北京鸭腹部脂肪组织的转录组特征分析

Transcriptome analysis of abdominal fats from Peking ducks by RNA-seq

鸭的基因组序列虽已释放,但其基因组信息,尤其是转录组信息仍需进一步开发。文章利用转录组测序分析了鸭的腹部脂肪组织转录组特征。共获得203 200 984个高质量测序数据,鉴定出18 464个基因表达(RPKM≥1),其中96.9%的基因RPKM值小于1 000。15 070个基因发生了可变剪切,剪切次数为35 913次。统计可变剪切类型发现,内含子保留所占比例最低,占所有可变剪切类型的1.17%,而第一外显子可变剪切、末端外显子可变剪切、外显子跳跃依次是3种比例最高的可变剪切类型,比例分别为45.92%,43.67%和6.23%。此外,利用这批转录组数据共检测出229 276个SNPs,其中转换是最主要的突变类型,占所有SNPs的73.28%。对SNP所在基因进行功能注释(GO)发现,这些基因涉及细胞组分、分子功能、生物学过程3大功能类别中广泛的生物功能,表明该研究开发的SNPs较为全面;通路分析(KEGG)发现,SNPs所在基因除了富集于脂类、能量代谢相关通路,更多的基因则富集于癌症、免疫以及内分泌系统相关的通路上,表明脂肪组织除了是能量储备组织,同时也是重要的免疫、内分泌组织。这些数据拓展了鸭的遗传信息,建立的SNPs数据库将有助于鸭分子标记辅助育种及功能基因定位。与癌症、免疫相关的SNPs可为癌症及免疫学研究提供候选遗传标记。

Although the duck genome sequence has been released,its genomic structure,especially its transcriptome characterization needs to be further studied. This study characterized the transcriptome of abdominal fat in ducks by using RNA-seq. In total,203 200 984 clean reads were obtained,and 18 464 genes were identified to be expressed in abdominal fat,among which 96. 9% genes＇ RPKM values were lower than 1 000. 15 070 genes had alternative splicing（ AS）,and the splicing times were 35 913. Intron retention was found to be the rarest AS type,while alternative first exons,alternative last exons and skipped exon were the three major types,with the proportions of45. 92%,43. 67% and 6. 23%,respectively. Using these transcriptome data,229 276 SNPs were called,among which transitions were the main type,accounting for 73. 28% of all the SNPs. Gene ontology（ GO） annotation analysis revealed that genes including these SNPs took part in numerous functions belonging to the three categories of cel-lular component,molecular function,and biological process,and further kyoto encyclopedia of genes and genomes（ KEGG） pathway analysis showed that most of these genes were related to cancer,immune system,and endocrine system,suggesting that the adipose tissue was an important immune and endocrine tissue,as well as an energy store tissue. These data could enlarge the genetic information of ducks. The numerous SNPs identified in this study would contribute to the molecular breeding and help in mapping the genes associated with important economic traits. The SNPs related with cancers and immune systems would serve as useful markers in related studies.