Evolutionary patterns and coevolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean.
The evolutionary dynamics of duplicated protein-encoding genes (PEGs) is well documented. However, the evolutionary patterns and consequences of duplicated MIRNAs and the potential influence on the evolution of their PEG targets are poorly understood. Here, we demonstrate the evolution of plant MIRNAs subsequent to a recent whole-genome duplication. Overall, the retention of MIRNA duplicates was correlated to the retention of adjacent PEG duplicates, and the retained MIRNA duplicates exhibited a higher level of interspecific preservation of orthologs than singletons, suggesting that the retention of MIRNA duplicates is related to their functional constraints and local genomic stability. Nevertheless, duplication status, rather than local genic collinearity, was the primary determinant of levels of nucleotide divergence of MIRNAs. In addition, the retention of duplicated MIRNAs appears to be associated with the retention of their corresponding duplicated PEG targets. Furthermore, we characterized the evolutionary novelty of a legume-specific microRNA (miRNA) family, which resulted from rounds of genomic duplication, and consequent dynamic evolution of its NB-LRR targets, an important gene family with primary roles in plant-pathogen interactions. Together, these observations depict evolutionary patterns and novelty of MIRNAs in the context of genomic duplication and evolutionary interplay between MIRNAs and their PEG targets mediated by miRNAs.
Department of Agronomy, Purdue University, West Lafayette, Indiana 47906.
Meixia
http://orcid.org/0000-0001-8812-8217
M
Zhao
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19716.
Blake C
http://orcid.org/0000-0003-3436-6097
BC
Meyers
College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
Chunmei
C
Cai
College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
Wei
http://orcid.org/0000-0003-3172-4397
W
Xu
Department of Agronomy, Purdue University, West Lafayette, Indiana 47906 College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China maj@purdue.edu.
Jianxin
http://orcid.org/0000-0002-1474-812X
J
Ma
D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D020131:Genes, Duplicate; D017343:Genes, Plant; D042822:Genomic Instability; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D013025:Glycine max / Q000235:genetics*; D013045:Species Specificity
D004251:DNA Transposable Elements; D035683:MicroRNAs