Expansion and evolutionary patterns of cysteine-rich peptides in plants
Abstract Background Cysteine-rich peptides (CRPs) are gaining recognition as regulators of cell–cell communication in plants. Results We identified 9556 CRPs in 12 plant species and analysed their evolutionary patterns. In most angiosperm plants, whole genome duplication and segmental duplication ar...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2017-08-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3948-3 |
| _version_ | 1811284237766098944 |
|---|---|
| author | Xing Liu Huping Zhang Huijun Jiao Leiting Li Xin Qiao Musana Rwalinda Fabrice Juyou Wu Shaoling Zhang |
| author_facet | Xing Liu Huping Zhang Huijun Jiao Leiting Li Xin Qiao Musana Rwalinda Fabrice Juyou Wu Shaoling Zhang |
| author_sort | Xing Liu |
| collection | DOAJ |
| description | Abstract Background Cysteine-rich peptides (CRPs) are gaining recognition as regulators of cell–cell communication in plants. Results We identified 9556 CRPs in 12 plant species and analysed their evolutionary patterns. In most angiosperm plants, whole genome duplication and segmental duplication are the major factors driving the expansion of CRP family member genes, especially signal peptides. About 30% of the CRP genes were found clustered on the chromosomes, except in maize (Zea mays). Considerable collinearities between CRP genes between or within species reveal several syntenic regions on the chromosomes. Different subfamilies display diverse evolutionary rates, suggesting that these subfamilies are subjected to different selective pressures. CRPs in different duplication models also show contrasting evolutionary rates, although the underlying mechanism is unclear because of the complexity of gene evolution. The 1281 positively selected genes identified are probably generated within a certain period of time. While most of these belonged to maize and sorghum (Sorghum bicolor), new CRP functions would also be expected. Up-regulation of 10 CRPs was observed in self-pollinated pear pistils and pollen tubes under self S-RNase treatments in vitro. The expression divergence between different CRP gene duplication types suggests that different duplication mechanisms affected the fate of the duplicated CRPs. Conclusion Our analyses of the evolution of the CRP gene family provides a unique view of the evolution of this large gene family. |
| first_indexed | 2024-04-13T02:25:36Z |
| format | Article |
| id | doaj.art-5121cc246a5546638143e64d6b0adfb4 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T02:25:36Z |
| publishDate | 2017-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-5121cc246a5546638143e64d6b0adfb42022-12-22T03:06:47ZengBMCBMC Genomics1471-21642017-08-0118111410.1186/s12864-017-3948-3Expansion and evolutionary patterns of cysteine-rich peptides in plantsXing Liu0Huping Zhang1Huijun Jiao2Leiting Li3Xin Qiao4Musana Rwalinda Fabrice5Juyou Wu6Shaoling Zhang7Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityCenter of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityCenter of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityCenter of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityCenter of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityCenter of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityCenter of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityCenter of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural UniversityAbstract Background Cysteine-rich peptides (CRPs) are gaining recognition as regulators of cell–cell communication in plants. Results We identified 9556 CRPs in 12 plant species and analysed their evolutionary patterns. In most angiosperm plants, whole genome duplication and segmental duplication are the major factors driving the expansion of CRP family member genes, especially signal peptides. About 30% of the CRP genes were found clustered on the chromosomes, except in maize (Zea mays). Considerable collinearities between CRP genes between or within species reveal several syntenic regions on the chromosomes. Different subfamilies display diverse evolutionary rates, suggesting that these subfamilies are subjected to different selective pressures. CRPs in different duplication models also show contrasting evolutionary rates, although the underlying mechanism is unclear because of the complexity of gene evolution. The 1281 positively selected genes identified are probably generated within a certain period of time. While most of these belonged to maize and sorghum (Sorghum bicolor), new CRP functions would also be expected. Up-regulation of 10 CRPs was observed in self-pollinated pear pistils and pollen tubes under self S-RNase treatments in vitro. The expression divergence between different CRP gene duplication types suggests that different duplication mechanisms affected the fate of the duplicated CRPs. Conclusion Our analyses of the evolution of the CRP gene family provides a unique view of the evolution of this large gene family.http://link.springer.com/article/10.1186/s12864-017-3948-3Cysteine-rich peptideExpression divergenceClustered genesDivergent evolution patternGene duplicationPositive selection |
| spellingShingle | Xing Liu Huping Zhang Huijun Jiao Leiting Li Xin Qiao Musana Rwalinda Fabrice Juyou Wu Shaoling Zhang Expansion and evolutionary patterns of cysteine-rich peptides in plants BMC Genomics Cysteine-rich peptide Expression divergence Clustered genes Divergent evolution pattern Gene duplication Positive selection |
| title | Expansion and evolutionary patterns of cysteine-rich peptides in plants |
| title_full | Expansion and evolutionary patterns of cysteine-rich peptides in plants |
| title_fullStr | Expansion and evolutionary patterns of cysteine-rich peptides in plants |
| title_full_unstemmed | Expansion and evolutionary patterns of cysteine-rich peptides in plants |
| title_short | Expansion and evolutionary patterns of cysteine-rich peptides in plants |
| title_sort | expansion and evolutionary patterns of cysteine rich peptides in plants |
| topic | Cysteine-rich peptide Expression divergence Clustered genes Divergent evolution pattern Gene duplication Positive selection |
| url | http://link.springer.com/article/10.1186/s12864-017-3948-3 |
| work_keys_str_mv | AT xingliu expansionandevolutionarypatternsofcysteinerichpeptidesinplants AT hupingzhang expansionandevolutionarypatternsofcysteinerichpeptidesinplants AT huijunjiao expansionandevolutionarypatternsofcysteinerichpeptidesinplants AT leitingli expansionandevolutionarypatternsofcysteinerichpeptidesinplants AT xinqiao expansionandevolutionarypatternsofcysteinerichpeptidesinplants AT musanarwalindafabrice expansionandevolutionarypatternsofcysteinerichpeptidesinplants AT juyouwu expansionandevolutionarypatternsofcysteinerichpeptidesinplants AT shaolingzhang expansionandevolutionarypatternsofcysteinerichpeptidesinplants |