蕎麥葉片及種子轉錄體分析

Abstract

本研究分析蕎麥種子及葉片轉錄體，分別讀取 143 M 及 247 M 條序列，共組裝 97,200及 74,544 條contigs，平均覆蓋率(coverage)分別約為 1,474 及 3,340 倍，contig 序列平均長度分別為 565 及 607 bp，全部拼接完成之序列分別為 54M 及 45M bp。葉片及種子序列混合拼接時，共可獲得106,190 條 contig，其中屬於種子和葉片者分別為 69,043 及 56,345 條，單獨存於種子或葉片者分別為 22,587 及 9,889 條。所有組裝成功之 contigs 進一步與資料庫比對，註解並進行基因功能分類檢索，分別依照細胞組成 (cellular component)、生理程序(biological process) 及分子功能進行分類。本研究同時檢索與種子蛋白質生合成相關基因，包括種子貯存蛋白、LEA protein, cupin 家族蛋白及過敏蛋白等基因，這些資訊可提供未來蕎麥栽培育種工作之參考。 In this study we surveyed the transcriptome of buckwheat seeds and leaves, 143 M and 247 M sequence are read and assembled into 97,200 and 74,544 contigs, the average coverage is 1474 and 3340, respectively. Average length of contigs is 565 and 607 bp, overall sequence assembled is 54 M and 45 M bp. When seed and leaf transcriptome are combined, a total of 106,190 contigs are assembled, in which 69,043 and 56,345 contigs belong to seeds and leaf, respectively. Of all the contigs, 22,857 and 9,889 are exclusively exist in seeds and leaves, respectively. After mixed assembling, 27,258 contigs, 25.6% of all assembled contigs, are considered false assembled as the RPKM value is 0 in both seed and leaf transcriptome. The successfully assembled contigs are then blasted with databases and annotated. The gene ontology (GO) is annotated according to cellular component, biological process and molecular functions. In the project, we are interested in seed properties include seed storage protein, LEA protein, cupin family and allergenic protein. All the above sequence are sorted and retrieved, which would be valuable for future breeding.