Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm
NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origi...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2017-06-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2017.01156/full |
| _version_ | 1831672075102715904 |
|---|---|
| author | Xiaoli Jin Jing Ren Eviatar Nevo Xuegui Yin Dongfa Sun Junhua Peng Junhua Peng |
| author_facet | Xiaoli Jin Jing Ren Eviatar Nevo Xuegui Yin Dongfa Sun Junhua Peng Junhua Peng |
| author_sort | Xiaoli Jin |
| collection | DOAJ |
| description | NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1) uneven constitution of Clusters of Orthologous Groups (COGs) and contrasting birth/death rates among subfamilies, and (2) two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses. |
| first_indexed | 2024-12-19T23:46:52Z |
| format | Article |
| id | doaj.art-a8cc22fc544142889d962cc3f530ddd7 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-19T23:46:52Z |
| publishDate | 2017-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-a8cc22fc544142889d962cc3f530ddd72022-12-21T20:01:17ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2017-06-01810.3389/fpls.2017.01156262248Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in AngiospermXiaoli Jin0Jing Ren1Eviatar Nevo2Xuegui Yin3Dongfa Sun4Junhua Peng5Junhua Peng6Department of Agronomy and the Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang UniversityHangzhou, ChinaShandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou UniversityDezhou, ChinaDepartment of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, IsraelDepartment of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, ChinaDepartment of Agronomy, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, ChinaDepartment of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, ChinaLife Science & Technology Center, and the State Key Lab of Crop Breeding Technology Innovation and Integration, China National Seed Group Co., Ltd.Wuhan, ChinaNAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1) uneven constitution of Clusters of Orthologous Groups (COGs) and contrasting birth/death rates among subfamilies, and (2) two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses.http://journal.frontiersin.org/article/10.3389/fpls.2017.01156/fullNAC transcription factorsgene duplicationevolution ratedivergent selectionangiosperm |
| spellingShingle | Xiaoli Jin Jing Ren Eviatar Nevo Xuegui Yin Dongfa Sun Junhua Peng Junhua Peng Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm Frontiers in Plant Science NAC transcription factors gene duplication evolution rate divergent selection angiosperm |
| title | Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm |
| title_full | Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm |
| title_fullStr | Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm |
| title_full_unstemmed | Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm |
| title_short | Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm |
| title_sort | divergent evolutionary patterns of nac transcription factors are associated with diversification and gene duplications in angiosperm |
| topic | NAC transcription factors gene duplication evolution rate divergent selection angiosperm |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2017.01156/full |
| work_keys_str_mv | AT xiaolijin divergentevolutionarypatternsofnactranscriptionfactorsareassociatedwithdiversificationandgeneduplicationsinangiosperm AT jingren divergentevolutionarypatternsofnactranscriptionfactorsareassociatedwithdiversificationandgeneduplicationsinangiosperm AT eviatarnevo divergentevolutionarypatternsofnactranscriptionfactorsareassociatedwithdiversificationandgeneduplicationsinangiosperm AT xueguiyin divergentevolutionarypatternsofnactranscriptionfactorsareassociatedwithdiversificationandgeneduplicationsinangiosperm AT dongfasun divergentevolutionarypatternsofnactranscriptionfactorsareassociatedwithdiversificationandgeneduplicationsinangiosperm AT junhuapeng divergentevolutionarypatternsofnactranscriptionfactorsareassociatedwithdiversificationandgeneduplicationsinangiosperm AT junhuapeng divergentevolutionarypatternsofnactranscriptionfactorsareassociatedwithdiversificationandgeneduplicationsinangiosperm |