The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming

• Published in: The Plant journal : for cell and molecular biology Vol. 118; no. 6; pp. 1848 - 1863
• Main Authors: Cherubino Ribeiro, Thales Henrique, Baldrich, Patricia, Oliveira, Raphael Ricon, Fernandes‐Brum, Christiane Noronha, Mathioni, Sandra Marisa, Sousa Cardoso, Thaís Cunha, Souza Gomes, Matheus, Amaral, Laurence Rodrigues, Pimenta de Oliveira, Kellen Kauanne, Reis, Gabriel Lasmar, Meyers, Blake C., Chalfun‐Junior, Antonio
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.06.2024
• Subjects: Coffea - genetics; Coffea - growth & development; Coffea arabica; Developmental stages; floral development; Flowers - genetics; Flowers - growth & development; Gene Expression Regulation, Plant; Gene sequencing; Growth stage; microRNA; MicroRNAs - genetics; mRNA; Nucleotides; phasiRNAs; Plant growth; Ribonucleic acid; RNA; RNA, Plant - genetics; small RNAs; Tetraploidy; tRFs; microRNA; floral development; Coffea arabica; tRFs; phasiRNAs; small RNAs
• ISSN: 0960-7412; 1365-313X; 1365-313X
• DOI: 10.1111/tpj.16713

SUMMARY Noncoding 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. Significance Statement Small RNAs in coffee floral development: unveiling stage‐specific accumulation patterns and regulatory networks.