The field of plant genome sequencing has grown rapidly in the past 20 years, leading to increases in the quantity and quality of publicly available genomic resources. The growing wealth of genomic ...data from an increasingly diverse set of taxa provides unprecedented potential to better understand the genome biology and evolution of land plants. Here we provide a contemporary view of land plant genomics, including analyses on assembly quality, taxonomic distribution of sequenced species and national participation. We show that assembly quality has increased dramatically in recent years, that substantial taxonomic gaps exist and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of study species. We identify numerous disconnects between the native range of focal species and the national affiliation of the researchers studying them, which we argue are rooted in colonialism-both past and present. Luckily, falling sequencing costs, widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps and empower a more global plant genomics community.
Aims and background
The resurrection plant
Myrothamnus flabellifolia
tolerates complete desiccation and is a great model for studying how plants cope with extreme drought. Root-associated microbes ...play a major role in stress tolerance and are an attractive target for enhancing drought tolerance in staple crops. However, how these dynamics play out under the most extreme water limitation remains underexplored. This study aimed to identify bacterial and fungal communities that tolerate extreme drought stress in the bulk soil, rhizosphere, and endosphere of
M. flabellifolia
.
Methods
High-throughput amplicon sequencing was used to characterise the microbial communities associated with
M. flabellifolia
.
Results
The bacterial phyla that were most abundant across all compartments were
Acidobacteriota, Actinobacteriota, Chloroflexota, Planctomycetota,
and
Pseudomonadota
, while the most abundant fungal phyla were
Ascomycota
and
Basidiomycota
. Although the bulk soil hosted multiple beneficial root-associated microbes, the rhizosphere compartment showed the highest functional diversity of bacteria and fungi. In contrast, the endosphere exhibited a low abundance and diversity of microbes. These findings share consistent with the theory that
M. flabellifolia
recruits soil microbes from the bulk to the rhizosphere and finally to the endosphere. It is possible that these microbes could promote drought tolerance in associated plant tissues.
Conclusion
We find that compartments act as the major driver of microbial diversity, but the soil physicochemical factors also influence microbial composition. These results suggest that the root-associated microbiome of
M. flabellifolia
is highly structured and may aid in plant function.
Desiccation tolerance has evolved recurrently across diverse land plant lineages as an adaptation for survival in regions where seasonal rainfall drives periodic drying of vegetative tissues. Growing ...interest in this phenomenon has fueled recent physiological, biochemical, and genomic insights into the mechanistic basis of desiccation tolerance. Although, desiccation tolerance is often viewed as binary and monolithic, substantial variation exists in the phenotype and underlying mechanisms across diverse lineages, heterogeneous populations, and throughout the development of individual plants. Most studies have focused on conserved responses in a subset desiccation‐tolerant plants under laboratory conditions. Consequently, the variability and natural diversity of desiccation‐tolerant phenotypes remains largely uncharacterized. Here, we discuss the natural variation in desiccation tolerance and argue that leveraging this diversity can improve our mechanistic understanding of desiccation tolerance. We summarize information collected from ~600 desiccation‐tolerant land plants and discuss the taxonomic distribution and physiology of desiccation responses. We point out the need to quantify natural diversity of desiccation tolerance on three scales: variation across divergent lineages, intraspecific variation across populations, and variation across tissues and life stages of an individual plant. We conclude that this variability should be accounted for in experimental designs and can be leveraged for deeper insights into the intricacies of desiccation tolerance.
Desiccation tolerance evolved recurrently across diverse plant lineages to enable survival in water limited conditions. Many resurrection plants are polyploid and several groups have hypothesized ...that polyploidy contributed to the evolution of desiccation tolerance. However, due to the vast phylogenetic distance between resurrection plant lineages, the rarity of desiccation tolerance, and the prevalence of polyploidy in plants, this hypothesis has been difficult to test. Here, we surveyed natural variation in morphological, reproductive, and desiccation tolerance traits across several cytotypes of a single species to test for links between polyploidy and increased resilience. We sampled multiple natural populations of the resurrection grass Microchloa caffra across an environmental gradient ranging from mesic to xeric in South Africa. We describe two distinct ecotypes of M. caffra that occupy different extremes of the environmental gradient and exhibit consistent differences in ploidy, morphological, reproductive, and desiccation tolerance traits in both field and common growth conditions. Interestingly, plants with more polyploid genomes exhibited consistently higher recovery from desiccation, were less reproductive, and larger than plants with smaller genomes and lower ploidy. These data suggest that selective pressures in increasingly xeric sites may play a role in maintaining and increasing desiccation tolerance that are mediated by changes in ploidy.
Summary
Tolerance to prolonged water deficit occurs along a continuum in plants, with dehydration tolerance (DhT) and desiccation tolerance (DT) representing some of the most extreme adaptations to ...water scarcity. Although DhT and DT presumably vary among individuals of a single species, this variability remains largely unstudied. Here, we characterized expression dynamics throughout a dehydration−rehydration time‐course in six diverse genotypes of the dioecious liverwort Marchantia inflexa. We identified classical signatures of stress response in M. inflexa, including major changes in transcripts related to metabolism, expression of LEA and ELIP genes, and evidence of cell wall remodeling. However, we detected very little temporal synchronization of these responses across different genotypes of M. inflexa, which may be related to genotypic variation among samples, constitutive expression of dehydration‐associated transcripts, the sequestration of mRNAs in ribonucleoprotein partials prior to drying, or the lower tolerance of M. inflexa relative to most bryophytes studied to date. Our characterization of intraspecific variation in expression dynamics suggests that differences in the timing of transcriptional adjustments contribute to variation among genotypes, and that developmental differences impact the relative tolerance of meristematic and differentiated tissues. This work highlights the complexity and variability of water stress tolerance, and underscores the need for comparative studies that seek to characterize variation in DT and DhT.
Significance Statement
We present a dehydration–rehydration transcriptome for the dehydration‐tolerant liverwort Marchantia inflexa. We detected substantial variation in gene expression among genotypes and tissues under dehydration conditions, underscoring the complexity of dehydration tolerance and highlighting the need for comparative studies that seek to explore variation in this remarkable trait.
We demonstrate a low-profile holographic imaging system at millimeter wavelengths based on an aperture composed of frequency-diverse metasurfaces. Utilizing measurements of spatially-diverse field ...patterns, diffraction-limited images of human-sized subjects are reconstructed. The system is driven by a single microwave source swept over a band of frequencies (17.5-26.5 GHz) and switched between a collection of transmit and receive metasurface panels. High fidelity image reconstruction requires a precise model for each field pattern generated by the aperture, as well as the manner in which the field scatters from objects in the scene. This constraint makes scaling of computational imaging systems inherently challenging for electrically large, coherent apertures. To meet the demanding requirements, we introduce computational methods and calibration approaches that enable rapid and accurate imaging performance.
Resurrection plants have an extraordinary ability to survive extreme water loss but still revive full metabolic activity when rehydrated. These plants are useful models to understand the complex ...biology of vegetative desiccation tolerance. Despite extensive studies of resurrection plants, many details underlying the mechanisms of desiccation tolerance remain unexplored. To summarize the progress in resurrection plant research and identify unexplored questions, we conducted a systematic review of 15 model angiosperm resurrection plants. This systematic review provides an overview of publication trends on resurrection plants, the geographical distribution of species and studies, and the methodology used. Using the Preferred Reporting Items for Systematic reviews and Meta-Analyses protocol we surveyed all publications on resurrection plants from 2000 and 2020. This yielded 185 empirical articles that matched our selection criteria. The most investigated plants were
(17.5%),
(13.7%),
(reclassified as
) (11.9%),
(8.5%), and
(8.1%), with all other species accounting for less than 8% of publications. The majority of studies have been conducted in South Africa, Bulgaria, Germany, and China, but there are contributions from across the globe. Most studies were led by researchers working within the native range of the focal species, but some international and collaborative studies were also identified. The number of annual publications fluctuated, with a large but temporary increase in 2008. Many studies have employed physiological and transcriptomic methodologies to investigate the leaves of resurrection plants, but there was a paucity of studies on roots and only one metagenomic study was recovered. Based on these findings we suggest that future research focuses on resurrection plant roots and microbiome interactions to explore microbial communities associated with these plants, and their role in vegetative desiccation tolerance.
The field of plant science has grown dramatically in the past two decades, but global disparities and systemic inequalities persist. Here, we analyzed ~300,000 papers published over the past two ...decades to quantify disparities across nations, genders, and taxonomy in the plant science literature. Our analyses reveal striking geographical biases-affluent nations dominate the publishing landscape and vast areas of the globe have virtually no footprint in the literature. Authors in Northern America are cited nearly twice as many times as authors based in Sub-Saharan Africa and Latin America, despite publishing in journals with similar impact factors. Gender imbalances are similarly stark and show remarkably little improvement over time. Some of the most affluent nations have extremely male biased publication records, despite supposed improvements in gender equality. In addition, we find that most studies focus on economically important crop and model species, and a wealth of biodiversity is underrepresented in the literature. Taken together, our analyses reveal a problematic system of publication, with persistent imbalances that poorly capture the global wealth of scientific knowledge and biological diversity. We conclude by highlighting disparities that can be addressed immediately and offer suggestions for long-term solutions to improve equity in the plant sciences.
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