基于山羊肌内前体脂肪细胞RNA-seq数据的新基因发掘与分析
Discovery and analysis of novel genes in goat intramuscular adipocytes before and after the differentiation based on the RNA-seq technique
王友利 1王永 1李志雄 1李艳艳 1朱江江 2熊燕 1林亚秋1
作者信息
- 1. 青藏高原动物遗传资源保护与利用教育部重点实验室,四川成都 610041;青藏高原动物遗传资源保护与利用四川省重点实验室,四川 成都 610041;西南民族大学生畜牧兽医学院,四川 成都 610041
- 2. 青藏高原动物遗传资源保护与利用教育部重点实验室,四川成都 610041;青藏高原动物遗传资源保护与利用四川省重点实验室,四川 成都 610041
- 折叠
摘要
为挖掘山羊(Capra hircus)肌内前体脂肪细胞分化前后的新基因并对其进行GO功能和KEGG通路富集分析.利用转录组测序(Transcriptome sequencing,RNA-seq)技术对山羊肌内前体脂肪细胞分化前后的两组细胞cDNA样品(n=3)进行高通量测序,有效数据与山羊参考基因组比对后利用StringTie软件组装新基因.基于|log2foldchange|＞0和P-adj＜0.05筛选获得差异表达新基因,并利用clusterProfiler R包针对GO和KEGG数据库对新基因进行GO功能及KEGG通路注释.结果表明,组装获得的201个新基因可定位在山羊29对常染色体上,且在染色体2、3、5、11、18和29上定位富集.山羊肌内脂肪细胞分化前后表达上调的新基因共28个,表达下调的新基因共57个.在GO功能富集方面,共21个新基因注释到277个GO功能亚类中,其中GO功能条目中参与生物过程、细胞组成和分子功能的基因分别占73.65％、3.97％和22.38％,且3个条目中显著富集的GO功能亚类分别与代谢功能、病毒组装和分子结合相关.此外,共21个新基因富集到16条KEGG通路中,其中氨基酸生物合成通路富集的新基因最多,为3个.研究结果挖掘了山羊肌内脂肪细胞分化前后的新基因201个,为揭示山羊肌内前体脂肪细胞分化相关的新基因并进一步完善山羊功能基因组提供基础数据.
Abstract
This study aimed to discover novel genes before and after the differentiation of goat intramuscular adipocytes and en-rich them to GO function and KEGG pathway.The RNA-seq technique was performed to carry out the high-throughput sequen-cing to cDNA samples(n=3)of goat intramuscular adipocytes before and after the differentiation.After aligning clean read to the goat reference genome,novel genes were assembled by String Tie.The differentially expressed novel genes were obtained ac-cording to the ratio that was defined as|log2foldchange|＞0 and P-adj＜0.05.GO function and KEGG pathway for novel genes were annotated using cluster Profiler R package against the GO and KEGG databases.These results showed that 201 novel genes obtained from the assembly were located to goat 29 pairs of autosomes,and abundantly located to the chromosome 2,3,5,11,18,and 29.The number of up-regulated novel genes was 28,while that of down-regulated was 57 before and after the differentia-tion of intramuscular adipocytes.In terms of GO function enrichment,a total of 21 novel genes were annotated to 277 GO func-tion subcategories.Further study showed that genes involved in biological process,cellular component and molecular function ac-count for 73.65％,3.97％and 22.38％of the GO terms,respectively.Also,the GO function subcategories significantly en-riched in these three terms were related to metabolism function,viral assembly,and molecular binding,respectively.Moreover,a total of 21 novel genes were enriched to 16 KEGG pathways,of which the biosynthesis of amino acids was the most enriched pathway including 3 novel genes.This study provided a basic data for revealing novel genes associated with goat intramuscular adipocytes differentiation and further improving the annotation of the goat function genome.
关键词
山羊基因组/肌内脂肪前体细胞/转录组测序/新基因Key words
goat genome/intramuscular preadipocyte/RNA-seq/novel gene引用本文复制引用
基金项目
国家自然科学基金项目(32072723)
国家自然科学基金项目(82002817)
国家自然科学基金项目(31902154)
西南民族大学中央高校基本科研业务费专项资金项目(ZYN2022109)
出版年
2024
NETL
NSTL
万方数据