In silico identification and characterization of conserved plant microRNAs in barley

Xiaoming Wu, Csaba Hornyik, Micha Bayer, David Marshall, Robbie Waugh, Runxuan Zhang

Research output: Contribution to journalArticleResearchpeer-review

1 Citation (Scopus)

Abstract

Background /Methodology: Taking advantage of a newly available barley (Hordeum vulgare) genome sequence assembly and increasing number of miRNAs identified in other plant species, we carried out computational analyses to identify and characterize miRNAs conserved in barley. We investigate the locations of miRNAs on the barley genome assembly and provide annotation of the functions of their predicted target genes. We compare our results to previous miRNA studies and publicly available barley small RNA libraries. Results: 116 mature miRNA sequences from 60 miRNA families have been found in the barley genome assembly by our miRNA identification pipeline. Closely related cereal crops contain most of the miRNA families that we found in the barley genome
assembly. Most miRNA genes were located in intergenic regions or introns. Among the 116 mature miRNAs predicted, 80 have been reported in previous barley miRNA studies. Eight mature miRNA sequences have never reported in the previous barley miRNA studies.
Conclusions: This in silico study has provided updated information in characterizing plant miRNAs in barley. The identified miRNA and
precursor sequences, their genomic locations as well as predicted target transcripts will serve as valuable resources for future studies.
Original languageEnglish
Pages (from-to)841-852
Number of pages12
JournalCentral European Journal of Biology
Volume9
Issue number9
DOIs
Publication statusPrint publication - 2014
Externally publishedYes

Fingerprint

Hordeum
MicroRNAs
microRNA
Computer Simulation
barley
genome assembly
Genes
Genome
RNA libraries
grain crops
intergenic DNA
Hordeum vulgare
introns
Intergenic DNA
genes
genomics
Introns
Crops

Keywords

  • Barley
  • Crop
  • Genome sequence
  • In silico
  • Small RNAs
  • microRNAs

Cite this

Wu, Xiaoming ; Hornyik, Csaba ; Bayer, Micha ; Marshall, David ; Waugh, Robbie ; Zhang, Runxuan. / In silico identification and characterization of conserved plant microRNAs in barley. In: Central European Journal of Biology. 2014 ; Vol. 9, No. 9. pp. 841-852.
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abstract = "Background /Methodology: Taking advantage of a newly available barley (Hordeum vulgare) genome sequence assembly and increasing number of miRNAs identified in other plant species, we carried out computational analyses to identify and characterize miRNAs conserved in barley. We investigate the locations of miRNAs on the barley genome assembly and provide annotation of the functions of their predicted target genes. We compare our results to previous miRNA studies and publicly available barley small RNA libraries. Results: 116 mature miRNA sequences from 60 miRNA families have been found in the barley genome assembly by our miRNA identification pipeline. Closely related cereal crops contain most of the miRNA families that we found in the barley genomeassembly. Most miRNA genes were located in intergenic regions or introns. Among the 116 mature miRNAs predicted, 80 have been reported in previous barley miRNA studies. Eight mature miRNA sequences have never reported in the previous barley miRNA studies.Conclusions: This in silico study has provided updated information in characterizing plant miRNAs in barley. The identified miRNA andprecursor sequences, their genomic locations as well as predicted target transcripts will serve as valuable resources for future studies.",
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In silico identification and characterization of conserved plant microRNAs in barley. / Wu, Xiaoming; Hornyik, Csaba; Bayer, Micha; Marshall, David; Waugh, Robbie; Zhang, Runxuan.

In: Central European Journal of Biology, Vol. 9, No. 9, 2014, p. 841-852.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - In silico identification and characterization of conserved plant microRNAs in barley

AU - Wu, Xiaoming

AU - Hornyik, Csaba

AU - Bayer, Micha

AU - Marshall, David

AU - Waugh, Robbie

AU - Zhang, Runxuan

PY - 2014

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N2 - Background /Methodology: Taking advantage of a newly available barley (Hordeum vulgare) genome sequence assembly and increasing number of miRNAs identified in other plant species, we carried out computational analyses to identify and characterize miRNAs conserved in barley. We investigate the locations of miRNAs on the barley genome assembly and provide annotation of the functions of their predicted target genes. We compare our results to previous miRNA studies and publicly available barley small RNA libraries. Results: 116 mature miRNA sequences from 60 miRNA families have been found in the barley genome assembly by our miRNA identification pipeline. Closely related cereal crops contain most of the miRNA families that we found in the barley genomeassembly. Most miRNA genes were located in intergenic regions or introns. Among the 116 mature miRNAs predicted, 80 have been reported in previous barley miRNA studies. Eight mature miRNA sequences have never reported in the previous barley miRNA studies.Conclusions: This in silico study has provided updated information in characterizing plant miRNAs in barley. The identified miRNA andprecursor sequences, their genomic locations as well as predicted target transcripts will serve as valuable resources for future studies.

AB - Background /Methodology: Taking advantage of a newly available barley (Hordeum vulgare) genome sequence assembly and increasing number of miRNAs identified in other plant species, we carried out computational analyses to identify and characterize miRNAs conserved in barley. We investigate the locations of miRNAs on the barley genome assembly and provide annotation of the functions of their predicted target genes. We compare our results to previous miRNA studies and publicly available barley small RNA libraries. Results: 116 mature miRNA sequences from 60 miRNA families have been found in the barley genome assembly by our miRNA identification pipeline. Closely related cereal crops contain most of the miRNA families that we found in the barley genomeassembly. Most miRNA genes were located in intergenic regions or introns. Among the 116 mature miRNAs predicted, 80 have been reported in previous barley miRNA studies. Eight mature miRNA sequences have never reported in the previous barley miRNA studies.Conclusions: This in silico study has provided updated information in characterizing plant miRNAs in barley. The identified miRNA andprecursor sequences, their genomic locations as well as predicted target transcripts will serve as valuable resources for future studies.

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