Deep reticulation: the long legacy of hybridization in vascular plant evolution

The Plant Journal, Journal Year: 2023, Volume and Issue: 114(4), P. 743 - 766

Published: Feb. 13, 2023

Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep scales largely obscure. Over the past decade, genomic phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, common throughout history plants, particularly various lineages flowering plants. However, studies also highlighted challenges disentangling signals ancient hybridization from other sources conflict (in particular, incomplete lineage sorting). Here, we provide critical review vascular outlining well-documented cases plant phylogeny, well unique to documenting versus recent hybridization. We definition for which, knowledge, explicitly attempted before. Further extent reticulation should remain an important research focus, especially because published examples likely represent tip iceberg terms total future increasingly explore macroevolutionary this process, impact on trajectories (e.g. how does influence trait evolution or generation biodiversity over time scales?), life ecological factors shape, shaped, frequency geologic phylogeny. Finally, consider implications ubiquitous conceptualize, analyze, classify Networks, opposed bifurcating trees, more accurate representations many cases, although ability infer, visualize, use networks comparative analyses is highly limited. Developing improved methods generation, visualization, represents direction biology. Current classification systems do generally allow recognition reticulate lineages, classifications themselves are based evidence chloroplast genome. Updating better reflect nuclear phylogenies, considering whether recognize systems, will challenge systematics community.

Language: Английский

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Chromosome‐scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata

New Phytologist, Journal Year: 2023, Volume and Issue: 238(5), P. 2016 - 2032

Published: Feb. 16, 2023

Summary Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability beautiful autumn coloration, with color changes from green yellow into red resulting the autumnal shifts leaf pigmentation. However, key genes molecular regulatory mechanisms for transition remain be investigated. First, we presented high‐quality chromosome‐scale assembly Q. . This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold 75.55 Mb; 2 n 24) harbors 31 584 protein‐coding genes. Second, our metabolome analyses uncovered pelargonidin‐3‐ O ‐glucoside, cyanidin‐3‐ ‐arabinoside, ‐glucoside as main pigments involved transition. Third, gene co‐expression further identified MYB‐bHLH‐WD40 (MBW) transcription activation complex central anthocyanin biosynthesis regulation. Notably, factor (TF) QdNAC ( QD08G038820 ) was highly co‐expressed this MBW may regulate accumulation chlorophyll degradation during senescence through direct interaction another TF, QdMYB QD01G020890 ), revealed by protein–protein DNA–protein assays. Our assembly, metabolome, transcriptome resources enrich genomics will facilitate upcoming exploration of values environmental important genus.

Language: Английский

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Resilience of genetic diversity in forest trees over the Quaternary

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Oct. 14, 2024

The effect of past environmental changes on the demography and genetic diversity natural populations remains a contentious issue has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses demographic inferences for seven widely distributed ecologically contrasting European forest tree species based concerted sampling 164 their ranges. For all species, effective size, N

Language: Английский

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Phylogenomic analyses re-evaluate the backbone of Corylus and unravel extensive signals of reticulate evolution

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: 204, P. 108293 - 108293

Published: Jan. 23, 2025

Language: Английский

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Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(7), P. 1639 - 1655

Published: Jan. 10, 2023

Understanding the evolutionary processes that shape landscape of genetic variation and influence response species to future climate change is critical for biodiversity conservation. Here, we sampled 27 populations across distribution range a dominant forest tree, Quercus acutissima, in East Asia, applied genome-wide analyses track history predict fate under climate. We found two groups (East West) Q. acutissima diverged during Pliocene. also heterogeneous genomic this species, which may have been shaped by population demography linked selections. Using genotype-environment association analyses, identified climate-associated SNPs diverse set genes functional categories, indicating model polygenic adaptation acutissima. further estimated three offset metrics quantify vulnerability due complex interplay between local migration. marginal are higher risk extinction because change, not be able suitable habitats maintain gene-environment relationships observed current detected reverse offsets northern China, currently present whole adapt conditions area. Overall, study illustrates how variation, provides comprehensive view maladaptation

Language: Английский

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A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis)

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 23, 2022

Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to widespread in East Asia. It a valuable woody indicator of local forest health, occupies dominant position ecosystems However, genomic resources from Q. are still lacking. Here, we present high-quality genome generated by PacBio HiFi Hi-C sequencing. The assembled size 787 Mb, with contig N50 26.04 Mb scaffold 64.86 comprising 12 pseudo-chromosomes. repetitive sequences constitute 67.6% the genome, which majority long terminal repeats, accounting for 46.62% genome. We used ab initio , RNA sequence-based homology-based predictions identify protein-coding genes. A total 32,466 genes were identified, 95.11% could be functionally annotated. Evolutionary analysis showed that was more closely related suber than lobata or robur. found no evidence species-specific whole duplications after had diverged. This study provides first assembly gene annotation data variabilis. These will inform design further breeding strategies, editing comparative genomics oak species.

Language: Английский

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Resilience of genetic diversity in forest trees over the Quaternary

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 6, 2023

Abstract The effect of past environmental changes on the demography and genetic diversity natural populations remains a contentious issue has rarely been investigated across multiple, phylogenetically distant species. Here, we performed comparative population genomic analyses demographic inferences for seven widely distributed ecologically contrasted European forest tree species based concerted sampling 164 their ranges. For all species, effective size, N e , increased or remained stable over many glacial cycles up to 15 million years in most extreme cases. Hence, surprisingly, drastic associated with Pleistocene have had little impact level dominant despite major shifts geographic Based trajectories time, can be divided into three groups, highlighting importance life history range size determining synchronous variation diversity, time. Altogether, our results indicate that trees were able retain evolutionary potential very long periods time strong changes. One-Sentence Summary Population reveal retained Quaternary.

Language: Английский

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Genomic basis of the distinct biosynthesis of β‐glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species

New Phytologist, Journal Year: 2024, Volume and Issue: 242(6), P. 2702 - 2718

Published: March 21, 2024

Summary Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used grape wine aging, feed additives, and human healthcare. However, the limited availability of a high‐quality reference genome oaks greatly hampered recognition mechanism HT biosynthesis. Here, genomes three Asian oak species ( Quercus variabilis , aliena dentata ) that have different contents were generated. Multi‐omics studies carried out to identify key genes regulating In vitro enzyme activity assay was also conducted. Dual‐luciferase yeast one‐hybrid assays reveal transcriptional regulation. Our results revealed β‐glucogallin biochemical marker for production cupules oaks. UGT84A13 confirmed as The differential expression rather than activity, main reason accumulation. Notably, sequence variations promoters led trans ‐activating activities WRKY32/59, explaining patterns among species. findings provide new trees give insights into regulation understanding biosynthesis closely related

Language: Английский

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HB26, a member of HD-Zip I subfamily, is involved in the regulation of hydrolysable tannin biosynthesis in the cupules of Quercus variabilis by transactivation of UGT84A13

Industrial Crops and Products, Journal Year: 2023, Volume and Issue: 200, P. 116866 - 116866

Published: May 13, 2023

Language: Английский

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Chromosome-scale genomes of Quercus sichourensis and Quercus rex provide insights into the evolution and adaptation of Fagaceae

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: April 1, 2024

Language: Английский

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