Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery

Harpal Singh, Krishan Mohan Rai, Santosh Kumar Upadhyay, Poonam Pant, Praveen Chandra Verma, Ajit Pratap Singh, Pradhyumna Kumar Singh

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Bryophytes are the first land plants but are scarcely studied at the molecular level. Here, we report transcriptome sequencing and functional annotation of Dumortiera hirsuta, as a representative bryophyte. Approximately 0.5 million reads with ~195 Mb data were generated by sequencing of mRNA using 454 pyrosequencer. De novo assembly of reads yielded 85,240 unigenes (12,439 contigs and 72,801 singletons). BlastX search at NCBI-NR database showed similarity of 33,662 unigenes with 10-(10) e-value. A total of 23,685 unigenes were annotated at TAIR10 protein database. The annotated unigenes were further classified using the Gene Ontology. Analysis at Kyoto Encyclopedia of Genes and Genomes pathway database identified 95 pathways with significant scores, among which metabolic and biosynthesis of secondary metabolite were the major ones. Phenylpropanoid pathway was elucidated and selected genes were characterized by real time qPCR. We identified 447 transcription factors belonging to 41 families and 1594 eSSRs in 1479 unigenes. D. hirsuta unigenes showed homology across the taxa from algae to angiosperm indicating their role as the connecting link between aquatic and terrestrial plants. This could be a valuable genomic resource for molecular and evolutionary studies. Further, it sheds light for the isolation and characterization of new genes with unique functions.

Original languageEnglish (US)
Pages (from-to)15350
JournalScientific reports
Volume5
DOIs
StatePublished - Oct 20 2015

Keywords

  • Bryophyta/genetics
  • Computational Biology/methods
  • Databases, Genetic
  • Expressed Sequence Tags
  • Gene Expression Profiling
  • Gene Expression Regulation, Enzymologic
  • Gene Expression Regulation, Plant
  • Genetic Markers
  • Genome, Plant
  • High-Throughput Nucleotide Sequencing
  • Microsatellite Repeats
  • Molecular Sequence Annotation
  • Stress, Physiological/genetics
  • Transcription Factors/genetics
  • Transcriptome

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't

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