Identification of genuine and novel miRNAs in Amaranthus hypochondriacus from high-throughput sequencing data

Marcelino Martínez Núñez, Magali Ruíz Rivas, Josefat Gregorio Jorge, Pedro Fernando Vera Hernández, Silvia Luna Suárez, Stefan de Folter, Ricardo A. Chávez Montes, Flor de Fátima Rosas Cárdenas

Research output: Contribution to journalArticlepeer-review

Abstract

Amaranth has been proposed as an exceptional alternative for food security and climate change mitigation. Information about the distribution, abundance, or specificity of miRNAs in amaranth species is scare. Here, small RNAs from seedlings under control, drought, heat, and cold stress conditions of the Amaranthus hypocondriacus variety “Gabriela” were sequenced and miRNA loci identified in the amaranth genome using the ShortStack software. Fifty-three genuine miRNA clustersthirty-nine belonging to conserved families, and fourteen novel, were identified. Identification of their target genes suggests that conserved amaranth miRNAs are involved in growth and developmental processes, as well as stress responses. MiR0005, an amaranth-specific miRNA, exhibited an unusual high level of expression, akin to that of conserved miRNAs. Overall, our results broaden our knowledge regarding the distribution, abundance and expression of miRNAs in amaranth, providing the basis for future research on miRNAs and their functions in this important species.

Original languageEnglish
Pages (from-to)88-103
Number of pages16
JournalGenomics
Volume113
Issue number1
DOIs
StatePublished - Jan 2021

Keywords

  • Abiotic stress
  • Amaranth
  • miRNA
  • miRNA loci
  • ShortStack
  • Small RNA sequencing

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