An official website of the United States government
ABSTRACT Yellow monkeyflowers (Mimulus guttatuscomplex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan‐genomics in this group, we present four chromosome‐scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a singleM. guttatuspopulation, one from the closely related selfing speciesM. nasutus, and one from a more divergent speciesM. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat‐rich, gene‐poor regions that large portions of the genome are unalignable across accessions. As a result, thisMimuluspan‐genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence–absence, investigate the recombination landscape using high‐resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high—even in regions of very low recombination—reaching ~3.2% within a singleM. guttatuspopulation, ~7% within the interfertileM. guttatusspecies complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolatedM. tilingii. Genome‐wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high‐recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation forMimulusresearch and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.
more »
« less
Transcriptome analyses of leaf architecture in Sansevieria support a common genetic toolkit in the parallel evolution of unifacial leaves in monocots
Abstract Planar structures dramatically increase the surface‐area‐to‐volume ratio, which is critically important for multicellular organisms. In this study, we utilize naturally occurring phenotypic variation among threeSansivieriaspecies (Asperagaceae) to investigate leaf margin expression patterns that are associated with mediolateral and adaxial/abaxial development. We identified differentially expressed genes (DEGs) between center and margin leaf tissues in two planar‐leaf speciesSansevieria subspicataandSansevieria trifasciataand compared these with expression patterns within the cylindrically leavedSansevieria cylindrica. TwoYABBYfamily genes, homologs ofFILAMENTOUS FLOWERandDROOPING LEAF, are overexpressed in the center leaf tissue in the planar‐leaf species and in the tissue of the cylindrical leaves. As mesophyll structure does not indicate adaxial versus abaxial differentiation, increased leaf thickness results in more water‐storage tissue and enhances resistance to aridity. This suggests that the cylindrical‐leaf inS. cylindricais analogous to the central leaf tissue in the planar‐leaf species. Furthermore, the congruence of the expression patterns of theseYABBYgenes inSansevieriawith expression patterns found in other unifacial monocot species suggests that patterns of parallel evolution may be the result of similar solutions derived from a limited developmental toolbox.
more »
« less
- Award ID(s):
- 1838291
- PAR ID:
- 10575419
- Publisher / Repository:
- Wiley Publishing
- Date Published:
- Journal Name:
- Plant Direct
- Volume:
- 7
- Issue:
- 8
- ISSN:
- 2475-4455
- Page Range / eLocation ID:
- 1-13
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
ABSTRACT Sister taxa that have diverged and persisted in sympatry have likely been exposed to the same general environmental changes throughout their evolutionary history and may thus exhibit similar phylogeographies. Here, we compare the phylogeographic patterns of two sister species of isopods (genusTylos) that have broadly overlapping distributions but distinct habitat preferences in the supralittoral zone of Chile. The dynamic geoclimatic history of this region during the Quaternary has been implicated in shaping the evolutionary histories of other coastal taxa.Tylos spinulosusis found in sandy beaches at latitudes ~27°–30° S, whereasTylos chilensishas been found in rocky shores at ~27°–33° S and at ~39°–42° S. We sampled both species across their ranges (collectively from 20 localities) and obtained sequences from at least one mitochondrial gene for 95 T. chilensisand 41 T. spinulosus. We used phylogenetics and population genetics methods to analyze four single‐gene and one concatenated datasets: 12S rDNA (n = 130); 16S rDNA (n = 31); Cytochrome oxidase subunit I (n = 28); Cytochrome b (n = 24); concatenation of the four genes (n = 24). Both species show high levels of isolation of local populations, consistent with expectations from their limited autonomous dispersal potential. However, they exhibit strikingly different mitochondrial phylogeographic patterns.Tylos chilensisshows evidence of multiple relatively deep divergence events leading to geographically restricted lineages that appear to have persisted over multiple glaciations. Surprisingly, one lineage ofT. chilensiswas found in geographically distant localities, suggesting the possibility of human‐mediated dispersal.Tylos spinulosusappears to have undergone a relatively recent bottleneck followed by a population/range expansion. Differences in life histories and habitat preferences or stochasticity may have contributed to these striking phylogeographic differences. Finally, the high levels of differentiation and isolation among populations indicate that they are highly vulnerable to extirpation. We discuss threats to their persistence and recommendations for their conservation.more » « less
-
ABSTRACT Necrotrophic pathogens cause serious threats to agricultural crops, and understanding the resistance genes and their genetic networks is key to breeding new plant cultivars with better resistance traits. AlthoughAlternaria alternatacauses black spot in important leafy brassica vegetables, and leads to significant loss of yield and food quality, little is known about plant–A. alternatainteractions. In this study, we used a unique and large collection of single, double and triple mutant lines of defence metabolite regulators inArabidopsisto explore how these transcription factors and their epistatic networks may influenceA. alternatainfections. This identified nine novel regulators and 20 pairs of epistatic interactions that modulateArabidopsisplants' defence responses toA. alternatainfection. We further showed that the glucosinolate 4‐methoxy‐indol‐3‐ylmethyl is the only glucosinolate consistently responsive toA. alternatainfection in Col‐0 ecotype. With the further exploration of the regulators and the genetic networks on modulating the accumulation of glucosinolates underA. alternatainfection, an inverted triangle regulatory model was proposed forArabidopsisplants' defence responses at a metabolic level and a phenotypic level.more » « less
-
SUMMARY Eudicot plant species have leaves with two surfaces: the lower abaxial and the upper adaxial surface. Each surface varies in a diversity of components and molecular signals, resulting in potentially different degrees of resistance to pathogens. We tested howBotrytis cinerea, a necrotroph fungal pathogen, interacts with the two different leaf surfaces across 16 crop species and 20 Arabidopsis genotypes. This showed that the abaxial surface is generally more susceptible to the pathogen than the adaxial surface. In Arabidopsis, the differential lesion area between leaf surfaces was associated with jasmonic acid (JA) and salicylic acid (SA) signaling and differential induction of defense chemistry across the two surfaces. When infecting the adaxial surface, leaves mounted stronger defenses by producing more glucosinolates and camalexin defense compounds, partially explaining the differential susceptibility across surfaces. Testing a collection of 96B. cinereastrains showed the genetic heterogeneity of growth patterns, with a few strains preferring the adaxial surface while most are more virulent on the abaxial surface. Overall, we show that leaf–Botrytis interactions are complex with host‐specific, surface‐specific, and strain‐specific patterns.more » « less
-
ABSTRACT Hybridization and interspecific gene flow play a substantial role in the evolution of plant taxa. The eastern North American white oak syngameon, a group of approximately 15 ecologically, morphologically and genomically distinguishable species, has long been recognised as a model system for studying introgressive hybridization in temperate trees. However, the prevalence, genomic context and environmental correlates of introgression in this system remain largely unknown. To assess introgression in the eastern North American white oak syngameon and population structure within the widespreadQuercus macrocarpa, we conducted a rangewide survey ofQ. macrocarpaand four sympatric eastern North American white oak species. Using a Hyb‐Seq approach, we assembled a dataset of 3412 thinned single‐nucleotide polymorphisms (SNPs) in 445 enriched target loci including 62 genes putatively associated with various ecological functions, as well as associated intronic regions and some off‐target intergenic regions (not associated with the exons). Admixture analysis and hybrid class inference demonstrated species coherence despite hybridization and introgressive gene flow (due to backcrossing of F1s to one or both parents). Additionally, we recovered a genetic structure withinQ. macrocarpaassociated with latitude. Generalised linear mixed models (GLMMs) indicate that proximity to range edge predicts interspecific admixture, but rates of genetic differentiation do not appear to vary between putative functional gene classes. Our study suggests that gene flow between eastern North American white oak species may not be as rampant as previously assumed and that hybridization is most strongly predicted by proximity to a species' range margin.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.1002/pld3.511
