Transcriptome analysis of goat ovaries and follicles based on high-throughput sequencing
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摘要:目的
比较山羊Capra hircus卵巢基质、大卵泡和小卵泡间的mRNA表达图谱，为探究卵泡发育机制提供一定的研究基础。
方法采用高通量测序技术对发情期川中黑山羊的卵巢基质、大卵泡和小卵泡进行转录组测序，利用生物信息学方法检测mRNA表达谱，筛选差异基因，对其进行GO和KEGG通路分析，最后随机抽取5个差异基因进行荧光定量PCR验证。
结果卵巢基质vs大卵泡、卵巢基质vs小卵泡和小卵泡vs大卵泡的差异表达基因分别为524、180和403个。筛选出INHA、TNFRSF19等15个与卵泡发育相关的基因，其主要富集在内质网蛋白质加工、类固醇生物合成、卵母细胞减数分裂等信号通路。通过qRT-PCR验证，定量结果与测序结果基本一致。
结论川中黑山羊卵巢基质、大卵泡和小卵泡的基因表达模式不同，小卵泡与卵巢基质的基因表达模式更相近。
Abstract:ObjectiveTo compare the expression profiles of mRNA among ovarian stroma, large follicles and small follicles of goat (Capra hircus), and lay a foundation for exploring the mechanism of follicular development.
MethodHigh-throughput sequencing technology was used to sequence the transcriptome of ovarian stroma, large follicles and small follicles in Chuanzhong black goats during estrus. The expression profiles of mRNA were detected by bioinformatics, and the differentially expressed genes were screened out. The GO and KEGG pathways of differentially expressed genes were analyzed. Finally, five differentially expressed genes were randomly selected and were verified by fluorescence quantitative PCR.
ResultThe differentially expressed genes of ovarian stroma vs large follicles, ovarian stroma vs small follicles and small follicles vs large follicles were 524, 180 and 403, respectively. Fifteen genes related to follicular development, such as INHA and TNFRSF19, were screened. They were mainly involved in endoplasmic reticulum protein processing, steroid biosynthesis, oocyte meiosis signaling pathway and so on. Quantitative results were basically consistent with sequencing results verified by qRT-PCR.
ConclusionThe gene expression profiles of ovarian stroma, large follicles and small follicles in Chuanzhong black goats are different, and the gene expression patterns of small follicles and ovarian stroma are relative more similar.
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Keywords:
- goat /
- ovarian stroma /
- follicle /
- transcriptome /
- high-throughput sequencing
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图 1 不同卵巢部位间差异表达基因的聚类图
O：卵巢基质；LF：大卵泡；SF：小卵泡；图例右侧的数字为基因表达上调或下调的倍数
Figure 1. Cluster analysis of differentially expressed genes among different parts of ovary
O: Ovarian stroma; LF: Large follicle; SF: Small follicle; Numbers by the legend are expression fold-changes for up- or down-regulated genes
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图 2 不同卵巢部位间差异表达基因的qRT-PCR验证
Figure 2. Quantitative identification of differentially expressed genes among different parts of ovary by qRT-PCR
表 1 用于qRT-PCR检测的基因引物
Table 1 Gene primers for qRT-PCR detection
基因
Gene引物序列(5′→3′)
Primer sequence扩增长度/bp
Product lengthCYP19A1 F: CCGAAGTTGTGCCTATTGC
R: GCTGGGACCTGGTATTGAG101 INHBA F: CATGTGGGAAAAGTGGGGGA
R: TCAAAGTGCAGCGTCTTCCT146 KITLG F: CATTTATCTTCAACTGCTCCTA
R: CCACCATCTCGCTTATCC191 SERP1 F: GTCTTCCTGTGCTCGCTCTTC
R: CGATTATGGCTTCCGATTTCA268 GPNMB F: CCTTGTCCTTTGCCTTCAC
R: AAATCCACCAGGGAGTCGT230 β-actin F: TGCTTCTAGGCGGACTGATT
R: TACAATCAAAGTCCTCGGCCAC106 
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表 2 测序数据质控
Table 2 Quality control of sequencing data
样品1)
Sample有效测序量
No. of clean reads有效测序的占比/%
Ratio of clean readsQ302)/% 样品1)
Sample有效测序量
No. of clean reads有效测序的占比/%
Ratio of clean readsQ302)/% O1 105 953 656 99.68 94.28 LF1 104 768 836 99.62 94.23 O2 102 197 046 99.34 92.71 LF2 100 396 168 99.70 94.85 O3 105 678 158 99.41 92.86 LF3 104 879 676 99.48 94.15 O4 101 844 278 99.44 92.86 LF4 102 209 432 99.37 92.57 O5 107 096 856 99.32 91.31 LF5 100 346 902 99.75 93.86 O6 104 231 700 99.57 92.09 LF6 101 449 700 99.50 92.26 SF1 102 014 414 99.69 94.88 SF4 105 756 846 99.19 91.52 SF2 102 993 890 99.45 94.24 SF5 103 645 956 99.58 93.79 SF3 106 653 668 99.77 94.11 SF6 106 529 902 99.45 92.38 1) O：卵巢基质；LF：大卵泡；SF：小卵泡；2) 碱基识别准确率在99.9%以上的碱基所占百分比
1) O: Ovarian stroma; LF: Large follicle; SF: Small follicle; 2) Percentage of bases with base recognition accuracy above 99.9%
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表 3 不同卵巢部位间排名前10位的差异表达基因
Table 3 Top ten differentially expressed genes among different parts of ovary
项目1)
Item基因
Genelog2(FC)2) P 项目1)
Item基因
Genelog2(FC)2) P 项目1)
Item基因
Genelog2(FC)2) P O vs LF EVI2A 1.69 3.45×10−6 O vs SF KCTD12 1.57 1.52×10−3 LF vs SF GLI1 2.13 1.22×10−6 IRF2BP2 1.24 5.84×10−7 CFD 1.43 3.02×10−4 SLC25A34 1.57 5.72×10−6 PNRC1 1.16 8.06×10−6 PTCH2 −2.23 2.59×10−3 PRRT2 1.35 2.55×10−5 GPR21 1.06 6.22×10−6 GDF5 −1.84 1.99×10−3 PPM1J 1.34 3.08×10−5 TMEM176B −1.86 1.27×10−5 GLI1 −1.48 3.80×10−4 TNRC6C 1.24 2.21×10−5 RDH11 −1.50 1.84×10−6 EMID1 −1.32 4.01×10−4 EFNB3 1.10 2.00×10−5 MINOS1 −1.37 6.17×10−6 MYCL −1.30 3.35×10−4 EFS 1.07 3.58×10−5 MPDU1 −1.09 1.09×10−5 DPEP3 −1.26 1.47×10−3 ADGRL1 1.04 1.63×10−5 NME1 −1.06 1.01×10−5 DPEP2 −1.23 1.68×10−3 KITLG −1.85 1.34×10−5 ARL2BP −1.05 3.12×10−6 CNRIP1 −1.20 1.81×10−3 TMEM176B −1.49 3.67×10−5 1) O：卵巢基质；LF：大卵泡；SF：小卵泡；2) FC:表达差异倍数
1) O: Ovarian stroma; LF: Large follicle; SF: Small follicle; 2) FC: Expression fold-change
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表 4 卵巢基质vs大卵泡部分差异表达基因的GO功能分类
Table 4 GO functional classification of partial differentially expressed genes in ovarian stroma vs large follicle
分类
Category条目
Term基因数目
Gene countP 生物学过程 Biological process RNA加工过程 RNA processing 5 2.70×10−2 细胞组分 Cellular component 细胞 Cell 66 1.90×10−2 细胞部分 Cell part 65 2.40×10−2 细胞内部 Intracellular 63 1.70×10−3 细胞内的部分 Intracellular part 55 6.00×10−3 细胞质 Cytoplasm 39 9.80×10−4 细胞内膜结合细胞器 Intracellular membrane-bounded organelle 36 2.50×10−2 膜结合细胞器 Membrane-bounded organelle 36 2.50×10−2 细胞质部分 Cytoplasmic part 28 2.80×10−2 分子功能 Molecular function 催化活性 Catalytic activity 51 8.20×10−4 磷酸核苷结合 Nucleotide phosphate binding 22 4.60×10−2 核苷酸结合 Nucleotide binding 22 4.60×10−2 转移酶活性 Transferase activity 21 1.50×10−2 转移酶活性(转移含磷基团)
Transferase activity (Transferring phosphorus-containing groups)12 2.70×10−2 异构酶活性 Isomerase activity 5 2.00×10−2
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表 5 卵巢基质vs小卵泡部分差异表达基因的GO功能分类
Table 5 GO functional classification of partial differentially expressed genes in ovarian stroma vs small follicle
分类
Category条目
Term基因数目
Gene countP 生物学过程 Biological process 初级代谢过程 Primary metabolic process 13 4.70×10−2 细胞对应激的反应 Cellular response to stress 4 4.40×10−2 分子功能 Molecular function 小分子结合 Small molecule binding 12 2.30×10−4 碳水化合物衍生物结合 Carbohydrate derivative binding 11 2.50×10−4 核苷酸结合 Nucleotide binding 11 5.90×10−4 磷酸核苷结合 Nucleoside phosphate binding 11 5.90×10−4 核糖核苷结合 Ribonucleoside binding 10 6.00×10−4 核苷结合 Nucleoside binding 10 6.00×10−4 嘌呤核苷三磷酸结合 Purine ribonucleoside triphosphate binding 10 6.00×10−4 嘌呤核苷结合 Purine nucleoside binding 10 6.00×10−4 嘌呤核糖核苷结合 Purine ribonucleoside binding 10 6.00×10−4 核糖核苷酸结合 Ribonucleotide binding 10 6.70×10−4
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表 6 小卵泡vs大卵泡部分差异表达基因的GO功能分类
Table 6 GO functional classification of partial differentially expressed genes in small follicle vs large follicle
分类
Category条目
Term基因数目
Gene countP 生物学过程
Biological process细胞进程 Cellular process 73 3.40×10−2 有机环状化合物代谢过程 Organic cyclic compound metabolic process 31 1.70×10−2 有机氮化合物代谢过程 Organonitrogen compound metabolic process 17 3.80×10−2 有机磷代谢过程 Organophosphate metabolic process 10 1.60×10−2 含核苷的小分子代谢过程 Nucleobase-containing small molecule metabolic process 9 3.50×10−2 嘌呤核糖核苷代谢过程 Purine ribonucleoside metabolic process 8 2.00×10−2 嘌呤核苷代谢过程 Purine nucleoside metabolic process 8 2.00×10−2 核糖核苷代谢过程 Ribonucleoside metabolic process 8 2.00×10−2 糖基化合物代谢过程 Glycosyl compound metabolic process 8 2.90×10−2 核苷代谢过程 Nucleoside metabolic process 8 2.90×10−2 细胞组分
Cellular component细胞内 Intracellular 64 2.70×10−3 细胞质 Cytoplasm 35 2.80×10−2 细胞质部分 Cytoplasmic part 29 2.30×10−2 线粒体 Mitochondrion 14 9.20×10−4 线粒体部分 Mitochondrial part 10 5.20×10−3 细胞器膜 Organelle membrane 10 2.30×10−2 线粒体膜 Mitochondrial membrane 9 5.70×10−3 细胞器包膜 Organelle envelope 9 9.00×10−3 线粒体包膜 Mitochondrial envelope 9 9.00×10−3 囊膜 Envelope 9 9.00×10−3 分子功能
Molecular function磷酸核苷结合 Nucleoside phosphate binding 28 2.90×10−3 核苷酸结合 Nucleotide binding 28 2.90×10−3 嘌呤核苷酸结合 Purine nucleotide binding 25 2.10×10−3 嘌呤核苷结合 Purine nucleoside binding 24 3.30×10−3 嘌呤核苷三磷酸结合 Purine ribonucleoside triphosphate binding 24 3.30×10−3 嘌呤核糖核苷结合 Purine ribonucleoside binding 24 3.30×10−3 核苷结合 Nucleoside binding 24 3.30×10−3 核糖核苷结合 Ribonucleoside binding 24 3.30×10−3 嘌呤核糖核苷酸结合 Purine ribonucleotide binding 24 4.10×10−3
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表 7 卵巢基质、大卵泡和小卵泡部分差异表达基因的KEGG代谢通路
Table 7 KEGG metabolic pathway of partial differentially expressed genes in ovarian stroma, large follicle and small follicle
项目1)
Item通路
Pathway数目
CountP O vs LF 代谢途径 Metabolic pathway 298 4.90×10−17 抗生素的生物合成 Antibiotic biosynthesis 79 1.30×10−14 氧化磷酸化 Oxidative phosphorylation 77 1.10×10−22 内质网蛋白质加工 Protein processing in endoplasmic reticulum 70 1.00×10−14 泛素介导的蛋白水解 Ubiquitin mediated proteolysis 34 6.30×10−3 细胞周期 Cell cycle 32 7.30×10−3 甲状腺激素信号通路 Thyroid hormone signaling pathway 29 5.00×10−3 柠檬酸循环 Citrate cycle 17 2.20×10−6 Notch信号通路 Notch signaling pathway 13 4.90×10−2 类固醇生物合成 Steroid biosynthesis 12 1.90×10−4 O vs SF 癌症的途径 Pathway in cancer 28 3.20×10−2 细胞周期 Cell cycle 25 4.50×10−9 抗生素的生物合成 Antibiotic biosynthesis 17 4.00×10−2 RNA转运 RNA transport 16 1.10×10−2 嘌呤代谢 Purine metabolism 15 3.70×10−2 卵母细胞减数分裂 Oocyte meiosis 13 8.30×10−3 嘧啶代谢 Pyrimidine metabolism 11 1.30×10−2 DNA复制 DNA replication 9 2.30×10−4 孕酮介导的卵母细胞成熟 Progesterone-mediated oocyte maturation 9 4.30×10−2 错配修复 Mismatch repair 8 8.90×10−5 SF vs LF 代谢途径 Metabolic pathway 248 5.60×10−4 氧化磷酸化 Oxidative phosphorylation 74 3.80×10−19 内质网蛋白质加工 Protein processing in endoplasmic reticulum 67 6.00×10−12 抗生素的生物合成 Antibiotic biosynthesis 54 7.80×10−4 泛素介导的蛋白水解 Ubiquitin mediated proteolysis 40 2.90×10−4 甲状腺激素信号通路 Thyroid hormone signaling pathway 32 1.40×10−3 AMPK信号通路 AMPK signaling pathway 32 8.70×10−3 蛋白酶体 Proteasome 31 1.10×10−12 Notch信号通路 Notch signaling pathway 15 1.50×10−2 类固醇生物合成 Steroid biosynthesis 9 2.10×10−2 1) O：卵巢基质；LF：大卵泡；SF：小卵泡
1) O: Ovarian stroma; LF: Large follicle; SF: Small follicle
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