Evolution of plant microRNA gene families

Li, Aili; Mao, Long

doi:10.1038/sj.cr.7310113

Cited by 151 publications

(112 citation statements)

References 47 publications

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“…In contrast, animal MIRNA genes in a cluster usually are not homologs although they are evolutionarily related, such as those in the miR-17 gene cluster. These non-homologous MIRNA genes could regulate multiple functionally related genes simultaneously [38].…”

Section: Highly Conserved Mir156b/c Among Cerealsmentioning

confidence: 99%

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

et al. 2007

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It has been shown that overexpression of MIR156b/c resulted in a bushy phenotype in maize and rice. Our results indicated that the MIR156b/c locus was highly conserved among cereals, but not in dicots and that genome duplication events played an important role in the evolution of the miR156 family. Genetic diversity investigation at the locus indicated that only $9% of nucleotide diversity observed in wild rice (O. rufigogon) was maintained in the cultivated rice and the neutral model was rejected (P < 0.05) based on Tajima's D and Fu and Li's D * and F * tests. To our knowledge, this is the first example of miRNA gene to be targeted by both natural and domestication selection in plants.

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Section: Highly Conserved Mir156b/c Among Cerealsmentioning

confidence: 99%

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

et al. 2007

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“…In contrast to most animal miRNAs, plant miRNAs are usually transcribed from large gene families consisting of multiple miRNA precursors (Li and Mao, 2007). Similar to protein-coding gene families, miRNA gene families, including the miR164 genes, probably originated from gene or genome duplications, and subsequently underwent functional diversification to acquire specific biological functions (Maher et al, 2006).…”

Section: Coordinate Control Of Multiple Mirnasmentioning

confidence: 99%

RBE controls microRNA164 expression to effect floral organogenesis

et al. 2012

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Genetic stocks and growth conditionsArabidopsis thaliana plants were grown at 22°C under 16-hour light/8-hour dark conditions. The rbe-2 (Salk_037010), rbe-3, mir164b-1 (Salk_136105), cuc1-1 and cuc2-1 seeds were obtained from the Arabidopsis Biology Resource Center (ABRC). mir164a-4 (GABI SUMMARYThe establishment and maintenance of organ boundaries are vital for animal and plant development. In the Arabidopsis flower, three microRNA164 genes (MIR164a, b and c) regulate the expression of CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, which encode key transcriptional regulators involved in organ boundary specification. These three miR164 genes are expressed in distinct spatial and temporal domains that are crucial for their function. Here, we show that the C2H2 zinc finger transcriptional repressor encoded by RABBIT EARS (RBE) regulates the expression of all three miR164 genes. Furthermore, we demonstrate that RBE directly interacts with the promoter of MIR164c and negatively regulates its expression. We also show that the role of RBE in sepal and petal development is mediated in part through the concomitant regulation of the CUC1 and CUC2 gene products. These results indicate that one role of RBE is to fine-tune miR164 expression to regulate the CUC1 and CUC2 effector genes, which, in turn, regulate developmental events required for sepal and petal organogenesis.KEY WORDS: Arabidopsis, miRNA, Flower development RBE controls microRNA164 expression to effect floral organogenesis

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“…For those miRNAs with multiple coding genes, the multiple coding genes were regarded as a miRNA gene family. For most arthropod species, the miRNA gene families are much smaller than those of plant species (Li et al, 2007;Nozawa et al, 2010). The miRNA origin for Arthropods is quite different from plants.…”

Section: Literature Review Mirnasmentioning

confidence: 99%

“…Previous miRNA studies indicated that miRNA families with larger size usually have relatively low abundance in plant species while those with smaller family size have higher abundance in animal species (Li et al, 2007). The largest miRNA family identified previously is the miRNA family miR395 in rice, which contains 24 perfectly matched coding genes (GUDDETI, 2005).…”

Section: Expansion Of Hessian Fly Mirna Familiesmentioning

confidence: 99%

Global analysis of microRNA species in the gall midgeMayetiola destructor

Du¹

2016

2016 International Congress of Entomology

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MicroRNA (miRNA) plays a role in nearly all the biological pathways and therefore may provide opportunities to develop new means to combat the Hessian fly, Mayetiola destructor, a destructive pest of wheat. This study presents a comprehensive analysis of miRNA species via deep-sequencing samples from Hessian fly second instar larvae, pupae and adults. A total of 921 unique miRNA species were identified from approximately 30 million sequence reads. Among the 921 miRNA species, only 22 were conserved among Hessian fly and other insect species, and 242 miRNA species were unique to Hessian fly, the remaining 657 share certain sequence similarities with pre-miRNA genes identified from various insect species. The abundance of the 921 miRNA species based on sequence reads varies greatly among the three analyzed stages, with 20 exclusively expressed in adults, two exclusively expressed in pupae and two exclusively expressed in second instar larvae. For miRNA species expressed in all stages, 722 were with reads lower than 10. The abundance of the remaining 199 miRNA species varied from zero to more than eight-fold differences among different stages. Putative miRNA-encoding genes were analyzed for each miRNA species. A single putative gene was identified for 594 miRNA species. Two putative genes were identified for 138 miRNA species. Three or more putative genes were identified for 86 miRNA species. The three largest families had 14, 23 and 34 putative coding genes, respectively. No gene was identified for the remaining 103 miRNA species. In addition, 1516 putative target genes were identified for 490 miRNA species based on known criteria for miRNA targets. The putative target genes are involved in a wide range of processes from nutrient metabolism to encoding effector proteins. Analysis of the expression patterns of miRNA and pre-miRNA for the miRNA family PC-5p-67443, which contains 91 genes, revealed that miRNA and pre-miRNA were expressed differently in different developmental stages, suggesting that different isogenes are regulated by different mechanisms, or pre-miRNAs had other functions in addition to as an intermediate for miRNA biogenesis. The large set of miRNA species identified here provides a foundation for future research on miRNA functions in Hessian fly and for comparative studies in other species. The differential expression patterns between a pre-miRNA and its encoded mature miRNA in a multigene family is an initial step toward understanding the functional significance of isogenes in dramatically expanded miRNA families.v

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Evolution of plant microRNA gene families

Cited by 151 publications

References 47 publications

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

Molecular evolution and selection of a gene encoding two tandem microRNAs in rice

RBE controls microRNA164 expression to effect floral organogenesis

Global analysis of microRNA species in the gall midgeMayetiola destructor

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