0.039 0.000 702 GO: 0019752 羧酸代谢过程
Carboxylic acid metabolic process0.037 0.000 818 GO: 0005575 细胞组分
Cellular_component0.661 0.081 363 GO: 0110165 细胞解构实体
Cellular anatomical entity0.594 0.061 953 GO: 0005576 细胞外区
Extracellular region0.053 0.000 702 细胞组分
Cellular componentGO: 0042995 细胞投影
Cell projection0.031 0.000 858 GO: 0099080 超分子复合物
Supramolecular complex0.030 0.001 038 GO: 0043167 离子结合
Ion binding0.325 0.014 108 GO: 0016787 水解酶活性
Hydrolase activity0.170 0.000 939 GO: 0036094 小分子结合
Small molecule binding0.163 0.000 962 分子功能
Molecular functionGO: 1901265 核苷磷酸结合
Nucleoside phosphate binding0.151 0.001 825 GO: 0000166 核苷酸结合
Nucleotide binding0.151 0.001 825 B_vs_C GO: 0044281 小分子代谢过程
Small molecule metabolic process0.063 0.097 450 GO: 0005975 碳水化合物代谢过程
Carbohydrate metabolic process0.030 0.000 614 GO: 0019637 有机磷代谢过程
Organophosphate metabolic process0.026 0.289 465 生物过程
Biological processGO: 0044283 小分子生物合成过程
Small molecule biosynthetic process0.021 0.076 630 GO: 0006091 前体代谢物和能量的产生
Generation of precursor metabolites and energy0.018 0.011 235 GO: 0005575 细胞组分
Cellular_component0.676 0.001 002 GO: 0110165 细胞解构实体
Cellular anatomical entity0.597 0.085 132 GO: 0031224 膜的内在成分
Intrinsic component of membrane0.307 0.071 058 细胞组分
Cellular componentGO: 0016021 膜的组成部分
Integral component of membrane0.306 0.087 041 GO: 000557 6 细胞外区
Extracellular region0.067 0.000 566 GO: 0043169 阳离子结合
Cation binding0.204 0.134 971 GO: 0046872 金属离子结合
Metal ion binding0.204 0.121 753 GO: 0016491 氧化还原酶活性
Oxidoreductase activity0.090 0.002 897 分子功能
Molecular functionGO: 0005215 转运蛋白活性
Transporter activity0.075 0.029 888 GO: 0005509 钙离子结合
Calcium ion binding0.073 0.000 626 C_ vs _D GO: 0005975 碳水化合物代谢过程
Carbohydrate metabolic process0.025 0.162 444 GO: 0044283 小分子生物合成过程
Small molecule biosynthetic process0.023 0.022 217 GO: 0007166 细胞表面受体信号通路
Cell surface receptor signaling pathway0.022 0.113 132 生物过程
Biological processGO: 0006790 硫化合物代谢过程
Sulfur compound metabolic process0.021 0.000 184 GO: 0032259 甲基化
Methylation0.020 0.014 144 GO: 0031224 膜的内在成分
Intrinsic component of membrane0.325 0.000 333 GO: 0016021 膜的组成部分
Integral component of membrane0.325 0.000 332 GO: 0005576 细胞外区
Extracellular region0.063 0.000 185 细胞组分
Cellular componentGO: 0005581 胶原蛋白三聚体
Collagen trimer0.031 0.000 184 GO: 0005615 细胞外空间
Extracellular space0.019 0.000 207 GO: 0003674 分子功能
Molecular_function0.820 0.000 312 GO: 0043169 阳离子结合
Cation binding0.214 0.000 417 GO: 0046872 金属离子结合
Metal ion binding0.214 0.000 382 分子功能
Molecular functionGO: 0140096 催化活性,作用于蛋白质
Catalytic activity, acting on a protein0.113 0.020 871 GO: 0016491 氧化还原酶活性
Oxidoreductase activity0.095 0.000 247 -
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