Characterization of small RNAs in Xenopus tropicalis gastrulae

Fernando Faunes, Leonardo I. Almonacid, Francisco Melo, Juan Larrain

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)


Here, we report and characterize deep sequencing data and bioinformatics analysis of small RNAs from Xenopus tropicalis gastrula. A total of 17,553,124 reads with perfect match to the genome derived from 2,616,053 unique sequences were identified. Seventy-seven percent of theses sequences were not found in previous reports from X. tropicalis oocytes and somatic tissues. Bioinformatics analyses indicate that a large fraction of the small RNAs are PIWI-interacting RNAs. Up to 23.9% of small RNAs mapped to transposable elements and 27% to genic regions. Most of abundant transposable derived small RNAs are found in oocyte and gastrula libraries, suggesting that transposon needs to be silenced also during early development. Additionally, miRNAs were identified and many of them are not present in oocytes, suggesting that miRNA expression is stage specific. To the best of our knowledge, this is the first high throughput data release and bioinformatics characterization of small RNAs during Xenopus development.

Original languageEnglish
Pages (from-to)260-270
Number of pages11
Issue number3
Publication statusPublished - Mar 2012


  • Early development process
  • Gastrulation process
  • Genomics process

ASJC Scopus subject areas

  • Endocrinology
  • Cell Biology
  • Genetics


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