Evolutionary Analysis and Functional Identification of Clock-Associated <i>PSEUDO-RESPONSE REGULATOR</i> (<i>PRRs</i>) Genes in the Flowering Regulation of Roses
Pseudo-response regulators (<i>PRRs</i>) are the important genes for flowering in roses. In this work, clock <i>PRRs</i> were genome-wide identified using Arabidopsis protein sequences as queries, and their evolutionary analyses were deliberated intensively in Rosaceae in cor...
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MDPI AG
2022-06-01
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| author | Abdul Jalal Jinrui Sun Yeqing Chen Chunguo Fan Jinyi Liu Changquan Wang |
| author_facet | Abdul Jalal Jinrui Sun Yeqing Chen Chunguo Fan Jinyi Liu Changquan Wang |
| author_sort | Abdul Jalal |
| collection | DOAJ |
| description | Pseudo-response regulators (<i>PRRs</i>) are the important genes for flowering in roses. In this work, clock <i>PRRs</i> were genome-wide identified using Arabidopsis protein sequences as queries, and their evolutionary analyses were deliberated intensively in Rosaceae in correspondence with angiosperms species. To draw a comparative network and flow of clock <i>PRRs</i> in roses, a co-expression network of flowering pathway genes was drawn using a string database, and their functional analysis was studied by silencing using VIGS and protein-to-protein interaction. We revealed that the clock <i>PRRs</i> were significantly expanded in Rosaceae and were divided into three major clades, i.e., <i>PRR5/9</i> (clade 1), <i>PRR3/7</i> (clade 2), and <i>TOC1/PRR1</i> (clade 3), based on their phylogeny. Within the clades, five clock <i>PRRs</i> were identified in <i>Rosa chinensis</i>. Clock <i>PRRs</i> had conserved RR domain and shared similar features, suggesting the duplication occurred during evolution. Divergence analysis indicated the role of duplication events in the expansion of clock <i>PRRs</i>. The diverse cis elements and interaction of clock <i>PRRs</i> with <i>miRNAs</i> suggested their role in plant development. Co-expression network analysis showed that the clock <i>PRRs</i> from <i>Rosa chinensis</i> had a strong association with flowering controlling genes. Further silencing of <i>RcPRR1b</i> and <i>RcPRR5</i> in <i>Rosa chinensis</i> using VIGS led to earlier flowering, confirming them as negative flowering regulators. The protein-to-protein interactions between <i>RcPRR1a</i>/<i>RcPRR5</i> and <i>RcCO</i> suggested that <i>RcPRR1a</i>/<i>RcPRR5</i> may suppress flowering by interfering with the binding of <i>RcCO</i> to the promoter of <i>RcFT</i>. Collectively, these results provided an understanding of the evolutionary profiles as well as the functional role of clock <i>PRRs</i> in controlling flowering in roses. |
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| spelling | doaj.art-18f2619bafca448ab249ed0108d90be02023-11-23T20:12:04ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-06-012313733510.3390/ijms23137335Evolutionary Analysis and Functional Identification of Clock-Associated <i>PSEUDO-RESPONSE REGULATOR</i> (<i>PRRs</i>) Genes in the Flowering Regulation of RosesAbdul Jalal0Jinrui Sun1Yeqing Chen2Chunguo Fan3Jinyi Liu4Changquan Wang5College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaPseudo-response regulators (<i>PRRs</i>) are the important genes for flowering in roses. In this work, clock <i>PRRs</i> were genome-wide identified using Arabidopsis protein sequences as queries, and their evolutionary analyses were deliberated intensively in Rosaceae in correspondence with angiosperms species. To draw a comparative network and flow of clock <i>PRRs</i> in roses, a co-expression network of flowering pathway genes was drawn using a string database, and their functional analysis was studied by silencing using VIGS and protein-to-protein interaction. We revealed that the clock <i>PRRs</i> were significantly expanded in Rosaceae and were divided into three major clades, i.e., <i>PRR5/9</i> (clade 1), <i>PRR3/7</i> (clade 2), and <i>TOC1/PRR1</i> (clade 3), based on their phylogeny. Within the clades, five clock <i>PRRs</i> were identified in <i>Rosa chinensis</i>. Clock <i>PRRs</i> had conserved RR domain and shared similar features, suggesting the duplication occurred during evolution. Divergence analysis indicated the role of duplication events in the expansion of clock <i>PRRs</i>. The diverse cis elements and interaction of clock <i>PRRs</i> with <i>miRNAs</i> suggested their role in plant development. Co-expression network analysis showed that the clock <i>PRRs</i> from <i>Rosa chinensis</i> had a strong association with flowering controlling genes. Further silencing of <i>RcPRR1b</i> and <i>RcPRR5</i> in <i>Rosa chinensis</i> using VIGS led to earlier flowering, confirming them as negative flowering regulators. The protein-to-protein interactions between <i>RcPRR1a</i>/<i>RcPRR5</i> and <i>RcCO</i> suggested that <i>RcPRR1a</i>/<i>RcPRR5</i> may suppress flowering by interfering with the binding of <i>RcCO</i> to the promoter of <i>RcFT</i>. Collectively, these results provided an understanding of the evolutionary profiles as well as the functional role of clock <i>PRRs</i> in controlling flowering in roses.https://www.mdpi.com/1422-0067/23/13/7335clock <i>PRRs</i>evolutionfloweringrose |
| spellingShingle | Abdul Jalal Jinrui Sun Yeqing Chen Chunguo Fan Jinyi Liu Changquan Wang Evolutionary Analysis and Functional Identification of Clock-Associated <i>PSEUDO-RESPONSE REGULATOR</i> (<i>PRRs</i>) Genes in the Flowering Regulation of Roses International Journal of Molecular Sciences clock <i>PRRs</i> evolution flowering rose |
| title | Evolutionary Analysis and Functional Identification of Clock-Associated <i>PSEUDO-RESPONSE REGULATOR</i> (<i>PRRs</i>) Genes in the Flowering Regulation of Roses |
| title_full | Evolutionary Analysis and Functional Identification of Clock-Associated <i>PSEUDO-RESPONSE REGULATOR</i> (<i>PRRs</i>) Genes in the Flowering Regulation of Roses |
| title_fullStr | Evolutionary Analysis and Functional Identification of Clock-Associated <i>PSEUDO-RESPONSE REGULATOR</i> (<i>PRRs</i>) Genes in the Flowering Regulation of Roses |
| title_full_unstemmed | Evolutionary Analysis and Functional Identification of Clock-Associated <i>PSEUDO-RESPONSE REGULATOR</i> (<i>PRRs</i>) Genes in the Flowering Regulation of Roses |
| title_short | Evolutionary Analysis and Functional Identification of Clock-Associated <i>PSEUDO-RESPONSE REGULATOR</i> (<i>PRRs</i>) Genes in the Flowering Regulation of Roses |
| title_sort | evolutionary analysis and functional identification of clock associated i pseudo response regulator i i prrs i genes in the flowering regulation of roses |
| topic | clock <i>PRRs</i> evolution flowering rose |
| url | https://www.mdpi.com/1422-0067/23/13/7335 |
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