Features of transcriptome in trioecious papaya revealed by a large-scale sequencing of ESTs and comparative analysis in higher plants

Fanchang Zeng, Qingyi Yu, Shaobin Hou, Paul H. Moore, Maqsudel Alam, Ray Ming

Research output: Contribution to journalArticlepeer-review


Papaya (Carica papaya L.) is a major fruit crop in tropical and subtropical regions worldwide. Papaya has three sex types, male, female, and hermaphrodite, and it is a model system for SunUp the evolution of plant sex chromosomes. Although the papaya genome has been sequenced, a systematic transcriptome analysis has not been performed. We report the generation of 75,847 raw sequences from Sanger sequencing of normalized cDNA libraries of the papaya cultivar SunUp prepared from 8 tissues collected from 14 developmental stages and the 3 sex types male, female and hermaphrodite. After trimming, processing and analysis, 16,362 unique sequences were obtained. Functional classification and domain analysis of the collection of unique ESTs indicates there are several protein families with functional domain, gene regulatory network and signal transduction that are involved in a variety of developmental processes including sex differentiation. Comparison of the trioecious papaya transcriptome with that of monoecious plants revealed a unique sex related transcriptome profile. In addition, 106 unigenes were assigned to X/Y chromosomes. Functional annotation revealed sex development related biological processes in which these sex unigenes are involved. Extensive simple sequence repeats (SSR) and single nucleotide polymorphhism (SNP) were identified in papaya ESTs. These sequences will be useful for developing new molecular markers for genetic mapping, detecting allelic polymorphisms associated with phenotypic variations, and facilitating gene cloning for sex determination and agronomically important traits.

Original languageEnglish (US)
Pages (from-to)450-460
Number of pages11
JournalPlant OMICS
Issue number6
StatePublished - 2014


  • Comparative transcriptome
  • Expressed sequence tags (ESTs)
  • Molecular polymorphisms
  • Papaya
  • Sex determination

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science

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