Multi-Omics Insights Into the Evolution of Angiosperm Resurrection Plants
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Annual Plant Reviews (2020) 3, 77–110 http://onlinelibrary.wiley.com doi: 10.1002/9781119312994.apr0730 MULTI-OMICS INSIGHTS INTO THE EVOLUTION OF ANGIOSPERM RESURRECTION PLANTS Rafe Lyall1 and Tsanko Gechev2 1Department of Bioinformatics and Mathematical Modelling, Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria 2Department of Molecular Stress Physiology, Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria Abstract: A small group of angiosperms possess vegetative desiccation tolerance (VDT). This unique ability allows them to withstand near total loss of cellular water and recover unharmed upon rehydration. Recently,omics technologies have begun to give greater insight into the mechanisms that regulate VDT. Several angiosperm resurrection plant genomes, from both monocot and eudicot lineages, have been sequenced in the past decade. Multiple transcriptomic and metabolomic analyses of desiccation and rehydration in resurrection plants have emphasised the impor- tance and ubiquity of known VDT responses, such as the induction of late embryo- genesis abundants (LEAs), sugars, and antioxidants. These studies have also con- firmed the similarity between VDT and the process of orthodox seed maturation drying, and highlighted the connection between embryonic, seedling, and vege- tative DT. However, the exact genes and pathways that regulate the acquisition of seed traits in leaves remain elusive. This article attempts to integrate what is currently understood about the evolution and regulation of VDT in angiosperm resurrection plants, drawing from the rapidly growing collection of omics datasets derived from these species. The limits of current knowledge, future research per- spectives, and the utility of VDT research as a resource for the improvement of drought tolerance in crop species are also discussed. Keywords: angiosperms, resurrection plants, seed maturation, drought, desicca- tion tolerance, abscisic acid, systems biology Annual Plant Reviews Online, Volume 3. Edited by Jeremy Roberts. © 2020 John Wiley & Sons, Ltd. Published 2020 by John Wiley & Sons, Ltd. 77 RLyall&TGechev 1 Introduction As sessile organisms, plants are unable to escape stressful conditions. Instead, they use a wide variety of molecular or behavioural mechanisms to min- imise the impact of biotic or abiotic stress. Dehydration is a stress common to nearly all land plants, and drought in particular has been and is one of the leading causes of reduced agricultural crop production and yield. The effect of drought on global agriculture is likely to worsen as global temper- atures rise while the demand for plant crops increases (Tilman et al., 2011; Sustainable Crop Production for Environmental and Human Health – The Future of Agriculture; Mittler and Blumwald, 2010). Commonly cultivated crops are not tolerant to water stress brought on by drought, something of particular relevance to small-scale or subsistence farmers that rely on rainfed irrigation (Lamaoui et al., 2018). The engineering of drought-resistant crop species through breeding or genetic engineering is one of the major goals of current crop plant research. Resurrection plants are those land plants that display vegetative desic- cation tolerance (VDT). VDT has been defined as the ability of a plant to > −1 lose nearly all cellular water ( 90%, or 0.1 g H2Og dry mass) and recover unharmed upon rehydration (Alpert, 2005). VDT is widespread in the plant kingdom, particularly in basal plants such as mosses and lichens, and is believed to have been the ancestral state of early land plants (Oliver et al., 2000; Fisher, 2008). However, VDT was progressively lost from the vegeta- tive tissues of tracheophytes, likely due to improvements in cellular water retention achieved through the evolution of the vascular system. It has been hypothesised that the ancestral VDT mechanisms were co-opted by early tracheophytes for abiotic stress response and for the protection of their repro- ductive propagules – spores, seeds, and pollen. Later, VDT re-evolved in the angiosperm lineage, giving rise to the approximately 135 known resurrection plant species – though this number may be higher (Oliver et al., 2005; Gaff and Oliver, 2013). The VDT strategy has a high metabolic cost and in angiosperms is usually associated with slow-growing plants in harsh environments where the trade-off provides an adaptive advantage against sensitive plants (Proctor and Tuba, 2002; Alpert, 2005). Nonetheless, this ability has made them an attractive model with which to study water stress, or as sources of novel secondary metabolites (Gechev et al., 2014; Hilhorst and Farrant, 2018). The rare but nonetheless widespread occurrence of resurrection plants within the angiosperm phylogeny implies that VDT has arisen indepen- dently numerous times (Figure 1). Additionally, it has been observed that many of the protective and regulatory mechanisms induced by angiosperm resurrection plants during desiccation are similar to those induced by maturing orthodox seeds. It has thus been proposed that the evolution of VDT in angiosperm resurrection plants occurred through co-option of the desiccation tolerance (DT) mechanisms already active in seeds (Illing Annual Plant Reviews Online, Volume 3. Edited by Jeremy Roberts. © 2020 John Wiley & Sons, Ltd. Published 2020 by John Wiley & Sons, Ltd. 78 Multi-Omics Insights into the Evolution of Angiosperm Resurrection Plants Figure 1 Occurrence of VDT within the angiosperm lineage. Most angiosperms are not tolerant of desiccation (shown in grey), though it is likely that this was the constitutive phenotype of the earliest land plants. Resurrection species, though individually rare, can nonetheless be found across diverse monocot and eudicot families. The inserts show growth mats of Xerophyta humilis on sandy soil, hydrated and desiccated fronds of Myrothamnus flabelliformis exhibiting leaf curling and pigment accumulation, and flowering Haberlea rhodopensis growing on a sheer rock surface. Classification of resurrection species as investigated in Porembski (2011), Tuba and Lichtenthaler (2011), and Artur et al. (2019). X. humilis and M. flabelliformis photographs by D. Wesuls (Jürgens et al., 2016). et al., 2005; Costa et al., 2017a; Giarola et al., 2017). As most angiosperms produce orthodox seeds, this would imply that the genetic capacity for VDT is common to many otherwise sensitive plants and could be leveraged for the improvement of drought tolerance in economically important crops. Annual Plant Reviews Online, Volume 3. Edited by Jeremy Roberts. © 2020 John Wiley & Sons, Ltd. Published 2020 by John Wiley & Sons, Ltd. 79 RLyall&TGechev This article will give an overview of what is currently known or predicted about the mechanisms of VDT in angiosperm resurrection plants. The focus is particularly on the relationship between VDT and embryonic DT found in orthodox seeds, as well as the use and integration of multiple omics technolo- gies to investigate the evolution and regulation of VDT. Lastly, current gaps in the knowledge of resurrection plants and possible directions for future research, particularly regarding the applicability towards drought-tolerant crops, are discussed. 1.1 Defining the Stress: Drought and Desiccation It is important to consider the differences between drought, dehydra- tion, and desiccation stress when comparing resurrection plants and desiccation-sensitive species. Both dehydration and desiccation relate to the internal water content of a plant, where the difference is largely a matter of degree of water lost. On the other hand, drought is a period of environmental water scarcity most often associated with plants grown on soil or in the field (Tardieu et al., 2018; Zhang and Bartels, 2018). Indeed, drought is most often simulated by manipulation of soil water contents in experimental systems. However, the existence of drought or even the extremity of the treatment does not necessarily reflect the internal water content or stress status of the treated plant (Bechtold, 2018; Chater et al., 2018). This is especially true when comparing species or ecotypes which may differ greatly in their degree of drought tolerance. Thus, plant adaptations to drought (low environmental water availability) are often independent of adaptations to dehydration specifically (low internal water content), despite the implicit connection between the two stresses (Blum and Tuberosa, 2018). Generally, plant adaptations to drought fall into one of three loose cate- gories: drought escape, drought avoidance/tolerance, and DT (Alpert, 2005; Kooyers, 2015). Drought escape is a behavioural strategy used by plants that cannot tolerate water loss. Instead, their growth and reproductive cycles are coordinated to occur only when there is sufficient water. Such plants bypass drought conditions at the population level by producing tolerant seeds (as in annuals), or on the individual level by dying back and re-growing from dormant storage tissues (as in perennial bulbs or shrubs). This is contrasted by drought tolerance, whereby plants remain metabolically active during periods of low water supply. Generally, this is achieved by maximising retained water – either constitutively, as observed in succulent species, or via stress-induced mechanisms that regulate stomatal closing and changes to leaves and roots that increase water uptake and reduce water loss. Nonethe- less, drought-tolerant plants will still die if their internal water contents drop below a critical level (Blum, 2010).