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PMID: 19936050 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

A genome-wide characterization of microRNA genes in maize.

PLoS genetics ·Vol. 5 ·No. 11 ·2009-11-00 ·Pages e1000716

Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D

Abstract

MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.

MeSH Terms
Base Sequence Conserved Sequence Gene Expression Profiling Gene Expression Regulation, Plant Genes, Plant Genetic Variation MicroRNAs/genetics Molecular Sequence Data Multigene Family Nucleotides/genetics Open Reading Frames/genetics Organ Specificity/genetics RNA Splicing/genetics RNA, Messenger/genetics,metabolism Sequence Homology, Nucleic Acid Sorghum/genetics Synteny/genetics Zea mays/genetics
Chemicals
MicroRNAs Nucleotides RNA, Messenger
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Zhang Lifang
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.
Chia Jer-Ming
Kumari Sunita
Stein Joshua C
Liu Zhijie
Narechania Apurva
Maher Christopher A
Guill Katherine
McMullen Michael D
Ware Doreen
Conflict of Interest

The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1000716
Published
2009-11-00
Epub
2009-00-20
Pages
e1000716
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC2773440
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pgen.1000716 PMC Full Text View journal details
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