《植物生理学报》 2017, 53(8): 1532-1538

基于RNA-Seq技术苹果基因结构优化与新转录本预测

倪伟, 高付凤, 杨恒峰, 张佳腾, 徐金, 毛志泉, 陈学森, 沈向^*

山东农业大学园艺科学与工程学院, 作物生物学国家重点实验室, 山东泰安271018

通信作者：沈；E-mail: guanshangguoshu@163.com

摘　要：

苹果(Malus domestica)已经完成全基因组测序并公布全基因组图谱, 但是基因注释信息很不完善, 因此本试验利用RNA-Seq技术对苹果已注释基因结构进行优化和新转录本预测。以‘富士’花后15、30、45、60 d的果肉为材料提取总RNA, 构建文库并使用Illumina双末端测序HiSeq 2500平台进行测序, 获得高质量的序列(clean reads)。将得到的结果与苹果‘金冠’参考基因组进行比对, 共优化了13 272个已注释基因的结构, 优化基因5′端和3′端数目分别为8 843个和8 955个, 另外, 共鉴定得到1 604个新的转录本, 部分基因参与了苹果的转录表达调控、生长调节、氨基酸和糖类等的代谢过程。

关键词：苹果; RNA-Seq; 基因结构优化; 新转录本预测

收稿：2016-12-26   修定：2017-07-04

资助：山东省现代农业产业技术体系创新团队(SDAIT-06-07)、现代农业产业技术体系建设专项经费(CARS-28)、公益性行业(农业)科研专项经费(201303093)和支撑计划专项经费(2014BAD6B102)。

Identification of novel transcripts and optimization of annotated genes in apple (Malus domestica) by RNA-Seq

NI Wei, GAO Fu-Feng, YANG Heng-Feng, ZHANG Jia-Teng, XU Jin, MAO Zhi-Quan, CHEN Xue-Sen, SHEN Xiang^∗

State Key Laboratory of Crop Biology, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China

Corresponding author: SHEN Xiang; E-mail: guanshangguoshu@163.com

Abstract:

Although the apple (Malus domestica) genome sequencing has been successfully accomplished and previous promulgated, it is incomplete in terms of the genic annotation information. In this study, we used the RNA-Seq technology to optimize the annotated gene organization and predicate the novel transcript. We use fruit after blooming 15, 30, 45, 60 days as material to isolated total RNA by ‘Fuji’. The cDNA library was constructed for the RNA samples and sequenced on the Illumina HiSeq 2500 platform. The obtained clean reads of high quality were assembled compared with the reference genome sequence, we had amended the 5′ ends or 3′ ends of the 13 727 genes in the original genome level, and optimized 8 843 5′ ends of genes, and 8 955 3′ ends of genes, respectively. Furthermore, 1 604 novel transcripts were identified, and the partial genic annotation information participated the apple metabolic process of transcription regulation, growth regulation, disease resistance, amino acids, and glycometabolism.

Key words: apple (Malus domestica); RNA-Seq; gene structural optimization; novel gene prediction