A comparative genomics examination of desiccation tolerance and sensitivity in two sister grass species - pnas.org
Significance
This is a significant sister group contrast comparative study of the underpinning genomics and evolution of desiccation tolerance (DT), a critical trait in the evolution of land plants. Our results revealed that the DT grass Sporobolus stapfianus is transcriptionally primed to tolerate a dehydration/desiccation event and that the desiccation response in the DT S. stapfianus is distinct from the water stress response of the desiccation-sensitive Sporobolus pyramidalis. Our results also show that the desiccation response is largely unique, indicating a recent evolution of this trait within the angiosperms, and that inhibition of senescence during dehydration is likely critical in rendering a plant desiccation tolerant.
Abstract
Desiccation tolerance is an ancient and complex trait that spans all major lineages of life on earth. Although important in the evolution of land plants, the mechanisms that underlay this complex trait are poorly understood, especially for vegetative desiccation tolerance (VDT). The lack of suitable closely related plant models that offer a direct contrast between desiccation tolerance and sensitivity has hampered progress. We have assembled high-quality genomes for two closely related grasses, the desiccation-tolerant Sporobolus stapfianus and the desiccation-sensitive Sporobolus pyramidalis. Both species are complex polyploids; S. stapfianus is primarily tetraploid, and S. pyramidalis is primarily hexaploid. S. pyramidalis undergoes a major transcriptome remodeling event during initial exposure to dehydration, while S. stapfianus has a muted early response, with peak remodeling during the transition between 1.5 and 1.0 grams of water (gH2O) g−1 dry weight (dw). Functionally, the dehydration transcriptome of S. stapfianus is unrelated to that for S. pyramidalis. A comparative analysis of the transcriptomes of the hydrated controls for each species indicated that S. stapfianus is transcriptionally primed for desiccation. Cross-species comparative analyses indicated that VDT likely evolved from reprogramming of desiccation tolerance mechanisms that evolved in seeds and that the tolerance mechanism of S. stapfianus represents a recent evolution for VDT within the Chloridoideae. Orthogroup analyses of the significantly differentially abundant transcripts reconfirmed our present understanding of the response to dehydration, including the lack of an induction of senescence in resurrection angiosperms. The data also suggest that failure to maintain protein structure during dehydration is likely critical in rendering a plant desiccation sensitive.
Desiccation tolerance (DT) is a fundamental trait that is widespread and developed early in the evolution of the land plants (1, 2), and it is believed to have been critical in the colonization of the land by green algae (3). In tracheophytes, DT is generally limited to reproductive propagules, such as seeds and spores, while vegetative desiccation tolerance (VDT) occurs in only 0.086% of known vascular plant species (4). Our understanding of VDT (and its relationship to seed DT) has broadened with the recent expansion of whole-genome sequencing of resurrection plants, tracheophytes that can survive the desiccation of their vegetative tissues. Since the release of the Boea hygrometrica genome sequence (5), the genomes of four other resurrection angiosperms [Xerophyta schlecteri (6), Oropetium thomaeum (7, 8), Lindernia brevidens (9), and Eragrostis nindensis (10)], two lycophytes [Selaginella tamariscina (11) and Selaginella lepidophylla (12)], and the bryophyte Syntrichia caninervis (13) have been published. Apart from the obvious benefits of obtaining genomic resources for individual resurrection species, the establishment of a collection of resurrection plant genomes offered the possibility of the reconstruction of an ancestral genome of a desiccation-tolerant progenitor that would reveal a genomic signature (blueprint) that defines a common mechanism for DT. However, a genomic blueprint for DT has not emerged (4), which may be related to the small number of genomes available and limited phylogenetic sampling, that all tracheophytes possess desiccation-tolerant propagules (seeds or spores), which would obfuscate the comparative analyses, or that the origin of DT lies deep in the land plant phylogeny and is thus cryptic in the recent plant lineages. It may also be a combination of these possibilities or that there is no genomic blueprint for this fundamental trait. Although a genomic blueprint for DT has not been revealed, comparative studies have demonstrated that certain gene families, such as those for early light-inducible proteins (ELIPs) and late embryogenesis-abundant proteins, have expanded in species that exhibit VDT (6, 14, 15).
A corollary to the ancestral reconstruction approach to understanding the evolution of VDT and the genomic aspect of its phenotypic expression is the comparison of the genomes of closely related species that contrast the two extremes: sensitivity and tolerance. Such closely related contrasting species pairings are rare in resurrection plants, but this approach has been applied, albeit with species pairs that are not as close as would be ideal. The genomes and dehydration–rehydration transcriptomes of two resurrection eudicots within the Linderniaceae family (16), the desiccation-tolerant L. brevidens and the desiccation-sensitive (DS) Lindernia subracemosa, were sequenced and compared (9). The comparison revealed that at least in the Lindernia lineage, VDT evolved via a combination of gene duplications in gene families that are functionally associated with the desiccation response and a network-level rewiring of gene expression in vegetative tissue commonly associated with seed desiccation. More recently, a comparative analysis of two contrasting grass genomes along with their respective desiccation-related transcriptomes, the desiccation-tolerant E. nindensis and the related DS cereal Eragrostis tef, reinforced the potential role of gene duplications in the evolution of DT (10). Although there is still a significant phylogenetic distance between these two Eragrostis species (17), the comparative analysis and its extension to include other C4 grasses, including the desiccation-tolerant O. thomaeum, revealed chromatin restructuring and methylation patterns associated with down-regulated genes and specific seed-related orthologs whose expression is associated with VDT. The comparative transcriptome analyses indicated that genes having important roles in seed development and DT are broadly expressed under dehydration in both sensitive and tolerant species, with just a few genes uniquely expressed in the tolerant plants.
In this study, we have chosen two phylogenetically closely related C4 grasses, the homoiochlorophyllous desiccation-tolerant Sporobolus stapfianus and the DS Sporobolus pyramidalis, to develop detailed comparative genomic and transcriptomic analyses to further explore genomic inferences into the evolution of VDT. S. stapfianus and S. pyramidalis are members of the same clade, clade A, in the Sporobolus family of the Sporobolinae subtribe of the Chloridoid grasses (18). S. stapfianus has been the subject of many mechanistic studies of its DT phenotype (19, 20) and along with S. pyramidalis, the subject of a detailed comparative leaf metabolomics study that highlighted differences in the metabolic responses of the two species to dehydration (21). We constructed Hi-C–derived assemblies of the sequenced genomes for both species and conducted transcript profiling analyses for parallel reductions in water contents for both species as well as a full desiccation drying series for S. stapfianus. We performed a detailed comparative genomic analysis for the two species and extended the analysis to include other grass species, both desiccation tolerant and DS. Our results offer insights into the mechanism and evolution of VDT in the Chloridoid grasses.
Results
Generating Genomic Resources for Sporobolus Grasses.
One-step flow cytometric assays generated size estimates for each of the Sporobolus genomes. The haploid genome of S. stapfianus had an average of 1,385 pg of DNA per nucleus, which is approximately equal to a complete genome sequence of 1.354 Gbp, and the haploid genome of S. pyramidalis had an average of 1,867 pg of DNA per nucleus, which is ∼1.826 Gbp (Table 1). Draft genome assemblies were generated for each grass using Illumina whole-genome shotgun sequencing combined with Chicago and Hi-C proximity ligation (Materials and Methods). The final assemblies consisted of 11,574 scaffolds with an N50 of 19.4 Mb for S. stapfianus and 2,518 scaffolds with an N50 of 21.6 Mb for S. pyramidalis, with the longest scaffolds for both species greater than 60 Mbp. Despite their high contiguity, the assembled genomes are smaller than the estimated genome size, at 1.080 and 1.055 Gbp for S. stapfianus and S. pyramidalis, respectively. These differences between the estimated and assembled genome sizes are likely caused by collapsed homologous regions in these complex polyploid species as described in detail below. Both genomes have similar levels of repetitive elements, 39.7 and 41.3% for S. stapfianus and S. pyramidalis, respectively (Table 2), with almost identical distributions of known repeat families (SI Appendix, Table S1). Gypsy and Copia retrotransposons are the most predominant families of the known repeats at 36 and 10 to 12%, respectively, for the two genomes.
The Sporobolus genomes were annotated using MAKER with a combination of RNASeq and PacBio Iso-Seq full-length transcripts as expressed sequence tag (EST) evidence and protein homology from other high-quality plant genomes. After filtering, the final annotations contained 52,208 and 51,207 gene models for S. stapfianus and S. pyramidalis, respectively (Table 2). Annotation completeness was assessed using Benchmarking Universal Single-Copy Orthologs (BUSCO) with the poales_odb10.2019–11-20 database of 4,896 conserved genes. The genome annotations recovered 93.5 and 92.4% of complete BUSCOs for S. stapfianus and S. pyramidalis, respectively, indicating that both genomes were well annotated and contained the vast majority of the coding portion of these two genomes (Table 3). Gene models were functionally annotated using a simplified maize–GAMER pipeline; 96% of genes were annotated with InterProScan domain/family information, and 66% were annotated with Gene Ontology (GO) descriptions for both genomes.
Comparative Genomics of Chloridoid Grasses.
Sporobolus belongs to the Chloridoideae subfamily of grasses, a large and diverse group of predominantly C4 species with remarkable drought, heat, and salinity tolerance. The orphan grain crops finger millet and teff are found within Chloridoideae, as are several model desiccation-tolerant plants in the genera Oropetium, Eragrostis, Tripogon, and Sporobolus among others. Most of the surveyed Chloridoideae species (∼90%) are polyploid, including species from many of the aforementioned taxa. The availability of several high-quality chloridoid genomes facilitates detailed comparative genomic comparisons within these grasses. Macrosynteny between S. stapfianus and S. pyramidalis shows a clear 2:3 pattern, consistent with the tetraploid and hexaploid nature of these grasses, respectively (Fig. 1 and SI Appendix, Fig. S1). Comparisons with the closely related diploid chloridoid grass O. thomaeum also revealed 1:2 and 1:3 patterns of synteny for S. stapfianus and S. pyramidalis, respectively, supporting their polyploidy (Fig. 1 and SI Appendix, Fig. S2). Although neither Sporobolus genome is scaffolded into complete chromosomes, large 20-Mb+-sized scaffolds are highly collinear with the Oropetium genome with few structural large-scale rearrangements (SI Appendix, Fig. S2), which is consistent with the unusually high conservation of karyotype and collinearity observed among other chloridoid grass genomes (22).
Macrosyntenic analysis between the Sporobolus species and O. thomaeum exposed an overall more complex polyploid structure than the more straightforward tetraploid and hexaploid compositions (SI Appendix, Fig. S2). Roughly half the hexaploid S. pyramidalis genome has the expected 3:1 pattern of syntenic blocks compared with O. thomaeum, while 37% is only 2:1. The pattern is similar for tetraploid S. stapfianus, where ∼44% of syntenic blocks are 2:1 to O. thomaeum as expected and ∼42% of blocks are 1:1 (SI Appendix, Fig. S2). Similar assembly issues were observed in the tetraploid chloridoid grass E. nindensis, where one to four regions were assembled for each syntenic region in O. thomaeum (10). These discrepancies, combined with differences between the estimated and assembled genome sizes, suggest the Sporobolus genomes were partially collapsed during assembly in homologous regions. S. pyramidalis and S. stapfianus may be segmental allopolyploids with varying degrees of homology between chromosomes from separate subgenomes. Partial collapse during assembly would result in divergent homologous regions assembling separately and highly similar regions collapsing, which is supported by the observation that the ratio of assembled syntenic blocks is maintained across large syntenic blocks and whole chromosomes in O. thomaeum. For instance, two homologous regions are assembled in S. pyramidalis for chromosomes 3 and 4 from O. thomaeum, while three regions in S. pyramidalis were identified for most of chromosome 2 in O. thomaeum. Similar patterns were observed between S. stapfianus and O. thomaeum. To account for these issues related to polyploidy, syntenic gene pairs and orthogroups were used for downstream comparative genomics and transcriptomics analyses between the Sporobolus genomes and other chloridoid grasses.
Transcriptional Landscape of Desiccation in S. pyramidalis and S. stapfianus.
We generated RNASeq data from RNA isolated from leaf tissues at different stages of dehydration for both species (SI Appendix, Fig. S3). Differentially expressed genes were identified using edgeR (23), and the resulting gene lists were assigned to GO biological process categories enrichment using the Cytoscape (23) plugin Bingo (24). These analyses indicate that S. pyramidalis and S. stapfianus transcriptomes respond differently to dehydration and share few biological process adaptations during the drying process. When water content decreases from 3 to 2 grams of water (gH2O) g−1 dry weight (dw), S. pyramidalis exhibits a strong response with 11,978 statistically differentially abundant transcripts (SDATs), in contrast to the more moderate response of 1,776 SDATs in S. stapfianus (Fig. 2 A and B). A GO enrichment analysis of SDAT lists further demonstrates that during the 3 to 2 gH2O g−1 dw water content transition, few biological processes are shared between the two species (Fig. 2 C and D and SI Appendix, Fig. S4). Some biological process categories, including response to heat and response to reactive oxygen species, are common to both species (SI Appendix, Fig. S4). Moreover, while S. pyramidalis responds to the change in water content from 3 to 2 gH2O g−1 dw by modulating processes involving the ribosome and the cell wall, S. stapfianus initiates alterations in the abundance of transcripts that relate to the response to oxidative stress, response to water deficit, and protein refolding (SI Appendix, Fig. S4).
As dehydration advances from 2 to 1.5 gH2O g−1 dw in S. pyramidalis, the functional categories of SDATs remain relatively unchanged from that activated at the initial loss of water, and as it is undergoing senescence during the 1.5 to 1 gH2O g−1 dw transition, further acclimation appears unlikely. By contrast, S. stapfianus exhibits an increase to 3,730 SDATs during the 2 to 1.5 gH2O g−1 dw transition, but starting at the 1.5 to 1 gH2O g−1 dw transition, it initiates a major remodeling of its transcriptome (SI Appendix, Fig. S3), as indicated by a significant increase to 14,557 and 16,047 SDATs during these two transitions in water content, respectively (Fig. 2D). Global transcriptional remodeling continues during the 0.75 to 0.5 gH2O g−1 dw transition, albeit at a lower degree, with 8,146 SDATs (Fig. 2D). When desiccated S. stapfianus plants are rehydrated, another strong transcriptome reprogramming, with 27,280 SDATs 12 h after rehydration, is evident and shifts to a transcriptome functional expression profile more similar to that of the fully hydrated control (SI Appendix, Fig. S3). Although S. stapfianus appeared morphologically fully recovered after 24 h of rehydration, the transcriptional profile is not equivalent to that observed in leaves of plants with a water content of 3 gH2O g−1 dw (SI Appendix, Fig. S3), with 24,659 SDATs between the two conditions (Fig. 2B). Leaves from plants 24 h after rehydration have up-regulated SDATs classified in ribosome biogenesis GO categories and down-regulated SDATs in photosynthesis categories, as well as remnants of stress-responsive adaptations, including the response to water categories, and altered metabolism, suggested by the presence of glucose 6-phosphate, fructose 1,6-bisphosphate, and several other metabolism-related categories (SI Appendix, Fig. S4B).
Syntenic Ortholog Transcripts Comparison of the Hydrated State in S. pyramidalis and S. stapfianus.
To directly compare the transcriptomes for S. stapfianus and S. pyramidalis and identify differentially regulated transcripts that relate to the differences between the two species in the hydrated state prior to dehydration, we created a custom list of syntenic ortholog "genes" (Materials and Methods). Differential expression was accomplished using a contrast S. stapfianus vs. S. pyramidalis in edgeR (23), and the resultant syntenic ortholog gene lists were probed with GO enrichment as described previously for the intraspecies dehydration transcriptome analyses. The analyses demonstrate that S. stapfianus and S. pyramidalis have very different transcriptional landscapes under hydrated conditions that reflect functionally different priorities for each species. The S. stapfianus transcriptome significantly favors nitrogen, starch, and photosynthetic metabolic processes, whereas the S. pyramidalis transcriptome significantly favors processes involved in growth, primarily the biogenesis of cell wall components (SI Appendix, Fig. S5A). These differences are also reflected at the cellular component and molecular levels (SI Appendix, Fig. S5 B and C), with the majority of cellular functions related to the chloroplast and photosystems in S. stapfianus and the symplast, cytoskeleton, cell wall, and cell wall modification activities in S. pyramidalis.
Syntenic Ortholog Protein Comparisons of Desiccation Response in S. pyramidalis and S. stapfianus.
To further compare the response of S. pyramidalis and S. stapfianus to dehydration, we performed a proteomic analysis using young leaves at 3 and 1.5 gH2O g−1 dw and focused on proteins encoded by syntenic genes in a comparison of enriched GO biological process categories of accumulating and decreasing proteins in both water content conditions (SI Appendix, Fig. S6). At 1.5 gH2O g−1 dw, S. pyramidalis had increased accumulation of proteins that are almost exclusively involved in stress responses; S. stapfianus had increased accumulation of stress response proteins but also, accumulated proteins involved in the response to misfolded proteins and protein catabolism (SI Appendix, Fig. S6A), and it decreased the abundance of proteins involved in energy production (SI Appendix, Fig. S6B). The protein data demonstrate that, as observed for the transcriptomic profiles, S. pyramidalis and S. stapfianus follow predominantly different approaches of protein accumulation in their response to dehydration.
Expression Dynamics of DS and Desiccation-Tolerant Grasses.
To explore the evolution of VDT in the Chloridoideae subfamily of grasses, we made use of several high-quality genomes with similar dehydration expression datasets that were available for this group of grasses: the desiccation tolerant (S. stapfianus, O. thomaeum, and E. nindensis) and the DS (E. tef and S. pyramidalis). To facilitate comparisons between species with different ploidy, we clustered genes into syntenic orthologs using MCScan (25) and orthologous groups (orthogroups) using OrthoFinder (26) and compared expression patterns between genes in the same orthogroups. We identified 49,418 orthogroups from OrthoFinder containing 806,075 genes across 23 diverse land plant genomes and focused the subsequent analyses on orthogroups, orthologs, or syntenic gene pairs present in the genome of all chloridoid grasses.
We first surveyed the global expression profiles of the five Chloridoid grasses under well-watered, drought/desiccation, and rehydration conditions using transformed expression data of 19,267 shared syntenic orthologs across all species. We applied a dimensionality reduction on the resulting expression matrix through principal component analysis. The first two principal components collectively explain 62% of the variance and separate the expression datasets by species and stress (Fig. 3). Well-watered RNASeq samples are found in a single tight cluster of all five species, while desiccation and rehydration samples are found in dispersed but distinct clusters. Samples from dehydration and rehydration time courses in the DT species fall into two clusters, with E. nindensis and O. thomaeum samples intertwined in one cluster and S. stapfianus in the second. The dehydration samples from the two DS species (E. tef and S. pyramidalis) clustered together in a third distinct cluster. Samples of E. nindensis and O. thomaeum are separated by relative water content in principal component (PC)1 and by dehydration vs. rehydration in PC2, but interestingly, they are not delineated by species. Together, these results indicate that expression patterns are broadly conserved in leaf samples of all species but that dehydration and rehydration samples are distinct between the three lineages of DT species and their DS relatives.
The same leaf RNASeq data were analyzed in a pairwise fashion to identify genes with significantly increased transcript abundance under dehydrating conditions in all five species. These SDATs were clustered based on orthogroup using OrthoFinder (as described above) and compared between species. Orthogroups were used in this set of analyses as they contained more genes than the synteny-based analyses, and orthogroups have better resolution of recently duplicated genes. Across the five sequenced chloridoid grasses, the largest number of up-regulated orthogroups under dehydrating conditions was observed between the two Sporobolus species (Fig. 4), as expected since they are sister taxa. The second largest number of up-regulated orthogroups was shared between the two Sporobolus species and O. thomaeum (Fig. 4), which is consistent with their phylogenetic placement within the Chloridoideae. Many other orthogroups are up-regulated similarly in all five species (Fig. 4). The orthogroups uniquely up-regulated in all VDT species are enriched in 214 biological process GO terms (SI Appendix, Fig. S7). Highly enriched GO terms include ultraviolet UV light response, chlorophyll catabolism, reactive oxygen species (ROS) metabolism, seed dormancy maintenance by abscisic acid (ABA), and gene expression in response to heat stress, among others (SI Appendix, Fig. S7A), These GO terms are consistent with well-characterized processes related to DT. Other GO terms with a lower magnitude of enrichment include those related to lipids, osmoprotectant biosynthesis, high light response, energy metabolism, protein degradation, and ABA signaling (SI Appendix, Fig. S7 B and C). Seventy-one biological process GO terms were uniquely up-regulated in only the DS species (SI Appendix, Fig. S8). These included several terms related to salicylic acid as well as ethylene and ABA signaling, arabinose biosynthesis, cell wall biogenesis, and notably, leaf senescence, among others (SI Appendix, Fig. S4). We then asked whether any of the GO terms uniquely up-regulated in DT species would overlap with those uniquely down-regulated in DS species and vice versa (SI Appendix, Table S3). The GO term "protein folding" was uniquely up-regulated in DT and down-regulated in DS species. Across these five species, most seed-related orthogroups are up-regulated similarly (SI Appendix, Fig. S9). There are no seed orthogroups that are up-regulated in all three DT species without also being up-regulated in one or more DS species.
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