Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains

• Published in: BMC plant biology Vol. 20; no. 1; p. 554
• Main Authors: Leal, Bárbara Simões Santos, Brandão, Marcelo Mendes, Palma-Silva, Clarisse, Pinheiro, Fabio
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 10.12.2020; BioMed Central; BMC
• Subjects: Adaptation; Adaptation, Physiological - genetics; Adaptive systems; Allopatric populations; Assortative mating; Biodiversity; Biological activity; Botanical research; Brazil; Calcium; Catalase; Coastal ecology; Coastal flora; Coastal plains; Discriminant analysis; Divergence; Divergent evolution; Ecological genomics; Ecosystem; Edaphic adaptation; Flooding; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation, Plant; Gene Ontology; Gene-Environment Interaction; Genes; Genetic aspects; Genetic Speciation; Genomes; Geography; Habitat (Ecology); Habitats; Hybridization, Genetic; Hybridization, Vegetable; Hybrids; Kinases; Natural history; Neotropical speciation; Ontology; Orchidaceae - classification; Orchidaceae - genetics; Orchids; Polyploidy; Populations; Principal Component Analysis; Principal components analysis; Protein kinase; Proteins; Restingas; Salinity; Signal transduction; Soil analysis; Species; Species Specificity; Sympatric populations; Sympatry; Transcription profile; Tropical Climate; Waterlogging; Wetlands; Brazil; Ecological genomics; Orchids; Neotropical speciation; Edaphic adaptation; Restingas; Transcription profile
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-020-02757-x

Closely related hybridizing species are ideal systems for identifying genomic regions underlying adaptive divergence. Although gene expression plays a central role in determining ecologically-based phenotypic differences, few studies have inferred the role of gene expression for adaptive divergence in Neotropical systems. In this study, we conduct genome-wide expression analysis alongside soil elemental analysis in sympatric and allopatric populations of Epidendrum fulgens and E. puniceoluteum (Orchidaceae), which occur in contrasting adjacent habitats in the Neotropical coastal plains. These species were highly differentiated by their gene expression profiles, as determined by 18-21% of transcripts. Gene ontology (GO) terms associated with reproductive processes were enriched according to comparisons between species in both allopatric and sympatric populations. Species showed differential expression in genes linked to salt and waterlogging tolerance according to comparisons between species in sympatry, and biological processes related to environmental stimulus appeared as representative among those transcripts associated with edaphic characteristics in each sympatric zone. Hybrids, in their turn, were well differentiated from E. fulgens, but exhibited a similar gene expression profile to flooding-tolerant E. puniceolutem. When compared with parental species, hybrids showed no transcripts with additive pattern of expression and increased expression for almost all transgressive transcripts. This study sheds light on general mechanisms promoting ecological differentiation and assortative mating, and suggests candidate genes, such as those encoding catalase and calcium-dependent protein kinase, underling adaptation to harsh edaphic conditions in the Neotropical coastal plains. Moreover, it demonstrates that differential gene expression plays a central role in determining ecologically-based phenotypic differences among co-occurring species and their hybrids.