A Genome-Wide Characterization of MicroRNA Genes in Maize 英文参考文献.docVIP

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A Genome-Wide Characterization of MicroRNA Genes in Maize 英文参考文献.doc

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A Genome-Wide Characterization of MicroRNA Genes in Maize 英文参考文献

AGenome-WideCharacterizationofMicroRNAGenesin Maize LifangZhang1,Jer-MingChia1,SunitaKumari1,JoshuaC.Stein1,ZhijieLiu1,ApurvaNarechania1, ChristopherA.Maher1,KatherineGuill2,MichaelD.McMullen2,3,DoreenWare1,4 * 1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America, 2Plant Genetics Research Unit, United States Department of Agriculture– AgricultureResearchService,Columbia,Missouri,UnitedStatesofAmerica,3DivisionofPlantSciences,UniversityofMissouriColumbia,Columbia,Missouri,UnitedStates ofAmerica,4Plant,Soil,andNutritionResearchUnit,UnitedStatesDepartmentofAgriculture–AgricultureResearchService,Ithaca,NewYork,UnitedStatesofAmerica 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 librariesthatwerepreparedfromanassortmentofmaizetissues.PCR–RACEamplificationof68miRNAtranscriptprecursors, 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 diversemaizeinbredlinesversusteosinteaccessionssuggestthatthematuremiRNAsareunderstrongpurifyingselection 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, duplicatedmiRNAgenesunderwentextensivegene-loss,with,35%ofancestralsitesretainedasduplicatehomoeologous miRNAgenes.Thisnumberishigherthanthatobservedwithprotein-codinggenes.Asearchforpu