A roadmap of phylogenomic methods for studying polyploid plant genera DOI Creative Commons
Weixuan Ning, Heidi M. Meudt, Jennifer A. Tate

et al.

Applications in Plant Sciences, Journal Year: 2024, Volume and Issue: 12(4)

Published: April 22, 2024

Phylogenetic inference of polyploid species is the first step towards understanding their patterns diversification. In this paper, we review challenges and limitations inferring relationships plants using traditional phylogenetic sequencing approaches, as well mischaracterization tree from single or multiple gene trees. We provide a roadmap to infer interspecific among lineages by comparing evaluating application current phylogenetic, phylogenomic, transcriptomic, whole-genome approaches different platforms. For reconstruction, assess following criteria: (1) amount prior information tools required capture genetic region(s) interest; (2) probability recovering homeologs for species; (3) time efficiency downstream data analysis. Moreover, discuss bioinformatic pipelines that can reconstruct networks relationships. summary, although phylogenomic have improved our reticulate in polyploid-rich genera, difficulties reliable orthologous genes sorting all homeologous copies allopolyploids remain challenge. future, assembled long-read will assist recovery identification copies, which be particularly useful reconstructing independent origins polyploids.

Language: Английский

Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants DOI Creative Commons
William J. Baker, Steven Dodsworth, Félix Forest

et al.

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1059 - 1065

Published: July 1, 2021

Language: Английский

Citations

57
Genomics of plant speciation DOI Creative Commons
Dan G. Bock,

Zhe Cai,

Cassandra Elphinstone

et al.

Plant Communications, Journal Year: 2023, Volume and Issue: 4(5), P. 100599 - 100599

Published: April 12, 2023

Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study other organisms while also additional ways which can form. Now, ability to sequence genomes at an unprecedented pace and scale allowed biologists settle decades-long debates tackle emerging challenges research. Here, we review these recent genome-enabled developments plant speciation. We discuss complications related identification reproductive isolation (RI) loci using analyses landscape genomic divergence highlight important role that structural variants speciation, as increasingly revealed by sequencing technologies. Further, genomics advanced what know routes formation, like hybridization or whole-genome duplication, casting doubt others, population bottlenecks genetic drift. While fast-track genes mutations confer RI, emphasize follow-up molecular field experiments remain critical. Nonetheless, clarified outsized ancient rather than mutations, particularly early during conclude highlighting promising avenues future study. These include expanding so far about epigenetic changes broadening scope taxonomic breadth studies, synthesizing information from extensive data already generated community.

Language: Английский

Citations

39
A plastid phylogenomic framework for the palm family (Arecaceae) DOI Creative Commons
Gang Yao, Yu‐Qu Zhang, Craig F. Barrett

et al.

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

Citations

33
Phylogenomic analyses re-evaluate the backbone of Corylus and unravel extensive signals of reticulate evolution DOI
Zhen Yang, Lisong Liang, Weibo Xiang

et al.

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

Published: Jan. 23, 2025

Language: Английский

Citations

1
A novel bHLH transcription factor, FabHLH110, is involved in regulation of anthocyanin synthesis in petals of pink-flowered strawberry DOI

Song Yang,

Ming Liu, Can Zhao

et al.

Plant Physiology and Biochemistry, Journal Year: 2025, Volume and Issue: 222, P. 109713 - 109713

Published: Feb. 28, 2025

Language: Английский

Citations

1
Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae) DOI Creative Commons
Diego F. Morales‐Briones, Berit Gehrke, Chien‐Hsun Huang

et al.

Systematic Biology, Journal Year: 2021, Volume and Issue: 71(1), P. 190 - 207

Published: May 5, 2021

Abstract Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits are typically designed to target single-copy genes, paralogs often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches processing data sets include random selection, manual pruning, and mainly, the removal entire genes that show any evidence paralogy. These prone errors orthology inference or removing large numbers genes. By valuable information could be used detect place WGD events discarded. Here, we an automated approach set 68 species Alchemilla s.l. (Rosaceae), widely distributed clade plants primarily temperate climate regions. Previous molecular phylogenetic studies chromosome both suggested ancient WGDs group. However, location putative parental lineages these remain unknown. taking into consideration inferring orthologs data, identified four nodes backbone elevated gene duplication. Furthermore, using gene-tree reconciliation approach, established autopolyploid origin nested allopolyploid major clades within showed utility tree-based methods, previously genomic transcriptomic sets, study complex scenarios polyploidy reticulate evolution sets.[Alchemilla; allopolyploidy; autopolyploidy; tree discordance; inference; paralogs; Rosaceae; enrichment; whole genome duplication.]

Language: Английский

Citations

43
Untying Gordian knots: unraveling reticulate polyploid plant evolution by genomic data using the large Ranunculus auricomus species complex DOI Creative Commons
Kevin Karbstein, Salvatore Tomasello, Ladislav Hodač

et al.

New Phytologist, Journal Year: 2022, Volume and Issue: 235(5), P. 2081 - 2098

Published: May 28, 2022

Summary Speciation via hybridization and polyploidization is a major evolutionary force in plant evolution but still poorly understood for neopolyploid groups. Challenges are attributed to high heterozygosity, low genetic divergence, missing information on progenitors, ploidy, reproduction. We study the large Eurasian Ranunculus auricomus species complex use comprehensive workflow integrating reduced‐representation sequencing (RRS) genomic data unravel reticulate evolution, genome diversity composition of polyploids. rely 97 312 restriction site‐associated DNA (RAD‐Seq) loci, 576 targeted nuclear genes (48 phased), 71 plastid regions derived from 78 polyploid apomictic taxa four diploid one tetraploid putative sexual progenitor species. applied (phylo)genomic structure, network, single nucleotide polymorphism (SNP)‐origin analyses. Results consistently showed only 3–5 supported geographically structured groups, each containing extant unknown Combined analyses demonstrated predominantly allopolyploid origins, involving 2–3 different Young allotetraploids were characterized by subgenome dominance nonhybrid SNPs, suggesting substantial post‐origin little lineage‐specific evolution. The biodiversity complexes can result multiple hybrid origins progenitors (e.g. homoeologous exchanges, segregation, gene flow). Reduced‐representation including multi‐approach efficient delimit shallow relationships.

Language: Английский

Citations

36
Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids DOI Creative Commons
Elvira Hörandl

Plants, Journal Year: 2022, Volume and Issue: 11(2), P. 204 - 204

Published: Jan. 13, 2022

Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because the complexity different evolutionary scenarios that do not fit with classical concepts. Polyploid complexes formed via combinations allopolyploidy, autopolyploidy homoploid hybridization persisting sexual reproduction, resulting in many discrete lineages have classified as species. facultative apomixis result complicated net-work like clusters, rarely agamospecies. Various case studies illustrate problems apply to traditional concepts hybrids polyploids. Conceptual progress can be made if lineage formation is accepted an inevitable consequence meiotic sex, which established already first eukaryotes a DNA restoration tool. The turnaround viewpoint sex forms helps overcome thinking "units". Lineage self-sustainability prerequisite speciation also applied Species delimitation aided by improved recognition various novel -omics methods, understanding meiosis functions, recognizing functional phenotypes considering morphological-physiological-ecological adaptations.

Language: Английский

Citations

32
homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes DOI Creative Commons
William A. Freyman, Matthew G. Johnson, Carl J. Rothfels

et al.

Methods in Ecology and Evolution, Journal Year: 2023, Volume and Issue: 14(5), P. 1230 - 1244

Published: March 13, 2023

Abstract Organisms such as allopolyploids and F1 hybrids contain multiple distinct subgenomes, each potentially with its own evolutionary history. These organisms present a challenge for multilocus phylogenetic inference other analyses since it is not apparent which gene copies from different loci are the same subgenome thus share an Here we introduce homologizer, flexible Bayesian approach that uses framework to infer phasing of across into their respective subgenomes. Through use simulation tests, demonstrate homologizer robust wide range factors, incomplete lineage sorting informativeness loci. Furthermore, establish utility on real data, by analysing dataset consisting nine diploids 19 tetraploids fern family Cystopteridaceae. Finally, describe how may be used beyond core functionality identify non‐homologous sequences, hidden paralogs or contaminants.

Language: Английский

Citations

22
Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex DOI Creative Commons
Ladislav Hodač, Kevin Karbstein, Salvatore Tomasello

et al.

Biology, Journal Year: 2023, Volume and Issue: 12(3), P. 418 - 418

Published: March 9, 2023

Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with morphological patterns. In such TCGs, mosaic-like character combinations conflicts data molecular phylogenies present major problem for classification. Here, we used the large polyploid apomictic European Ranunculus auricomus to study relationships among five diploid sexual progenitor 75 derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal stem leaves, receptacles), genomic (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed clusters correspond groupings basal leaves concatenated traits, were best resolved data; (2) described taxa usually overlap within trait morphospace except those at space edges; (3) phenotypes are highly influenced by parental subgenome composition lesser extent climatic factors; (4) allopolyploid compared their progenitor, resemble mosaic ecological intermediate transgressive biotypes. The joint evaluation phylogenomic, phenotypic, reproductive, supports revision purely descriptive, subjective traditional classifications.

Language: Английский

Citations

20