Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants
Abstract Background Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth and development. Integrated phylogenomic synteny network analyses were able to provide novel insights into the evolution of the ARF gene family. Results Here, mor...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-05-01
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| Series: | Plant Methods |
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| Online Access: | http://link.springer.com/article/10.1186/s13007-020-00609-1 |
| _version_ | 1818047882211622912 |
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| author | Bei Gao Liuqiang Wang Melvin Oliver Moxian Chen Jianhua Zhang |
| author_facet | Bei Gao Liuqiang Wang Melvin Oliver Moxian Chen Jianhua Zhang |
| author_sort | Bei Gao |
| collection | DOAJ |
| description | Abstract Background Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth and development. Integrated phylogenomic synteny network analyses were able to provide novel insights into the evolution of the ARF gene family. Results Here, more than 3500 ARFs collected from plant genomes and transcriptomes covering major streptophyte lineages were used to reconstruct the broad-scale family phylogeny, where the early origin and diversification of ARF in charophytes was delineated. Based on the family phylogeny, we proposed a unified six-group classification system for angiosperm ARFs. Phylogenomic synteny network analyses revealed the deeply conserved genomic syntenies within each of the six ARF groups and the interlocking syntenic relationships connecting distinct groups. Recurrent duplication events, such as those that occurred in seed plants, angiosperms, core eudicots and grasses contributed to the expansion of ARF genes which facilitated functional diversification. Ancestral transposition activities in important plant families, including crucifers, legumes and grasses, were unveiled by synteny network analyses. Ancestral gene duplications along with transpositions have profound evolutionary significance which may have accelerated the functional diversification process of paralogues. Conclusions The broad-scale family phylogeny in combination with the state-of-art phylogenomic synteny network analyses not only allowed us to infer the evolutionary trajectory of ARF genes across distinct plant lineages, but also facilitated to generate a more robust classification regime for this transcription factor family. Our study provides insights into the evolution of ARFs which will enhance our current understanding of this important transcription factor family. |
| first_indexed | 2024-12-10T10:12:51Z |
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| id | doaj.art-98307001d27f40cfbf54144199ab6cba |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-12-10T10:12:51Z |
| publishDate | 2020-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-98307001d27f40cfbf54144199ab6cba2022-12-22T01:53:04ZengBMCPlant Methods1746-48112020-05-0116111310.1186/s13007-020-00609-1Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plantsBei Gao0Liuqiang Wang1Melvin Oliver2Moxian Chen3Jianhua Zhang4State Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of ForestryUSDA-ARS, Plant Genetics Research Unit, University of MissouriCAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesState Key Laboratory of Agrobiotechnology, The Chinese University of Hong KongAbstract Background Auxin response factors (ARFs) have long been a research focus and represent a class of key regulators of plant growth and development. Integrated phylogenomic synteny network analyses were able to provide novel insights into the evolution of the ARF gene family. Results Here, more than 3500 ARFs collected from plant genomes and transcriptomes covering major streptophyte lineages were used to reconstruct the broad-scale family phylogeny, where the early origin and diversification of ARF in charophytes was delineated. Based on the family phylogeny, we proposed a unified six-group classification system for angiosperm ARFs. Phylogenomic synteny network analyses revealed the deeply conserved genomic syntenies within each of the six ARF groups and the interlocking syntenic relationships connecting distinct groups. Recurrent duplication events, such as those that occurred in seed plants, angiosperms, core eudicots and grasses contributed to the expansion of ARF genes which facilitated functional diversification. Ancestral transposition activities in important plant families, including crucifers, legumes and grasses, were unveiled by synteny network analyses. Ancestral gene duplications along with transpositions have profound evolutionary significance which may have accelerated the functional diversification process of paralogues. Conclusions The broad-scale family phylogeny in combination with the state-of-art phylogenomic synteny network analyses not only allowed us to infer the evolutionary trajectory of ARF genes across distinct plant lineages, but also facilitated to generate a more robust classification regime for this transcription factor family. Our study provides insights into the evolution of ARFs which will enhance our current understanding of this important transcription factor family.http://link.springer.com/article/10.1186/s13007-020-00609-1AuxinARFTranscription factorGene duplicationGenomic synteny |
| spellingShingle | Bei Gao Liuqiang Wang Melvin Oliver Moxian Chen Jianhua Zhang Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants Plant Methods Auxin ARF Transcription factor Gene duplication Genomic synteny |
| title | Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants |
| title_full | Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants |
| title_fullStr | Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants |
| title_full_unstemmed | Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants |
| title_short | Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants |
| title_sort | phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants |
| topic | Auxin ARF Transcription factor Gene duplication Genomic synteny |
| url | http://link.springer.com/article/10.1186/s13007-020-00609-1 |
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