Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs.
Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial. Here, we examine the origin, evolution, and potential roles in local adaptation of Populus-specific miRNAs, which originated after the recent salicoid-specific, whole-genome duplication. RNA sequencing was used to generate extensive, comparable miRNA and gene expression data for six tissues. A natural population of Populus trichocarpa and closely related species were used to study the divergence rates, evolution, and adaptive variation of miRNAs. MiRNAs that originated in 5' untranslated regions had higher expression levels and their expression showed high correlation with their host genes. Compared with conserved miRNAs, a significantly higher proportion of Populus-specific miRNAs appear to target genes that were duplicated in salicoids. Examination of single nucleotide polymorphisms in Populus-specific miRNA precursors showed high amounts of population differentiation. We also characterized the newly emerged MIR6445 family, which could trigger the production of phased small interfering RNAs from NAC mRNAs, which encode a transcription factor with primary roles in a variety of plant developmental processes. Together, these observations provide evolutionary insights into the birth and potential roles of Populus-specific miRNAs in genome maintenance, local adaptation, and functional innovation.
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.|Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
Jianbo
J
Xie
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.|Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
Xiaohui
X
Yang
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.|Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
Yuepeng
Y
Song
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.|Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
Qingzhang
Q
Du
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.|Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
Ying
Y
Li
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.|Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
Jinhui
J
Chen
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.|Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
Deqiang
D
Zhang
D000222:Adaptation, Physiological; D001483:Base Sequence; D055162:Biocatalysis; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D018628:Gene Dosage; D020440:Gene Duplication; D005787:Gene Frequency / Q000235:genetics; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D016366:Open Reading Frames / Q000235:genetics; D032107:Populus / Q000235:genetics*; D013045:Species Specificity
D035683:MicroRNAs
Populus-specific; functional innovation; local adaptation; micro-RNA (miRNA); whole-genome duplication (WGD)