RNA-Seq 揭示了热带草原和季节性干旱森林的热带树木对干旱的不同响应。

RNA-Seq reveals different responses to drought in Neotropical trees from savannas and seasonally dry forests.

机构信息

Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil.

Laboratório de Genética e Genômica de Plantas, Escola de Agronomia, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil.

出版信息

BMC Plant Biol. 2021 Oct 12;21(1):463. doi: 10.1186/s12870-021-03244-7.

DOI:10.1186/s12870-021-03244-7

PMID:34641780

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8507309/

Abstract

BACKGROUND

Water is one of the main limiting factors for plant growth and crop productivity. Plants constantly monitor water availability and can rapidly adjust their metabolism by altering gene expression. This leads to phenotypic plasticity, which aids rapid adaptation to climate changes. Here, we address phenotypic plasticity under drought stress by analyzing differentially expressed genes (DEG) in four phylogenetically related neotropical Bignoniaceae tree species: two from savanna, Handroanthus ochraceus and Tabebuia aurea, and two from seasonally dry tropical forests (SDTF), Handroanthus impetiginosus and Handroanthus serratifolius. To the best of our knowledge, this is the first report of an RNA-Seq study comparing tree species from seasonally dry tropical forest and savanna ecosystems.

RESULTS

Using a completely randomized block design with 4 species × 2 treatments (drought and wet) × 3 blocks (24 plants) and an RNA-seq approach, we detected a higher number of DEGs between treatments for the SDTF species H. serratifolius (3153 up-regulated and 2821 down-regulated under drought) and H. impetiginosus (332 and 207), than for the savanna species. H. ochraceus showed the lowest number of DEGs, with only five up and nine down-regulated genes, while T. aurea exhibited 242 up- and 96 down-regulated genes. The number of shared DEGs among species was not related to habitat of origin or phylogenetic relationship, since both T. aurea and H impetiginosus shared a similar number of DEGs with H. serratifolius. All four species shared a low number of enriched gene ontology (GO) terms and, in general, exhibited different mechanisms of response to water deficit. We also found 175 down-regulated and 255 up-regulated transcription factors from several families, indicating the importance of these master regulators in drought response.

CONCLUSION

Our findings show that phylogenetically related species may respond differently at gene expression level to drought stress. Savanna species seem to be less responsive to drought at the transcriptional level, likely due to morphological and anatomical adaptations to seasonal drought. The species with the largest geographic range and widest edaphic-climatic niche, H. serratifolius, was the most responsive, exhibiting the highest number of DEG and up- and down-regulated transcription factors (TF).

摘要

背景

水是植物生长和作物生产力的主要限制因素之一。植物不断监测水分供应情况，并通过改变基因表达迅速调整新陈代谢。这导致表型可塑性，有助于快速适应气候变化。在这里，我们通过分析四个亲缘关系相近的新热带紫葳科树种（两种来自热带稀树草原，两种来自季节性干旱热带森林）在干旱胁迫下的差异表达基因（DEG）来研究表型可塑性：两种来自热带稀树草原的是 Handroanthus ochraceus 和 Tabebuia aurea，两种来自季节性干旱热带森林的是 Handroanthus impetiginosus 和 Handroanthus serratifolius。据我们所知，这是首次报道比较季节性干旱热带森林和热带稀树草原生态系统树种的 RNA-Seq 研究。

结果

使用完全随机区组设计，4 个物种×2 个处理（干旱和湿润）×3 个区组（24 株植物）和 RNA-seq 方法，我们检测到处理之间季节性干旱热带森林物种 H. serratifolius（干旱时 3153 个上调和 2821 个下调）和 H. impetiginosus（332 个上调和 207 个下调）的差异表达基因数量高于热带稀树草原物种。H. ochraceus 的差异表达基因数量最少，只有 5 个上调和 9 个下调基因，而 T. aurea 则有 242 个上调和 96 个下调基因。物种之间的共享差异表达基因数量与起源地或系统发育关系无关，因为 T. aurea 和 H. impetiginosus 与 H. serratifolius 具有相似数量的差异表达基因。所有四个物种都有很少的富集基因本体（GO）术语，并且通常表现出不同的水分亏缺响应机制。我们还从几个家族中发现了 175 个下调和 255 个上调转录因子，表明这些主调控因子在干旱响应中很重要。

结论

我们的研究结果表明，亲缘关系相近的物种可能在基因表达水平上对干旱胁迫有不同的反应。热带稀树草原物种在转录水平上对干旱的反应似乎较小，可能是由于对季节性干旱的形态和解剖学适应。具有最大地理范围和最广泛的土壤-气候生态位的物种 H. serratifolius 反应最为灵敏，表现出最多数量的差异表达基因和上调及下调转录因子（TF）。