Elsevier

Gene

Volume 694, 30 April 2019, Pages 50-62
Gene

Research paper
Comparative analysis of two sister Erythrophleum species (Leguminosae) reveal contrasting transcriptome-wide responses to early drought stress

https://doi.org/10.1016/j.gene.2019.01.027Get rights and content

Highlights

  • RNA-seq approach was used to analyze drought response in two Erythrophleum species.

  • Gene expression changes at early and late stages of drought were analyzed.

  • Expression profiles showed a species-dependent regulation of the DEGs.

  • E. ivorense is characterized by a late response to drought.

  • E. suaveolens displays a prompt response to drought.

Abstract

With the ongoing climate change, African rainforests are expected to experience severe drought events in the future. In Africa, the tropical genus Erythrophleum (Fabaceae) includes two forest sister timber tree species displaying contrasting geographical distributions. Erythrophleum ivorense is adapted to wet evergreen Guineo-Congolian forests, whereas E. suaveolens occurs in a wider range of climates, being found in moist dense forests but also in gallery forests under a relatively drier climate. This geographical distribution pattern suggests that the two species might cope differently to drought at the genomic level. Yet, the genetic basis of tolerance response to drought stress in both species is still uncharacterized. To bridge this gap, we performed an RNA-seq approach on seedlings from each species to monitor their transcriptional responses at different levels of drought stress (0, 2 and 6 weeks after stopping watering seedlings).

Monitoring of wilting symptoms revealed that E. suaveolens displayed an earlier phenotypic response to drought stress than E. ivorense. At the transcriptomic level, results revealed 2020 (1204 down-regulated/816 up-regulated) and 1495 differentially expressed genes (DEGs) in response to drought stress from a total of 67,432 and 66,605 contigs assembled in E. ivorense and E. suaveolens, respectively. After identifying 30,374 orthologs between species, we found that only 7 of them were DEGs shared between species, while 587 and 458 were differentially expressed only in E. ivorense or E. suaveolens, respectively. GO and KEGG enrichment analysis revealed that the two species differ in terms of significantly regulated pathways as well as the number and expression profile of DEGs (Up/Down) associated with each pathway in the two stress stages. Our results suggested that the two studied species react differently to drought. E. suaveolens seems displaying a prompt response to drought at its early stage strengthened by the down-regulation of many DEGs encoding for signaling and metabolism-related pathways. A considerable up-regulation of these pathways was also found in E. ivorense at the late stage of drought, suggesting this species may be a late responder. Overall, our data may serve as basis for further understanding the genetic control of drought tolerance in tropical trees and favor the selection of crucial genes for genetically enhancing drought resistance.

Introduction

Drought has been long recognized as one of the most important environmental factors driving the geographical distribution of plant species. It poses tremendous threat to sustainable agriculture and forestry worldwide as it severely impairs the survival of plants, mainly in water-limited ecosystems (Liu et al., 2017; Yang et al., 2018). Tropical ecosystems support around half of all terrestrial plant and animal species, including 96% of tree species, and represent 34% of gross primary terrestrial productivity (Corlett, 2016). Drought events frequency and water scarcity are predicted to increase progressively as an outcome of global climatic changes (Wuebbles et al., 2014; Sprenger et al., 2016), with profound impacts on the vegetation of the Amazonian, Asian and African tropical regions (Solomon et al., 2007; Buytaert et al., 2011; Kirtman et al., 2013; Bonal et al., 2016). Nowadays, African rainforests are subject to deforestation and habitat degradation (Mayaux et al., 2004; Duveiller et al., 2008), which make them highly susceptible to droughts resulting from the expected climatic changes.

The tropical genus Erythrophleum includes two large sister tree species geographically widespread in the tropical African rainforest and characterized by their high economic and socio-cultural value: E. suaveolens and E. ivorense (Fabaceae–Caesalpinioideae). Although they are morphologically very similar to each other, these species display a parapatric distribution and grow in different climatic environments, representing a wide range of biotic and abiotic conditions that may be associated with adaptive natural genetic variation (Duminil et al., 2010). Erythrophleum ivorense is restricted to the wet and evergreen Guineo-Congolian forests (>2000 mm rainfall) bordering the gulf of Guinea, from Guinea to Gabon. In contrast, E. suaveolens has a wide geographical distribution extending from Senegal east to Sudan and Kenya, and south to Mozambique and Zimbabwe, and is adapted to the more seasonal climate of semi-deciduous Guineo-Congolian forests (>1600 mm rainfall) and the drier climate of forest–savanna mosaic landscapes (1100–1600 mm rainfall) (Vivien and Faure, 1985; Akoègninou et al., 2006; Duminil et al., 2013). The respective geographical distributions of the two species suggest that they probably respond to environmental stresses differently at the genomic level. We therefore hypothesized that these sister species may use divergent regulatory and metabolic pathways during their interaction with different abiotic constraints.

Due to their contrasting ecological features, these species are promising evolutionary models of rainforest species. Recent investigations, mainly focusing on the patterns of genetic variation and demographic changes, have pointed out a substantial spatial genetic structure in these species, associated to rainfall gradients and past climatic changes (Duminil et al., 2010; Duminil et al., 2013; Duminil et al., 2015). However, the genetic bases and molecular mechanisms underlying their response to environmental variation have not been yet investigated, while sister species adapted to contrasted environments offer the possibility to compare the expression of very similar genomes showing different adaptations. Here we assume that the wider geographical distribution of E. suaveolens, compared to E. ivorense, might be attributed to its better adaptation to severe environmental constraints, including drought.

Deciphering the underlying molecular mechanism of plant responses under drought stress remains a major challenge in biology. Drought tolerance involving the interplay of a vast array of mechanisms, its genetic control is difficult to determine without detailed genetic and sequence information (Liang et al., 2017; Tricker et al., 2018). In general, drought resistance in plants could be related to various molecular mechanisms controlled at hormonal and transcriptomic level (Yıldırım and Kaya, 2017). According to Yates et al. (2014), the typical response to drought is to reduce the water loss by closing stomata and diminishing photosynthesis. At the molecular level, plants react to drought by changing the expression profiles of a large set of genes encoding for several pathways and transcription factors (TFs) with up- as well as down-regulation (Gao et al., 2015; Jia et al., 2016). The response starts by a step of stress perception that triggers common pathways (‘plant hormone signal transduction’, ‘Calcium signaling pathway’ and ‘MAPK signaling pathway’), and many TFs (ATHB7, NAC and WRKY) involved in signal transduction. Then, a modification in expression profiles occurs in a cascade of genes involved in several pathways related to carbohydrate metabolism, oxidative phosphorilation, glycolysis, photosynthesis, transcription, nucleotide and antioxidants metabolisms in order to adjust the reduced water.

A deep transcriptomic analysis, via massively parallel cDNA sequencing technology, or RNA sequencing (RNA-seq), could provide detailed information about gene expression at the mRNA level. Nowadays, this approach is widely used for quantitative transcriptome profiling, accurate quantification of gene expression and detecting differentially expressed genes in order to unravel a diversity of stress responses at a transcriptome-wide level. RNA-seq is a cost and time-effective approach, and it has been recently used to analyze global gene expression in plant responses to various abiotic stresses such as drought (Huang et al., 2015; Fracasso et al., 2016; de Freitas Guedes et al., 2018), cold and salt for model and non-model plant species.

In the present study, using an RNA-seq approach, our major interest was to characterize the leaf transcriptomes of E. suaveolens and E. ivorense seedlings under drought stress in order to: 1) characterize the immediate gene expression response to mild short-term drought stress in the two species at the genome wide level, 2) identify the strategy employed to cope with severe drought-stress exposure and the main metabolic pathways involved, and 3) determine the differences in drought response between the two species.

Section snippets

Plant material and drought stress experiment

Seeds of E. ivorense and E. suaveolens used for the experiment were collected from mother trees originating from two different localities in Cameroon: Korup (5° 03′ 55″N; 8° 51′ 28″E) and Mindourou (3° 23′ 03″N; 14° 30′ 20″E), respectively. Collected seeds were first grown in a greenhouse at Gembloux Agro-Bio Tech, Belgium for ten months. In October 2016, seedlings were moved to a controlled glasshouse set to 25 °C for 12-h days and 22 °C for 12-h nights at the Laboratory of Plant Ecology,

Phenotypic and physiological response to drought stress

Results showed that for seedlings of both species the soil water content dropped from c. 50% in the control samples (T0) to c. 20% in the 2 weeks-stressed plants and to c. 5% at 6 weeks of treatment (Fig. 1). We noticed that first signs of wilting (slightly wilted stage) appeared at two weeks in E. suaveolens and at four weeks in E. ivorense (Fig.1). After five weeks, wilting symptoms increased rapidly, especially in E. ivorense, so that the two species displayed the same mean wilting stage at

Discussion

Water availability is a critical driver of the geographical distribution and abundance of plant species (Kunstler et al., 2016), which could explain the parapatric distribution of sister Erythrophleum species: E. ivorense is distributed in evergreen rainforests, whereas E. suaveolens is found in semi-evergreen and in gallery forests under more seasonal and/or drier climates (Duminil et al., 2013), suggesting that it might be more adapted to survive drought stress. Our RNA-Seq based comparative

Conclusion

The present study represents a first attempt in using the RNA-seq approach to unravel the genetic basis of drought stress response in E. ivorense and E. suaveolens, two sister tree species characterized by contrasting geographical distribution and ecological amplitude in the African rainforests. The high quality and comprehensiveness of the de novo assembled transcriptomes generated for both species allowed the identification of a large number of DEGs implicated in diverse signaling and

Conflict of interest

The authors have no conflicts of interest to declare.

Acknowledgements

We thank Wallonie-Bruxelles International (WBI) for the provided Postdoctoral Fellowships attributed to M.N. The genetic analyses were funded by the F.R.S. - FNRS (grants n° J.0292.17F and T.0163.13) and the Belgian Science Policy Office (Belspo, project AFRIFORD). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CÉCI), funded by the Fonds de la Recherche Scientifique de Belgique (F.R.S. - FNRS) under Grant No. 2.5020.11. We would like also to

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