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Studies on evolution of exons and introns in fungi

Research Project

Project/Area Number 25440188
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Evolutionary biology
Research InstitutionToyama Prefectural University

Principal Investigator

Nishida Hiromi  富山県立大学, 工学部, 教授 (60301115)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2014: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2013: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywords菌類 / 進化 / エキソン / イントロン / 塩基組成 / 塩基配列 / ヌクレオソーム / 連続2塩基配列出現頻度 / Saitoella complicata / transcribed RNA / nucleosome / evolution / base composition / genome signature / exon and intron / ヒストン / ゲノムDNA / 等電点 / 菌類進化 / 2塩基配列出現頻度 / アスペルギルス
Outline of Final Research Achievements

Eukaryotic chromosomal DNA binds to core histones (2 copies of H2A, H2B, H3, and H4 each), resulting in the formation of nucleosomes. The isoelectric point values of fungal histones were not clearly correlated with the chromosomal GC contents. Next, we showed that the frequency of the dinucleotide sequences AA (TT), AT, and TA in introns was more than that in exons. On the other hand, the frequency of CC (GG), CG, and GC in exons was more than that in introns. Among the other dinucleotides, some sequences had species-specific pattern. Enriched and depleted dinucleotides distribution of the archiascomycetous yeast Saitoella complicata around the midpoints of highly positioned nucleosome dyads was not similar to that of the phylogenetically close yeast but similar to the basidiomycete Mixia osmundae, which has similar genomic GC content to that of S. complicata.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (9 results)

All 2016 2015 2014 Other

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Open Access: 4 results,  Acknowledgement Compliant: 4 results) Presentation (4 results) Remarks (1 results)

  • [Journal Article] Genome-wide maps of nucleosomes of the trichostatin A treated and untreated archiascomycetous yeast Saitoella complicata2016

    • Author(s)
      Kenta Yamauchi, Shinji Kondo, Makiko Hamamoto, Yutaka Suzuki, Hiromi Nishida
    • Journal Title

      AIMS Microbiology

      Volume: 2 Issue: 1 Pages: 69-91

    • DOI

      10.3934/microbiol.2016.1.69

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Draft genome sequence of the archiascomycetous yeast Saitoella complicata.2015

    • Author(s)
      Yamauchi K, Kondo S, Hamamoto M, Takahashi Y, Ogura Y, Hayashi T, Nishida H
    • Journal Title

      Genome Announcements

      Volume: 3 Issue: 3

    • DOI

      10.1128/genomea.00220-15

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Relationship between chromosomal GC content and isoelectric points of histones in fungi2015

    • Author(s)
      Hiromi Nishida
    • Journal Title

      The Journal of General and Applied Microbiology

      Volume: 61 Issue: 1 Pages: 24-26

    • DOI

      10.2323/jgam.61.24

    • NAID

      130005061414

    • ISSN
      0022-1260, 1349-8037
    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Conserved and varied dinucleotide sequences in the genomes of three Aspergillus species2014

    • Author(s)
      Hiromi Nishida
    • Journal Title

      Recent Advances in DNA & Gene Sequences

      Volume: 8 Issue: 1 Pages: 10-14

    • DOI

      10.2174/2352092208666141013231001

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 菌類ヌクレオソーム形成とDNA塩基配列2016

    • Author(s)
      山内健太,居島冴香,近藤伸二,西田洋巳
    • Organizer
      第10回日本ゲノム微生物学会
    • Place of Presentation
      東京
    • Year and Date
      2016-03-05
    • Related Report
      2015 Annual Research Report
  • [Presentation] 古生子嚢菌類Saitoella complicataのRNAマップ解析およびヌクレオソームマップ解析2015

    • Author(s)
      山内健太, 近藤伸二, 浜本牧子, 鈴木穣, 西田洋巳
    • Organizer
      2015年度日本農芸化学会中部・関西支部合同大会
    • Place of Presentation
      射水
    • Year and Date
      2015-09-20
    • Related Report
      2015 Annual Research Report
  • [Presentation] 菌類のヌクレオソームマップ解析から見えること

    • Author(s)
      西田洋巳
    • Organizer
      第6回北陸合同バイオシンポジウム
    • Place of Presentation
      国民宿舎能登小牧台
    • Related Report
      2013 Research-status Report
  • [Presentation] 菌類におけるエキソン、イントロン、塩基組成とヌクレオソーム形成

    • Author(s)
      西田洋巳
    • Organizer
      日本農芸化学会2014年度大会 シンポジウム「微生物ゲノム設計の時代に塩基組成の機能と進化を再考する」
    • Place of Presentation
      明治大学生田キャンパス
    • Related Report
      2013 Research-status Report
  • [Remarks] Fungal Nucleosome Database

    • URL

      https://sites.google.com/site/microbioinformatics/home/fungal-nucleosome-database

    • Related Report
      2015 Annual Research Report

URL: 

Published: 2014-07-25   Modified: 2019-07-29  

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