Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming

Journal of Systematics and Evolution, Journal Year: 2020, Volume and Issue: 58(5), P. 673 - 695

Published: April 11, 2020

Abstract With more than 300 species, the Magnoliaceae family represents a major Magnoliid lineage that is disjunctly distributed in Asia and New World. The classification of Magnolia s.l. has been highly controversial among taxonomists, varying from one genus with several subgenera, sections, subsections to (up 16) genera. We conducted comprehensive phylogenetic study on basis sequences complete chloroplast genomes broad taxon sampling 86 species. analyses strongly support 15 clades within due non‐monophyly subgen. , previous subgeneric treatment recognizes three not supported. Based phylogenetic, morphological, geographic evidence, we recognize two subfamilies Magnoliaceae: Liriodendroideae Magnolioideae, each genus, Liriodendron respectively. herein classified into sections: sects. Manglietia, Michelia Gwillimia Gynopodium Kmeria Maingola Oyama Rytidospermum Splendentes Talauma Tuliparia Macrophylla Tulipastrum Yulania .

Language: Английский

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A new classification of Cyperaceae (Poales) supported by phylogenomic data

Journal of Systematics and Evolution, Journal Year: 2021, Volume and Issue: 59(4), P. 852 - 895

Published: May 9, 2021

Abstract Cyperaceae (sedges) are the third largest monocot family and of considerable economic ecological importance. Sedges represent an ideal model to study evolutionary biology due their species richness, global distribution, large discrepancies in lineage diversity, broad range preferences, adaptations including multiple origins C 4 photosynthesis holocentric chromosomes. Goetghebeur′s seminal work on published 1998 provided most recent complete classification at tribal generic level, based a morphological inflorescence, spikelet, flower, embryo characters, plus anatomical other information. Since then, several family‐level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after last comprehensive family, we present first family‐wide phylogenomic targeted sequencing Angiosperms353 probe kit sampling 311 accessions. In addition, 62 accessions available from GenBank were mined for overlapping reads included analyses. Informed by this backbone phylogeny, new tribal, subtribal, levels is proposed. The majority previously recognized suprageneric groups supported, time, establish support tribe Cryptangieae as clade genus Koyamaea . We provide taxonomic treatment identification keys diagnoses 2 subfamilies, 24 tribes, 10 subtribes, basic information 95 genera. includes five subtribes Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, Oreobolinae.

Language: Английский

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A framework infrageneric classification ofCarex(Cyperaceae) and its organizing principles

Journal of Systematics and Evolution, Journal Year: 2020, Volume and Issue: 59(4), P. 726 - 762

Published: Dec. 28, 2020

Abstract Phylogenetic studies of Carex L. (Cyperaceae) have consistently demonstrated that most subgenera and sections are para‐ or polyphyletic. Yet, taxonomists continue to use in classification. Why? The Global Group (GCG) here takes the position historical continued serves (i) organize our understanding lineages , (ii) create an identification mechanism break ~2000 species into manageable groups stimulate its study, (iii) provide a framework recognize morphologically diagnosable within . Unfortunately, current phylogenetic relationships is not yet sufficient for global reclassification genus Linnean infrageneric (sectional) framework. Rather than leaving classification state, which misleading confusing, we take intermediate steps implementing recently revised subgeneric using combination informally named clades formally reflect state knowledge. This hybrid presented order corresponding linear arrangement on ladderized phylogeny, largely based recent phylogenies published by GCG. It organizes six subgenera, are, turn, subdivided 62 plus 49 informal groups. will serve as roadmap research enabling further development complete presenting relevant morphological geographical information where possible standardizing formal sectional names.

Language: Английский

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Carex maolanensis (Cyperaceae), a new species from Guizhou, China

Phytotaxa, Journal Year: 2021, Volume and Issue: 525(2), P. 137 - 146

Published: Nov. 15, 2021

Carex maolanensis, a new species of Cyperaceae is described and illustrated from Guizhou, China. The belongs to sect. Decorae, it similar C. jizhuangensis, but differs in having short rhizome, 3–7 spikes per node, terminal androgynous, female glumes awned. morphology perigynium achene maolanensis jizhuangensis compared. According the IUCN Red List criteria, may be turned out Endangered (EN) or Vulnerable (VU), however, for present, better classified as Data Deficient (DD) because field survey necessary. A revised identification key Decorae China provided.

Language: Английский

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A new classification ofCarex(Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree

Botanical Journal of the Linnean Society, Journal Year: 2020, Volume and Issue: 194(2), P. 141 - 163

Published: June 4, 2020

Abstract The field of systematics is experiencing a new molecular revolution driven by the increased availability high-throughput sequencing technologies. As these techniques become more affordable, genomic resources have increasingly far-reaching implications for our understanding Tree Life. With c. 2000 species, Carex (Cyperaceae) one five largest genera angiosperms and two among monocots, but phylogenetic relationships between main lineages are still poorly understood. We designed Cyperaceae-specific HybSeq bait kit using transcriptomic data siderosticta Cyperus papyrus. identified 554 low-copy nuclear orthologous loci, targeting total length 1 Mbp. Our shared loci with recently published angiosperm-specific Anchored Hybrid Enrichment kit, which enabled us to include compile from different sources. used Cyperaceae sequence 88 spp., including samples all major clades in genus. For first time, we present tree based on hundreds (308 exon matrices, 543 intron matrices 66 plastid matrices), demonstrating that there six strongly supported Carex: Siderostictae, Schoenoxiphium, Unispicate, Uncinia, Vignea Core clades. Based results, suggest revised subgeneric treatment provide lists species belonging each subgenera. results will inform future biogeographic, taxonomic, dating evolutionary studies step towards classification seems likely stand test time.

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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Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats

New Phytologist, Journal Year: 2023, Volume and Issue: 242(2), P. 727 - 743

Published: Nov. 27, 2023

Poales are one of the most species-rich, ecologically and economically important orders plants often characterise open habitats, enabled by unique suites traits. We test six hypotheses regarding evolution assembly in closed habitats throughout world, examine whether diversification patterns demonstrate parallel evolution. sampled 42% species obtained taxonomic biogeographic data from World Checklist Vascular Plants database, which was combined with open/closed habitat scored experts. A dated supertree constructed. integrated spatial phylogenetics regionalisation analyses, historical biogeography ancestral state estimations. Diversification result dynamic evolutionary processes that vary across lineages, time space, prominently tropical southern latitudes. Our results reveal recurrent trait transitions species-rich families Poaceae Cyperaceae. Smaller display divergent trajectories. The have achieved global dominance via notable, spatially phylogenetically restricted divergences into strictly habitats.

Language: Английский

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Genomic hotspots of chromosome rearrangements explain conserved synteny despite high rates of chromosome evolution in a holocentric lineage

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(24)

Published: July 24, 2023

Holocentric organisms, unlike typical monocentric have kinetochore activity distributed along almost the whole length of chromosome. Because this, chromosome rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for extraordinary rates evolution that many lineages exhibit. Long blocks genome synteny been reported animals with chromosomes despite high rearrangements. Nothing is known from plants, however, fact holocentricity appears played a key role diversification one largest angiosperm genera, Carex (Cyperaceae). In current study, we compared genomes species distantly related Cyperaceae characterize conserved rearranged regions. Our analyses span divergence times ranging between 2 50 million years. We also C. scoparia chromosome-level assembly linkage map same study at population level suppression recombination patterns. found longer than expected under null model random rearrangement breakpoints, even very species. repetitive DNA be non-randomly associated holocentromeres regions genome. The evidence sedges suggests genomic hotspots shape recombination, gene order crossability sedges. This finding help explain why able maintain cohesion face interspecific

Language: Английский

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History and evolution of the afroalpine flora: in the footsteps of Olov Hedberg

Alpine Botany, Journal Year: 2021, Volume and Issue: 132(1), P. 65 - 87

Published: July 19, 2021

Abstract The monumental work of Olov Hedberg provided deep insights into the spectacular and fragmented tropical alpine flora African sky islands. Here we review recent molecular niche modelling studies re-examine Hedberg’s hypotheses conclusions. Colonisation started when mountain uplift established harsh diurnal climate with nightly frosts, accelerated throughout last 5 Myr (Plio-Pleistocene), resulted in a rich local endemics. Recruitment was dominated by long-distance dispersals (LDDs) from seasonally cold, remote areas, mainly Eurasia. only rarely followed substantial diversification. Instead, most larger genera even species colonised afroalpine habitat multiple times independently. Conspicuous parallel evolution occurred among mountains, e.g., gigantism Lobelia Dendrosenecio dwarf shrubs Alchemilla . Although ~ 8 treeline 1000 m lower than today during Last Glacial Maximum, genetic data suggest that shaped strong intermountain isolation interrupted rare LDDs rather ecological connectivity. new evidence points to much younger more dynamic island scenario envisioned Hedberg: is unsaturated fragile, it repeatedly disrupted Pleistocene oscillations, harbours taxonomic diversity unique but severely depauperated frequent bottlenecks cycles colonisation, extinction, recolonisation. level intrapopulation variation alarmingly low, many may be vulnerable extinction because warming increasing human impact.

Language: Английский

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Chromosome-Scale Genome Assembly for Clubrush (Bolboschoenus planiculmis) Indicates a Karyotype with High Chromosome Number and Heterogeneous Centromere Distribution

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(3)

Published: March 1, 2024

Abstract Bolboschoenus planiculmis (F.Schmidt) T.V.Egorova is a typical wetland plant in the species-rich Cyperaceae family. This species contributes prominently to carbon dynamics and trophic integration ecosystems. Previous studies have reported that chromosomes of B. are holocentric; i.e. they kinetic activity along their entire length carry multiple centromeres. feature was suggested lead rapid genome evolution through chromosomal fissions fusions participate diversification ecological success genus. However, specific mechanism remains uncertain, partly due scarcity genetic information on Bolboschoenus. We present here first chromosome-level assembly for planiculmis. Through high-quality long-read short-read data, together with chromatin conformation using Hi-C technology, ultimate 238.01 Mb contig N50 value 3.61 Mb. Repetitive elements constituted 37.04% genome, 18,760 protein-coding genes were predicted. The low proportion long terminal repeat retrotransposons (∼9.62%) similar other species. Ks (synonymous substitutions per synonymous site) distribution no recent large-scale duplication this genome. haploid contained large number 54 pseudochromosomes small mean size 4.10 Mb, covering most karyotype. results centromere detection support not all centromeres, indicating more efforts needed fully reveal style holocentricity cyperids its evolutionary significance.

Language: Английский

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