De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB
De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB
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DOI：
10.1093/pcp/pcu184
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发表时间：
2015-01-01
影响因子：
4.9
通讯作者：
Matsuoka, Makoto
中科院分区：
文献类型：
--
作者：
Aya, Koichiro;Kobayashi, Masaaki;Matsuoka, Makoto
在植物进化过程中，蕨类植物最初进化为一种主要的维管植物，具有独特的生活史，其中单倍体和二倍体世代完全分离。然而，由于遗传资源水平低，限制了对陆生植物生理事件的研究，也阻碍了陆生植物进化史的研究。在这项研究中，以确定一个全面的目录的转录本和表征其表达性状的蕨类海金沙，9个不同的RNA样品分离原叶体，营养叶，根茎和孢子叶测序使用罗氏454 GSFLX和Illumina HiSeq测序仪。高质量的454个GS-FLX和Illumina HiSeq读段的杂交组装产生了一组37，830个同种型，平均长度为1，444 bp。使用4个开放阅读框架（ORF）预测因子，从总共37，830个转录异构体和95个重叠群中鉴定出38，142个代表性ORF，这些ORF通过在几个公共数据库中搜索来注释。此外，还利用L. japonicum和5种模式植物中发现了不同的谱系特异性基因，包括在陆地植物谱系中检测到的基因和仅在L.山茱萸我们还研究了所有重叠群/同种型的表达模式，沿着与L. japonicum中表达，并使用统计表达分析鉴定了组织特异性转录物。最后，我们开发了一个公共网络资源，L。japonicum转录组数据库http：//bioinf.mind.meiji.ac.jp/kanikusa/，这为加速蕨类植物的分子研究提供了重要机会。
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 GSFLX 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. japonicumand 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.