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Analyses of random BAC clone sequences of Japanese cedar, Cryptomeria japonica

  • Miho Tamura
  • Yosuke Hisataka
  • Etsuko Moritsuka
  • Atsushi Watanabe
  • Kentaro Uchiyama
  • Norihiro Futamura
  • Kenji Shinohara
  • Yoshihiko Tsumura
  • Hidenori TachidaEmail author
Original Paper
Part of the following topical collections:
  1. Genome Biology

Abstract

Conifers have larger genomes than most angiosperms, long generation times, and undergone relatively few chromosome duplications during their evolution. Thus, conifers are interesting targets for molecular evolutionary studies. Despite this, there have been few studies regarding their genome structure, and these studies are mostly limited to the Pinaceae. Our target species, Cryptomeria japonica, belongs to the Cupressaceae family, which is phylogenetically separated from the Pinaceae family by a few hundred million years, and is the most important timber tree in Japan, making investigation of its genome structure both interesting and worthwhile. We analyzed the sequences of eight random bacterial artificial chromosome (BAC) clones from C. japonica and compared them with sequences of comparable size from eight other model plants, including Arabidopsis thaliana and Pinus taeda. From this analysis, we identified several features of the C. japonica genome. First, the genome of C. japonica has many divergent repetitive sequences, similar to those of Physcomitrella patens and P. taeda. Additionally, some C. japonica transposable elements (TEs) seem to have been active until recently, and some might be unidentified novel TEs. We also found a putative protein-coding gene with a very long intron (approximately 70 kb). The three Pinaceae species whose genome sequences have been determined share these features, despite the few hundred million years of independent evolution separating the Pinaceae species from C. japonica.

Keywords

BAC clone Cupressaceae Repeat elements Intron length 

Notes

Acknowledgments

We would like to thank Alfred E. Szmidt, Junko Kusumi, and two anonymous referees for constructive comments on earlier drafts of the manuscript. This study was partially supported by the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry and by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (nos. 22370083 and 26291082).

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

Nucleotide sequences were deposited with the DNA Data Bank of Japan (DDBJ).

Supplementary material

11295_2015_859_MOESM1_ESM.docx (13.5 mb)
ESM 1 (DOCX 13806 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Miho Tamura
    • 1
  • Yosuke Hisataka
    • 1
  • Etsuko Moritsuka
    • 2
  • Atsushi Watanabe
    • 3
  • Kentaro Uchiyama
    • 4
  • Norihiro Futamura
    • 5
  • Kenji Shinohara
    • 5
  • Yoshihiko Tsumura
    • 4
    • 6
  • Hidenori Tachida
    • 2
    Email author
  1. 1.Graduate School of Systems Life SciencesKyushu UniversityFukuokaJapan
  2. 2.Department of Biology, Faculty of SciencesKyushu UniversityFukuokaJapan
  3. 3.Department of Forest Environmental Science, Faculty of AgricultureKyushu UniversityFukuokaJapan
  4. 4.Department of Forest GeneticsForestry and Forest Products Research InstituteTsukubaJapan
  5. 5.Department of Molecular and Cell BiologyForestry and Forest Products Research InstituteTsukubaJapan
  6. 6.Faculty of Life & Environmental SciencesUniversity of TsukubaTsukubaJapan

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