The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming
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Wiley
2024
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| author | Thales Henrique Cherubino Ribeiro Patricia Baldrich Raphael Ricon de Oliveira Christiane Noronha Fernandes‐Brum Sandra Marisa Mathioni Thaís Cunha de Sousa Cardoso Matheus de Souza Gomes Laurence Rodrigues do Amaral Kellen Kauanne Pimenta de Oliveira Gabriel Lasmar dos Reis Blake C. Meyers Antonio Chalfun‐Junior |
| author_facet | Thales Henrique Cherubino Ribeiro Patricia Baldrich Raphael Ricon de Oliveira Christiane Noronha Fernandes‐Brum Sandra Marisa Mathioni Thaís Cunha de Sousa Cardoso Matheus de Souza Gomes Laurence Rodrigues do Amaral Kellen Kauanne Pimenta de Oliveira Gabriel Lasmar dos Reis Blake C. Meyers Antonio Chalfun‐Junior Thales Henrique Cherubino Ribeiro Patricia Baldrich Raphael Ricon de Oliveira Christiane Noronha Fernandes‐Brum Sandra Marisa Mathioni Thaís Cunha de Sousa Cardoso Matheus de Souza Gomes Laurence Rodrigues do Amaral Kellen Kauanne Pimenta de Oliveira Gabriel Lasmar dos Reis Blake C. Meyers Antonio Chalfun‐Junior |
| collection | Wiley Open Access |
| contents | The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming Thales Henrique Cherubino Ribeiro Patricia Baldrich Raphael Ricon de Oliveira Christiane Noronha Fernandes‐Brum Sandra Marisa Mathioni Thaís Cunha de Sousa Cardoso Matheus de Souza Gomes Laurence Rodrigues do Amaral Kellen Kauanne Pimenta de Oliveira Gabriel Lasmar dos Reis Blake C. Meyers Antonio Chalfun‐Junior The Plant Journal SUMMARYNoncoding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in the Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up to anthesis. We combined these data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiple in silico tools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs, and tRFs. Our differential and co‐expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs, and phasiRNAs preferentially accumulate in a stage‐specific manner. Members of the miR482/miR2118 superfamily and their 21‐nucleotide phasiRNAs originating from resistance genes show a robust co‐expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family stage‐specific manner, related to modulated hormonal responses and transcription factor expression. 10.1111/tpj.16713 http://onlinelibrary.wiley.com/termsAndConditions#am |
| doi_str_mv | 10.1111/tpj.16713 |
| format | Artículo Open Access |
| id | wiley_oa_10_1111_tpj_16713 |
| institution | Wiley Open Access |
| license_str_mv | http://onlinelibrary.wiley.com/termsAndConditions#am |
| publishDate | 2024 |
| publisher | Wiley |
| record_format | wiley_oa |
| spellingShingle | The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming Thales Henrique Cherubino Ribeiro Patricia Baldrich Raphael Ricon de Oliveira Christiane Noronha Fernandes‐Brum Sandra Marisa Mathioni Thaís Cunha de Sousa Cardoso Matheus de Souza Gomes Laurence Rodrigues do Amaral Kellen Kauanne Pimenta de Oliveira Gabriel Lasmar dos Reis Blake C. Meyers Antonio Chalfun‐Junior The Plant Journal The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming Thales Henrique Cherubino Ribeiro Patricia Baldrich Raphael Ricon de Oliveira Christiane Noronha Fernandes‐Brum Sandra Marisa Mathioni Thaís Cunha de Sousa Cardoso Matheus de Souza Gomes Laurence Rodrigues do Amaral Kellen Kauanne Pimenta de Oliveira Gabriel Lasmar dos Reis Blake C. Meyers Antonio Chalfun‐Junior The Plant Journal SUMMARYNoncoding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in the Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up to anthesis. We combined these data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiple in silico tools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs, and tRFs. Our differential and co‐expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs, and phasiRNAs preferentially accumulate in a stage‐specific manner. Members of the miR482/miR2118 superfamily and their 21‐nucleotide phasiRNAs originating from resistance genes show a robust co‐expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family stage‐specific manner, related to modulated hormonal responses and transcription factor expression. 10.1111/tpj.16713 http://onlinelibrary.wiley.com/termsAndConditions#am |
| title | The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming |
| topic | The Plant Journal |
| url | https://onlinelibrary.wiley.com/doi/10.1111/tpj.16713 |