基于RNA-Seq技术的塔里木马鹿毛色相关差异表达基因筛选及初步分析

doi:10.11843/j.issn.0366-6964.2020.10.009

摘要/Abstract

摘要： 旨在基于RNA-Seq技术对塔里木马鹿毛色相关基因进行筛选及分析。采用Illumina Hi Seq TM2000测序平台对塔里木马鹿和天山马鹿的皮肤组织进行转录组测序，所得序列经质控、组装后比对到NR、Swiss-Prot、COG、KOG、KEGG、GO和Pfam数据库中注释，并对差异表达基因进行筛选、功能注释和富集分析。结果表明，测序获得25 038个有注释信息的Unigenes，比对分析显示，塔里木马鹿与天山马鹿有922个差异表达基因，其中上调表达基因495个，下调表达基因427个；GO功能富集分析结果显示，568个差异表达基因富集到61个GO条目上，分别参与了生物学过程、细胞组分及分子功能；KEGG代谢通路富集分析发现，在差异表达基因中富集最显著的代谢通路是ECM-受体相互作用。利用实时荧光定量PCR（qRT-PCR）方法分析与塔里木马鹿毛色相关的7个候选基因的转录水平变化来验证转录组测序结果的准确性和可靠性，这些基因的表达趋势与转录组测序结果相一致。ECM-受体相互作用、蛋白质消化与吸收、PI3K-Akt信号通路及与黑色素合成相关的酪氨酸等通路可能与塔里木马鹿的毛色有关；候选基因MITF、Ggt1、VDR、PTPRF、CⅡTA、ARPC5L、POMC等可能在塔里木马鹿毛色形成过程中发挥重要作用。本研究结果为今后塔里木马鹿毛色相关基因的分子调控机制方面及挖掘潜在的新基因提供了丰富的试验数据。

关键词: 塔里木马鹿, RNA-Seq技术, 毛色, 差异表达基因, qRT-PCR

Abstract: The aim of this study was to screen and analyze the hair color related genes of Tarim red deer based on RNA-Seq technology. Using Illumina Hi Seq TM2000 sequencing platform, the skin tissue of Tarim red deer and Tianshan red deer were sequenced by transcriptome. After quality control and assembly, the obtained sequences were compared with the annotations in NR, Swiss-Prot, COG, KOG, KEGG, GO and Pfam databases, and the differentially expressed genes were screened, functional annotated and enriched. The results showed that 25 038 Unigenes with annotated information were obtained by sequencing. The comparative analysis showed that there were 922 differentially expressed genes between Tarim red deer and Tianshan red deer, of which 495 were up-regulated and 427 were down-regulated. The results of GO functional enrichment analysis showed that 568 differentially expressed genes were enriched in 61 GO terms and participated in biological processes, cell components and molecular functions, respectively. The enrichment analysis of KEGG metabolic pathway showed that the most significant metabolic pathway enriched by differentially expressed genes was the ECM-receptor interaction. Real-time fluorescence quantitative PCR (qRT-PCR) was used to analyze the transcriptional level changes of 7 candidate genes related to hair color to verify the accuracy and reliability of transcriptome sequencing results. The expression trend of these genes was consistent with the transcriptome sequencing results. ECM-receptor interaction, protein digestion and absorption, PI3K-Akt signaling pathway and tyrosine related to melanin synthesis may be related to regulation of hair color of Tarim red deer; Candidate genes MITF, Ggt1, VDR, PTPRF, CⅡTA, ARPC5L, POMC may play an important role in hair color formation of Tarim red deer. The results of this study will provide abundant experimental data for studying the molecular regulatory mechanism of hair color related genes and exploring the potential new genes in Tarim red deer.

Key words: Cervus elaphus yarkandensis, RNA-Seq technology, hair color, differentially expressed genes, qRT-PCR

中图分类号:

Q953.3

苏比奴尔·艾力, 塔依尔江·麦麦提, 布威海丽且姆·阿巴拜科日, 马合木提·哈力克. 基于RNA-Seq技术的塔里木马鹿毛色相关差异表达基因筛选及初步分析[J]. 畜牧兽医学报, 2020, 51(10): 2413-2424.

Subinur ELI, Tayerjan MAMAT, Buweihailiqiemu ABABAIKERI, Mahmut HALIK. Screening and Preliminary Analysis of Tarim Red Deer (Cervus elaphus yarkandensis) Hair Color Differentially Expressed Genes Based on RNA-Seq[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(10): 2413-2424.

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