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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #207857
Title: Evolution of Arabidopsis microRNA families through duplication events

Author
item MAHER, CHRISTOPHER - COLD SPRING HARBOR LAB
item STEIN, LINCOLN - COLD SPRING HARBOR LAB
item Ware, Doreen

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/9/2007
Publication Date: 3/2/2007
Citation: Maher, C., Stein, L., Ware, D. 2007. Evolution of Arabidopsis microRNA families through duplication events. Genome Research. 16:510-519.

Interpretive Summary: MicroRNAs (miRNAs), nucleotide sequences 20-22 bases in length, are processed from larger precursors transcribed from non-protein-coding genes. These precursors are products of a ribonuclease III-like nuclease known as DICER-LIKE (dcl1). In plants, miRNAs have been shown to control developmental processes such as meristem cell identity, organ polarity, and developmental timing by reducing transcript accumulation or inhibiting translation of their respective coding gene targets. Recently the research community has placed great emphasis on the identification of microRNAs and the spatial and temporal regulation of microRNA genes. To understand how microRNA genes evolve, we looked at several rapidly evolving families in Arabidopsis thaliana. We found that they arise from a process of genome-wide duplication, tandem duplication, and segmental duplication followed by dispersal and diversification, similar to the process that drives the evolution of protein gene families. Large-scale expression data, such as massive parallel signature sequencing (MPSS) and expressed sequence tag (EST) data, captures sequences expressed within a given tissue, allowing examination of the transcription patterns of miRNAs. We found that sequence diversification of duplicated miRNA genes was accompanied in some cases by a change in spatial and temporal expression patterns, suggesting that duplicated copies acquire new functionality as they evolve. A better understanding of gene function and the ability to control gene expression during plant development has the potential to improve crop yields, increase resistance to disease, and increase the adaptability of the plant to its environment.

Technical Abstract: Recently there has been a great interest in the identification of microRNAs and their targets as well as understanding the spatial and temporal regulation of microRNA genes. To understand how microRNA genes evolve, we looked at several rapidly evolving families in Arabidopsis thaliana, and found that they arise from a process of genome-wide duplication, tandem duplication, and segmental duplication followed by dispersal and diversification, similar to the processes that drive the evolution of protein gene families. Using multiple expression datasets to examine the transcription patterns of different members of the microRNA families, we find the sequence diversification of duplicated microRNA genes to be accompanied by a change in spatial and temporal expression patterns, suggesting that duplicated copies acquire new functionality as they evolve.