Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission
Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically importa...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2019-04-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/6677.pdf |
| _version_ | 1797424772678680576 |
|---|---|
| author | Yanqing Zhang Zaohai Zeng Chengjie Chen Caiqin Li Rui Xia Jianguo Li |
| author_facet | Yanqing Zhang Zaohai Zeng Chengjie Chen Caiqin Li Rui Xia Jianguo Li |
| author_sort | Yanqing Zhang |
| collection | DOAJ |
| description | Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes (LcARFs) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs. Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA-ARF (miRN43-ARF9) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E, 7A/7B, 9A/9B, 16A/16B, while a few LcARFs, such as LcARF5A/B, might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission. |
| first_indexed | 2024-03-09T08:06:36Z |
| format | Article |
| id | doaj.art-8fe3c09fa605409f8f197cb94c79467e |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:06:36Z |
| publishDate | 2019-04-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-8fe3c09fa605409f8f197cb94c79467e2023-12-02T23:48:16ZengPeerJ Inc.PeerJ2167-83592019-04-017e667710.7717/peerj.6677Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscissionYanqing ZhangZaohai ZengChengjie ChenCaiqin LiRui XiaJianguo LiAuxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes (LcARFs) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs. Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA-ARF (miRN43-ARF9) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E, 7A/7B, 9A/9B, 16A/16B, while a few LcARFs, such as LcARF5A/B, might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission.https://peerj.com/articles/6677.pdfLitchiAuxinAuxin response factorsmiRNAAbscission |
| spellingShingle | Yanqing Zhang Zaohai Zeng Chengjie Chen Caiqin Li Rui Xia Jianguo Li Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission PeerJ Litchi Auxin Auxin response factors miRNA Abscission |
| title | Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission |
| title_full | Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission |
| title_fullStr | Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission |
| title_full_unstemmed | Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission |
| title_short | Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission |
| title_sort | genome wide characterization of the auxin response factor arf gene family of litchi litchi chinensis sonn phylogenetic analysis mirna regulation and expression changes during fruit abscission |
| topic | Litchi Auxin Auxin response factors miRNA Abscission |
| url | https://peerj.com/articles/6677.pdf |
| work_keys_str_mv | AT yanqingzhang genomewidecharacterizationoftheauxinresponsefactorarfgenefamilyoflitchilitchichinensissonnphylogeneticanalysismirnaregulationandexpressionchangesduringfruitabscission AT zaohaizeng genomewidecharacterizationoftheauxinresponsefactorarfgenefamilyoflitchilitchichinensissonnphylogeneticanalysismirnaregulationandexpressionchangesduringfruitabscission AT chengjiechen genomewidecharacterizationoftheauxinresponsefactorarfgenefamilyoflitchilitchichinensissonnphylogeneticanalysismirnaregulationandexpressionchangesduringfruitabscission AT caiqinli genomewidecharacterizationoftheauxinresponsefactorarfgenefamilyoflitchilitchichinensissonnphylogeneticanalysismirnaregulationandexpressionchangesduringfruitabscission AT ruixia genomewidecharacterizationoftheauxinresponsefactorarfgenefamilyoflitchilitchichinensissonnphylogeneticanalysismirnaregulationandexpressionchangesduringfruitabscission AT jianguoli genomewidecharacterizationoftheauxinresponsefactorarfgenefamilyoflitchilitchichinensissonnphylogeneticanalysismirnaregulationandexpressionchangesduringfruitabscission |