The rubber tree kinome: Genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

Lucas Borges Dos Santos; Alexandre Hild Aono; Felipe Roberto Francisco; Carla Cristina da Silva; Livia Moura Souza; Anete Pereira de Souza

doi:10.3389/fpls.2023.1068202

The rubber tree kinome: Genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

Front Plant Sci. 2023 Feb 7:14:1068202. doi: 10.3389/fpls.2023.1068202. eCollection 2023.

Authors

Lucas Borges Dos Santos¹, Alexandre Hild Aono¹, Felipe Roberto Francisco¹, Carla Cristina da Silva¹, Livia Moura Souza^{1

2}, Anete Pereira de Souza^{1

3}

Affiliations

¹ Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil.
² São Francisco University (USF), Itatiba, Brazil.
³ Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil.

Abstract

The protein kinase (PK) superfamily constitutes one of the largest and most conserved protein families in eukaryotic genomes, comprising core components of signaling pathways in cell regulation. Despite its remarkable relevance, only a few kinase families have been studied in Hevea brasiliensis. A comprehensive characterization and global expression analysis of the PK superfamily, however, is currently lacking. In this study, with the aim of providing novel inferences about the mechanisms associated with the stress response developed by PKs and retained throughout evolution, we identified and characterized the entire set of PKs, also known as the kinome, present in the Hevea genome. Different RNA-sequencing datasets were employed to identify tissue-specific expression patterns and potential correspondences between different rubber tree genotypes. In addition, coexpression networks under several abiotic stress conditions, such as cold, drought and latex overexploitation, were employed to elucidate associations between families and tissues/stresses. A total of 1,809 PK genes were identified using the current reference genome assembly at the scaffold level, and 1,379 PK genes were identified using the latest chromosome-level assembly and combined into a single set of 2,842 PKs. These proteins were further classified into 20 different groups and 122 families, exhibiting high compositional similarities among family members and with two phylogenetically close species Manihot esculenta and Ricinus communis. Through the joint investigation of tandemly duplicated kinases, transposable elements, gene expression patterns, and coexpression events, we provided insights into the understanding of the cell regulation mechanisms in response to several conditions, which can often lead to a significant reduction in rubber yield.

Keywords: Hevea brasiliensis; RNA-sequencing; coexpression networks; kinase family; tandem duplications; transposanable elements.

Grants and funding

This work was supported by grants from the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Computational Biology Programme). LBS received an undergraduate fellowship from FAPESP (2019/19340-2); AA received a PhD fellowship from FAPESP (2019/03232-6); FF received a PhD fellowship from FAPESP (2018/18985-7); and AS received research fellowships from CNPq (312777/2018).