title: De novo transcriptome assembly of a fern, Lygodium japonicum, and a web resource database, Ljtrans DB.
abstract: 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 http://bioinf.mind.meiji.ac.jp/kanikusa/, which provides important opportunities to accelerate molecular research in ferns.
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan aya.koichiro329@gmail.com.
authors.forename: Koichiro
authors.initials: K
authors.lastname: Aya
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Japan.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Kobayashi
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan.
authors.forename: Junmu
authors.initials: J
authors.lastname: Tanaka
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Japan Tsukuba Division, Mitsubishi Space Software Co., Ltd., Ibaraki, Japan.
authors.forename: Hajime
authors.initials: H
authors.lastname: Ohyanagi
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Suzuki
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Yano
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Japan.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Takano
authors.affiliation: School of Agriculture, Meiji University, Kawasaki, 214-8571 Japan CREST, JST, Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Matsuoka
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D030541:Databases, Genetic; D029624:Ferns / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA; D059467:Transcriptome
keywords: De novo assembly; Fern; Plant evolution; RNA-Seq; Transcriptome resource