Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil.
Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil.
BMC Plant Biol. 2020 Dec 10;20(1):554. 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.
密切相关的杂交种是识别适应分歧背后基因组区域的理想系统。尽管基因表达在决定基于生态的表型差异方面起着核心作用，但很少有研究推断基因表达在新热带系统中的适应分歧中的作用。在这项研究中，我们在同域和异域种群的 Epiden-drum fulgens 和 E. puniceoluteum（Orchidaceae）中进行了全基因组表达分析，这些物种存在于新热带沿海平原的对比相邻栖息地。
这些物种的基因表达谱高度分化，通过 18-21%的转录本确定。根据同域和异域种群中物种之间的比较，与生殖过程相关的基因本体论（GO）术语丰富。根据同域物种之间的比较，物种在与耐盐和耐淹水相关的基因中表现出差异表达，与环境刺激相关的生物过程似乎是与每个同域区土壤特征相关的转录本的代表。杂种与 E. fulgens 分化良好，但表现出与耐淹水的 E. puniceoluteum 相似的基因表达谱。与亲本物种相比，杂种没有表现出累加表达模式的转录本，并且几乎所有的超亲转录本的表达都增加了。
这项研究揭示了促进生态分化和同型交配的一般机制，并提出了候选基因，如编码过氧化氢酶和钙依赖性蛋白激酶的基因，这些基因是适应新热带沿海平原恶劣土壤条件的基础。此外，它表明基因表达的差异在决定共存物种及其杂种的基于生态的表型差异方面起着核心作用。
