Parasitic angiosperms: How often and how many?

Taxon, Journal Year: 2020, Volume and Issue: 69(1), P. 5 - 27

Published: Feb. 1, 2020

Abstract Angiosperms that morphologically and physiologically attach to other flowering plants by means of a haustorium have evolved 12 times independently resulting in 292 genera ca. 4750 species. Although hemiparasites predominate, holoparasitism has all but two clades, Cassytha (Lauraceae) Krameria (Krameriaceae). Santalales contains the largest number (179) species (2428) among parasitic plant lineages whereas Orobanchaceae is single family with 102 over 2100 This review presents current state knowledge on molecular phylogenetic relationships clades angiosperms. These methods been particularly important revealing closest non‐parasitic relatives holoparasites, exhibit reduced morphologies, increased substitution rates, frequent horizontal gene transfers, which confound phylogenetics. comprehensive phylogenies are still lacking for many large genera, nearly complete generic level sampling exists, thus allowing unprecedented understanding evolutionary within these fascinating plants.

Language: Английский

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Plastid phylogenomic insights into relationships of all flowering plant families

BMC Biology, Journal Year: 2021, Volume and Issue: 19(1)

Published: Oct. 28, 2021

Abstract Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding their evolution early diversification. The plastome, typically mapped as a circular genome, has been most important molecular data source for plant phylogeny reconstruction decades. Results Here, we assembled by far largest plastid dataset angiosperms, composed 80 genes from 4792 plastomes 4660 species in 2024 genera representing all currently recognized families. Our tree (PPA II) is essentially congruent with those previous phylogenomic analyses generally provides greater clade support. In PPA II tree, 75% nodes or ordinal 78% were resolved high bootstrap support (BP ≥ 90). We obtained strong many interordinal interfamilial that poorly previously within core eudicots, such Dilleniales, Saxifragales, Vitales being successive sisters to remaining rosids, Santalales, Berberidopsidales, Caryophyllales asterids. However, placement magnoliids, although sister other Mesangiospermae , not well supported disagrees topologies inferred nuclear data. Relationships among five major clades intractable despite increased sampling, probably due an ancient rapid radiation. Conclusions provide comprehensive date well-resolved which together foundation future evolutionary studies flowering plants.

Language: Английский

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Asterid Phylogenomics/Phylotranscriptomics Uncover Morphological Evolutionary Histories and Support Phylogenetic Placement for Numerous Whole-Genome Duplications

Molecular Biology and Evolution, Journal Year: 2020, Volume and Issue: 37(11), P. 3188 - 3210

Published: June 26, 2020

Abstract Asterids are one of the most successful angiosperm lineages, exhibiting extensive morphological diversity and including a number important crops. Despite their biological prominence value to humans, deep asterid phylogeny has not been fully resolved, evolutionary landscape underlying radiation remains unknown. To resolve phylogeny, we sequenced 213 transcriptomes/genomes combined them with other data sets, representing all accepted orders nearly families asterids. We show supported monophyly asterids, Berberidopsidales as sister except Icacinales, Aquifoliales, Bruniales, Icacinaceae Ehretiaceae. Novel taxon placements benefited from expanded sampling living collections botanical gardens, resolving hitherto uncertain relationships. The remaining ambiguous here likely due limited could be addressed in future relevant additional taxa. Using our well-resolved reference, divergence time estimates support an Aptian (Early Cretaceous) origin asterids before Cretaceous–Paleogene boundary. Ancestral state reconstruction at family level suggests that ancestor was woody terrestrial plant simple leaves, bisexual, actinomorphic flowers free petals anthers, superior ovary style, drupaceous fruits. Whole-genome duplication (WGD) analyses provide strong evidence for 33 WGDs Berberidopsidales, four suprafamilial seven familial/subfamilial WGDs. Our results advance understanding numerous novel insights into diversification evolution.

Language: Английский

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Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

American Journal of Botany, Journal Year: 2020, Volume and Issue: 107(5), P. 790 - 805

Published: May 1, 2020

Premise Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well‐documented phenomenon at shallow evolutionary levels but has been poorly investigated deep of plant phylogeny. Determining the extent cytonuclear discordance across major lineages essential not only for elucidating processes, also evaluating currently used framework phylogeny, which largely based on plastid genome. Methods We present phylogenomic examination angiosperm clade ( Asteridae ) sequence data from nuclear, plastid, mitochondrial genomes as means accepted relationships inferred plastome exploring potential sources genomic conflict in this group. Results recovered least five instances well‐supported concerning placements asterid (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis , Icacinaceae). attribute to combination incomplete lineage sorting hybridization, latter supported part by previously whole‐genome duplications. Conclusions Our results challenge several long‐standing hypotheses have implications morphological character evolution importance ancient duplications early evolution. These findings highlight value reevaluating broad‐scale green‐plant phylogeny with data.

Language: Английский

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A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification

Journal of Systematics and Evolution, Journal Year: 2019, Volume and Issue: 57(6), P. 695 - 718

Published: Nov. 1, 2019

Abstract The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion our knowledge phylogenetic history and many molecular studies focusing on biogeography particular groups during last few decades, global analysis diversification is still lacking. For this purpose, we built hitherto most comprehensive Carex‐ dated phylogeny based three markers (ETS–ITS– matK ), using previous phylogenomic Hyb‐Seq framework, sampling two‐thirds its all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, rate analyses were conducted to elucidate macroevolutionary patterns. Our results reveal that originated late Eocene E Asia, where it probably remained until synchronous main subgeneric lineages Oligocene. Asia supported as cradle diversification, well “museum” extant diversity. Subsequent “out‐of‐Asia” colonization patterns feature multiple asymmetric dispersals clustered toward present times among Hemisphere regions, major regions acting both source sink (especially North America), several independent events Southern We detected 13 notable shifts 10 My, including remarkable radiations America New Zealand, which occurred concurrently Neogene cooling, suggests involved new into novel niche space.

Language: Английский

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Darwin review: angiosperm phylogeny and evolutionary radiations

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2019, Volume and Issue: 286(1899), P. 20190099 - 20190099

Published: March 27, 2019

Darwin's dual interests in evolution and plants formed the basis of evolutionary botany, a field that developed following his publications on both topics. Here, we review many contributions to plant biology—from origins angiosperms reproduction, carnivory, movement—and note he expected one day there would be ‘true’ genealogical tree for plants. This view fuelled phylogenetics. With perhaps nearly 400 000 species, have diversified rapidly since their origin Early Cretaceous, often through what appear rapid radiations. We describe these patterns, evaluate possible drivers radiations, consider how new approaches studies diversification can contribute our understanding angiosperm diversity, suggest directions further insight into evolution.

Language: Английский

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Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant GenusPolemonium(Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

Systematic Biology, Journal Year: 2020, Volume and Issue: 70(1), P. 162 - 180

Published: June 24, 2020

Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose challenges inferring evolutionary histories. Most existing methods reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as cause intra- or intergenomic discordance. Here, we utilize variety methods, including those to infer networks, account both ILS and introgression nuclear cytoplasmic-nuclear discordance using phylogenomic the flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse Western North America with known suspected gene flow between species. We find widespread among loci can be explained by reticulate evolution history Polemonium. Furthermore, histories organellar genomes show strong inferred species tree genome. Discordance plastid genome is not completely ILS, one case detected events. Our results suggest multiple processes have been involved does accurately reflect relationships. discuss several potential causes this discordance, which emerging suggests more across Tree Life than previously thought. [Cyto-nuclear genomic capture, Polemoniaceae, Polemonium, reticulations.].

Language: Английский

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Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(2)

Published: Feb. 1, 2022

Abstract Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite importance supergenes in adaptation, little is known on how they originate. A classic example supergene S locus controlling heterostyly, a floral heteromorphism occurring 28 angiosperm families. In Primula, heterostyly characterized by cooccurrence two complementary, self-incompatible morphs and controlled five genes clustered hemizygous, ca. 300-kb locus. Here, we present first chromosome-scale genome assembly any heterostylous species, that Primula veris (cowslip). By leveraging high contiguity P. comparative analyses, demonstrated S-locus evolved via asynchronous gene duplications independent translocations. Furthermore, discovered new whole-genome duplication Ericales specific to lineage. We also propose mechanism for origin hemizygosity nonhomologous recombination involving newly pairs CFB flanking Finally, detected only weak signatures degeneration locus, as predicted hemizygous supergenes. The study provides useful resource future research addressing key questions evolution general particular: How do arise? What role architecture complex adaptations? Is molecular across angiosperms similar Primula?

Language: Английский

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The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)

Genome Biology and Evolution, Journal Year: 2019, Volume and Issue: 11(12), P. 3353 - 3371

Published: Nov. 7, 2019

Abstract The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed of >1,000 species. Here, we report the chromosome-scale de novo assembly genome annotation williamsianum basis for continued study this large genus. We created multiple short fragment genomic libraries, were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) fragScaff scaffolding library, improved decreasing number scaffolds increasing scaffold length. Chromosome-scale performed proximity-guided (LACHESIS) chromatin conformation capture (Hi-C) data. further refined linkage groups defined restriction-site associated DNA (RAD) parents progeny genetic cross. resulting map confirmed LACHESIS clustering ordering onto chromosomes rectified large-scale inversions. Assessments R. gene estimate them to be 89% 79% complete, respectively. Predicted coding sequences from used in syntenic analyses generating age distributions synonymous substitutions/site between paralgous pairs, identified whole-genome duplications (WGDs) williamsianum. then analyzed other publicly available Ericaceae genomes shared WGDs. Based on our spatial temporal paralogous find evidence two shared, ancient WGDs Vaccinium (cranberry/blueberry) members that predate family and, one case, Ericales order.

Language: Английский

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Angiosperms at the edge: Extremity, diversity, and phylogeny

Plant Cell & Environment, Journal Year: 2020, Volume and Issue: 43(12), P. 2871 - 2893

Published: Sept. 21, 2020

Abstract A hallmark of flowering plants is their ability to invade some the most extreme and dynamic habitats, including cold dry biomes, a far greater extent than other land plants. Recent work has provided insight phylogenetic distribution evolutionary mechanisms which have enabled this success, yet needed synthesis perspectives with plant physiological traits, morphology, genomic diversity. Linking these disparate components will not only lead better understand parallelism diversification two strategies, but also provide framework for directing future research. We summarize primary structural traits involved in response cold‐ drought stress, outline adaptations, describe recurring association changes rapid events that occurred multiple lineages over past 15 million years. Across threefold facets dry‐cold correlation (traits, phylogeny, time) we stress contrast between (a) amazing diversity solutions developed face environments (b) broad adaptations cases may hint at deep common origins.

Language: Английский

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