De novo transcriptome assembly of a fern, lygodium japonicum, and a web resource database, ljtrans DB

Koichiro Aya*, Masaaki Kobayashi, Junmu Tanaka, Hajime Ohyanagi, Takayuki Suzuki, Kenji Yano, Tomoyuki Takano, Kentaro Yano, Makoto Matsuoka

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

39 Scopus citations


During plant evolution, ferns originally evolved as a major vascular plant with a distinctive life cycle in which the haploid and diploid generations are completely separated. However, the low level of genetic resources has limited studies of their physiological events, as well as hindering research on the evolutionary history of land plants. In this study, to identify a comprehensive catalog of transcripts and characterize their expression traits in the fern Lygodium japonicum, nine different RNA samples isolated from prothalli, trophophylls, rhizomes and sporophylls were sequenced using Roche 454 GS-FLX and Illumina HiSeq sequencers. The hybrid assembly of the high-quality 454 GS-FLX and Illumina HiSeq reads generated a set of 37,830 isoforms with an average length of 1,444 bp. Using four open reading frame (ORF) predictors, 38,142 representative ORFs were identified from a total of 37,830 transcript isoforms and 95 contigs, which were annotated by searching against several public databases. Furthermore, an orthoMCL analysis using the protein sequences of L. japonicum and five model plants revealed various sets of lineage-specific genes, including those detected among land plant lineages and those detected in only L. japonicum. We have also examined the expression patterns of all contigs/isoforms, along with the life cycle of L. japonicum, and identified the tissue-specific transcripts using statistical expression analyses. Finally, we developed a public web resource, the L. japonicum transcriptome database at, which provides important opportunities to accelerate molecular research in ferns.

Original languageEnglish (US)
Pages (from-to)e5
JournalPlant and Cell Physiology
Issue number1
StatePublished - Jan 1 2015
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2014 The Author.


  • De novo assembly
  • Fern
  • Plant evolution
  • RNA-Seq
  • Transcriptome resource

ASJC Scopus subject areas

  • Physiology
  • Plant Science
  • Cell Biology


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