基于RNA-Seq技术的野生和圈养塔里木马鹿皮肤组织转录组比较分析

Comparative Transcriptome Analysis of Skin Tissue of Wild and Captive Tarim Red Deer Based on RNA-Seq

为探寻野生和圈养塔里木马鹿(Cervus elaphus yarkandensis)的基因表达谱是否存在差异,并进一步筛选该物种适应干旱环境的相关基因,利用RNA-Seq技术对野生和圈养塔里木马鹿的皮肤组织进行转录组测序,对测序数据质控后比对参考基因组,筛选差异表达基因并对其进行功能注释和富集分析,利用qRT-PCR方法对转录组测序结果进行可靠性检测。结果显示:与圈养塔里木马鹿相比,在野生塔里木马鹿皮肤组织中共有3 303个差异表达基因,包括上调表达基因1 535个,下调表达基因1 768个,其中上调表达基因显著富集在221个GO terms和12个KEGG通路上,下调表达基因显著富集在1 104个GO terms和38个KEGG通路上;qRT-PCR分析结果显示,转录组测序结果可靠。相比于圈养塔里木马鹿,皮肤和表皮发育相关基因、DNA损伤修复相关基因、转谷氨酰胺酶编码基因和热休克蛋白家族基因在野生塔里木马鹿皮肤组织中上调表达,表明这些基因可能直接或间接参与塔里木马鹿在极端干旱炎热环境中的皮肤保护策略,通过最大限度地减少水分流失和调节体温来保护机体免受外界刺激的损伤。皮肤发育相关基因(K2C6A)、热应激相关基因(HSPA4、TRAP1和HSPH1)和氧化应激相关基因(PRDX2和PRDX6)在塔里木马鹿干旱环境适应性中可能发挥潜在作用。

To investigate whether there are differences in gene expression profiles between wild and captive Tarim red deer(Cervus elaphus yarkandensis) and to further screen genes related to the adaptation of this species to an arid-desert environment, the transcriptome sequencing was performed on skin tissues of wild and captive Tarim red deer using RNASeq technology. The sequencing data was compared with the reference genome after quality control, the differentially expressed genes were screened and their functional annotation and enrichment analysis were performed, and the reliability of transcriptome sequencing results was tested by qRT-PCR. The results showed that compared with captive Tarim red deer, there were 3,303 differentially expressed genes in skin tissue of wild Tarim red deer, including 1,535 up-regulated genes and 1,768 down-regulated genes. The up-regulated genes were significantly enriched in 221 GO terms and 12 KEGG pathways, and the down-regulated genes were significantly enriched in 1,104 GO terms and 38 KEGG pathways, and qRT-PCR analysis showed that the transcriptome sequencing results were reliable. Compared with captive Tarim red deer, the genes related to skin and epidermis development, DNA damage repair, as well as transglutaminase coding genes and heat shock protein family genes were up-regulated in the skin tissues of wild Tarim red deer, suggesting that these genes may be directly or indirectly involved in skin protection strategies of this species to its extremely dry and hot environment, and that these genes protect the body from external stimuli by minimizing water loss and regulating body temperature. Among them, the genes related to skin development(K2C6A), heat stress(HSPA4, TRAP1 and HSPH1) and oxidative stress(PRDX2 and PRDX6) may play potential roles in the adaptability of Tarim red deer to arid environment.