Abstract
BackgroundClosely 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.ResultsThese 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.ConclusionsThis 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.
Highlights
Related hybridizing species are ideal systems for identifying genomic regions underlying adaptive divergence
We investigate the genetic basis of adaptation in two closely related Neotropical orchids [28], the diploid Epidendrum fulgens and tetraploid E. puniceoluteum, which hybridize in the Atlantic coastal plains in southeast Brazil, a narrow vegetation physiognomy known as restingas [29, 30]
Linear Discriminant Analysis (LDA) demonstrates that the discrimination between E. fulgens and E. puniceouteum sites in such hybrid zones is highly correlated with the Reference transcriptome We generated 9.53 × to 1.73 × paired-end raw reads per root-derived sample of E. fulgens, E. puniceoluteum, and hybrids, with PHRED score rates Q30 varying from 98.05 to 98.24% (Table S4)
Summary
Related hybridizing species are ideal systems for identifying genomic regions underlying adaptive divergence. 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. Part of the genes whose expression is associated with adaptive divergence may affect fitness, thereby contributing to ecologicallydriven reproductive isolation [21, 23]. Establishing these links is challenging due to the complex patterns of gene expression and scattered information on the genomic architecture for non-model organisms, differential gene expression can be used to generate further hypotheses about molecular mechanisms involved in reproductive isolation (e.g., [14, 24])
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