Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 65(2), P. 299 - 323

Published: Nov. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

Language: Английский

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A plastid phylogenomic framework for the palm family (Arecaceae)

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: March 8, 2023

Abstract Background Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies large families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, a family ca. 181 genera and 2600 important components tropical rainforests bearing great cultural economic significance. Taxonomy phylogeny have been extensively investigated by series molecular phylogenetic in last two decades. Nevertheless, some relationships within not yet well-resolved, especially at tribal generic levels, consequent impacts for downstream research. Results Plastomes 182 palm representing 111 were newly sequenced. Combining these previously published plastid DNA data, we able to sample 98% conduct investigation family. Maximum likelihood analyses yielded robustly supported hypothesis. Phylogenetic among all five subfamilies 28 tribes most inter-generic also resolved strong support. Conclusions inclusion nearly generic-level coupled genomes strengthened understanding plastid-based palms. This comprehensive genome dataset complements growing body nuclear genomic data. Together, datasets form novel baseline palms an increasingly robust framework future comparative biological this exceptionally plant

Language: Английский

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The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP)

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled size of was 1.84 Gb, contig N50 ca. 45 Mb scaffold 92 Mb. Identified repeats constituted approximately 57% genome, 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that magnolias form sister clade eudicots order Ceratophyllales, while monocots are other core angiosperms. our total 21 individuals 5 remnant populations as well 22 specimens belonging 8 related Magnoliaceae species, resequenced. results showed had higher genetic diversity (θw = 0.01126 θπ 0.01158) than species in Magnoliaceae. However, population structure suggested differentiation among very low. Analyses demographic history using different models consistently revealed 2 bottleneck events occurred. contemporary effective estimated be 10.9. patterns loads (inbreeding numbers deleterious mutations) constructive strategies conservation these sinica. Overall, will valuable genomic resource

Language: Английский

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Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 187, P. 107869 - 107869

Published: July 8, 2023

Language: Английский

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Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(11), P. 2850 - 2868

Published: Feb. 27, 2023

The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related the evolutionary processes component species under paleoclimatic change, potentially reflected in dynamic history broadleaved forests (EBLFs) East Asia. However, knowledge about shift with impact change using genomic data remains rare. Here, we focus on Litsea complex (Lauraceae), a key lineage dominant EBLFs, gain insights into how shifted, providing origin historical dynamics EBLFs Asia Cenozoic climate change. We reconstructed robust phylogeny genome-wide single-nucleotide variants (SNVs) eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modelling reconstruction were employed estimate its pattern. Taking account studies other plant lineages dominating Asia, it was revealed that prototype probably emerged Early Eocene (55-50 million years ago [Ma]), facilitated by greenhouse warming. As response cooling drying Middle Late (48-38 Ma), habits evolved Up Miocene (23 prevailing Asian monsoon increased extreme seasonal precipitation accelerated emergence lineages, ultimately shaped vegetation resembling today.

Language: Английский

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(3), P. 546 - 578

Published: Jan. 30, 2024

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of angiosperms in fossil record was referred to Darwin as "abominable mystery," hence contributing heightened interest angiosperm evolution. display wide ranges morphological, physiological, and ecological characters, some which have probably influenced their species richness. evolutionary analyses these characteristics help address questions diversification require well resolved phylogeny. Following great successes phylogenetic using plastid sequences, dozens thousands nuclear genes from next-generation sequencing been used phylogenomic analyses, providing phylogenies new insights into evolution angiosperms. In this review we focus on recent large clades, orders, families, subdivisions families provide a summarized Nuclear Phylogenetic Tree Angiosperm Families. newly established relationships highlighted compared previous results. sequenced genomes Amborella, Nymphaea, Chloranthus, Ceratophyllum, monocots, Magnoliids, basal eudicots, facilitated phylogenomics among five major clades. All but one 64 orders were included except placements several orders. Most robust highly supported placements, especially for within important families. Additionally, examine divergence time estimation biogeographic basis frameworks discuss differences analyses. Furthermore, implications ancestral reconstruction characters groups, limitations current studies, taxa that future attention.

Language: Английский

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Transcriptome data analysis provides insights into the conservation of Michelia lacei, a plant species with extremely small populations distributed in Yunnan province, China

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: March 19, 2024

Abstract Background Michelia lacei W.W.Smith (Magnoliaceae), was classified as a Plant Species with Extremely Small Populations (PSESP) by the Yunnan Provincial Government in both action plans of 2012 and 2021. This evergreen tree is known for its high ornamental scientific value, but it faces significant threats due to extremely small population size narrow geographical distribution. The study aims understand genetic structure, diversity, demographic history this species inform conservation strategies. Results analysis transcriptome data from 64 individuals across seven populations M. identified three distinct clusters generated 104,616 single-nucleotide polymorphisms (SNPs). KM ex-situ population, originating Longling County, exhibited unique features, suggesting limited gene flow. diversity substantial, differences between populations, particularly lineage OTHER lineage. Demographic inferred indicated experienced declines during glaciations, followed periods recovery. We estimated effective (Ne) lineages 1,000 years ago were 85,851 416,622, respectively. Gene flow suggested past showed no recent A total 805 outlier SNPs, associated four environmental factors, suggest potential local adaptation showcase species' adaptive potential. Particularly, BZ displayed 515 loci, highlighting strong within group. Conclusions comprehensive genomic provides valuable insights into background highlights urgent need efforts. underscores importance methods, such seed collection vegetative propagation, safeguard promote restoration. preservation like MC crucial maintaining diversity. In-situ measures, including establishment in-situ sites community engagement, are essential enhance protection awareness ensure long-term survival threatened plant species.

Language: Английский

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Historical climate change and vicariance events contributed to the intercontinental disjunct distribution pattern of ash species (Fraxinus, Oleaceae)

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: May 20, 2024

The Northern Hemisphere temperate forests exhibit a disjunct distributional pattern in Europe, North America, and East Asia. Here, to reveal the promoter of intercontinental distribution, Fraxinus was used as model organism integrate abundant fossil evidence with high-resolution phylogenies phytogeographic analysis. We constructed robust phylogenetic tree using genomic data, reconstructed geographic ancestral areas, evaluated effect incorporating information on biogeographic history. relationships were highly resolved divided into seven clades. originated western America during Eocene, six dispersal events five vicariance occured. Results suggest that climate change contributed distribution Fraxinus. Moreover, results highlight necessity integrating relationship improve reliability inferred our understanding processes underlying distributions.

Language: Английский

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Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 198, P. 108120 - 108120

Published: June 7, 2024

Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one major eukaryotic supergroups. Due to their ecological impact as primary producer, ochrophytes are relatively well-studied compared rest yet evolutionary relationships remain poorly understood. This in part due number missing lineages large-scale multigene analyses, and an apparently rapid radiation leading many short internodes between ochrophyte subgroups tree. These also found across deep-branching stramenopiles with limited signal, leaving controversial overall. We have addressed this issue other recently, now examine whether contentious within may be resolved help filling updated phylogenomic dataset ochrophytes, along exploring various gene filtering criteria identify most phylogenetically informative genes. generated ten new transcriptomes from culture collections single-cell isolation environmental sample, added these existing dataset, examined effects selecting genes high signal or low noise. For some previously relationships, we find variety analyses consistently unite unstable groupings strong statistical support. example, recovered robust grouping Eustigmatophyceae Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed sister-lineage Pinguiophyceae. Selecting data quality more stable topologies. Overall, adding under-represented groups different still crucial resolving discrete properties affect differently. something which explored further our understanding molecular evolution stramenopiles.

Language: Английский

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Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests

BMC Plant Biology, Journal Year: 2022, Volume and Issue: 22(1)

Published: Jan. 13, 2022

Abstract Background The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the of this biome, we generated a molecular phylogeny one its essential plant groups, tribe Perseeae (Lauraceae). Results Our plastid tree topologies were robust to analyses based on different regions and strategies for data partitioning, nucleotide substitution saturation, gap handling. We found that comprised six major clades began colonize EBLFs Asia in early Miocene. diversification rates accelerated twice late Conclusions findings suggest intensified precipitation Miocene may have facilitated range expansions establishment within biome. By Miocene, species had become rapid.

Language: Английский

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