Generation of Siebold's beech draft genome toward an improvement of functional genomics of trees in Fagales

2015 Fiscal Year Final Research Report

• Project/Area Number: 26660121
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Forest science
• Research Institution: Hokkaido University
• Principal Investigator: SAITO Hideyuki 北海道大学, (連合)農学研究科(研究院), 講師 (70312395)
• Co-Investigator(Kenkyū-buntansha): SESE Jun 国立研究開発法人産業技術総合研究所, 人工知能研究センター, 研究チーム長 (40361539) ; OGURA Atsushi 長浜バイオ大学, バイオサイエンス学部, 准教授 (60465929)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Keywords: 機能ゲノム学 / ドラフトゲノム / RNA-seq / DNA-seq / 次世代シーケンス / ゲノムアセンブリ / ブナ（Fagus crenata）

Outline of Final Research Achievements

We generated a draft genome of Fagus crenata (Fagaceae), as a case study of tree in Fagales, with some considerations of the methods about its assembly and gene prediction. A software of Platanus resulted in the highest quality of the genome assemble compared to others, SOAPdenove and ALLPaths-LG, due to the efficient algorithm of De novo assembly to frequent heterozygous genome. This result suggest that F. crenata genome has heterozygous as a long-living plant with self-incompatibility. De novo assembly of RNA-seq. showed non-convergence relationship between RNA-sequence volume (<73 Gb) and predicted gene number, suggesting unavailable method for gene prediction in F. crenata. Gene expression pattern is helpful information for associating the gene annotation in the candidate of the family. Finally, F crenata draft genome (Ver. 3) was generated (523 Mbp with gap) with 96.9% coverage.

Free Research Field

森林生理生態学