De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris

Shan Ce Niu, Qing Xu, Guo Qiang Zhang, Yong Qiang Zhang, Wen Chieh Tsai, Jui Ling Hsu, Chieh Kai Liang, Yi Bo Luo, Zhong Jian Liu

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)

Abstract

Orchids are renowned for their spectacular flowers and ecological adaptations. After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris, we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds. Our aims were to contribute to a better understanding of the molecular mechanisms driving the analysed tissue characteristics and to enrich the available data for P. equestris. Here, we present three databases. The first dataset is the RNA-Seq raw reads, which can be used to execute new experiments with different analysis approaches. The other two datasets allow different types of searches for candidate homologues. The second dataset includes the sets of assembled unigenes and predicted coding sequences and proteins, enabling a sequence-based search. The third dataset consists of the annotation results of the aligned unigenes versus the Nonredundant (Nr) protein database, Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) databases with low e-values, enabling a name-based search.

Original languageEnglish
Article number201683
JournalScientific Data
Volume3
DOIs
Publication statusPublished - 2016 Sep 27

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences

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