Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species DOI Creative Commons
Irene T. Liao, Karen E. Sears, Lena C. Hileman

et al.

Applications in Plant Sciences, Journal Year: 2024, Volume and Issue: 13(1)

Published: Dec. 25, 2024

Abstract Premise Orthology inference is crucial for comparative genomics, and multiple algorithms have been developed to identify putative orthologs downstream analyses. Despite the abundance of proposed solutions, including publicly available benchmarks, it difficult assess which tool most suitable plant species, commonly complex genomic histories. Methods We explored performance four orthology algorithms—OrthoFinder, SonicParanoid, Broccoli, OrthNet—on eight Brassicaceae genomes in two groups: one group comprising only diploids another set diploids, mesopolyploids, recent hexaploid genome. Results The composition orthogroups reflected species' ploidy histories, with diploid having a higher proportion identical orthogroups. While + had lower compositions, average degree similarity between was not different from set. Discussion Three Broccoli—are helpful initial predictions. produced using OrthNet were generally outliers but could still provide detailed information about gene colinearity. With our dataset, slight discrepancies found across algorithms, necessitating additional analyses such as tree fine‐tune results.

Language: Английский

Phylogenetic and genomic mechanisms shaping glucosinolate innovation DOI Creative Commons
Kevin A. Bird,

Amanda Agosto Ramos,

Daniel J. Kliebenstein

et al.

Current Opinion in Plant Biology, Journal Year: 2025, Volume and Issue: 85, P. 102705 - 102705

Published: March 30, 2025

Plants have created an immense diversity of specialized metabolites to optimize fitness within a complex environment. Each plant lineage has novel often using the classical duplication/neo-functionalization model, but this is constrained by undersampled genera and absence high-quality genomes. Phylogenetically resolved genomes, deeper chemical sampling mechanistic assessment glucosinolate in Brassicales beginning fill understanding how novelty arises. This showing that small-scale duplications like tandem or distal events may more influence on formation metabolic novelty. Similarly, gene loss playing significant role across entire genera. Finally, work pathway not defined endpoint being used as launching pad for creation other metabolites. In combination, potential combining genomes with balanced phylogenetic develop improved models metabolite evolution occurs.

Language: Английский

Citations

0
The Role of Meiotic Drive in Chromosome Number Disparity Between Heterosporous and Homosporous Plants DOI
Sylvia P. Kinosian, Michael S. Barker

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 7, 2025

ABSTRACT In vascular plants, heterosporous lineages typically have fewer chromosomes than homosporous lineages. The underlying mechanism causing this disparity has been debated for over half a century. Although reproductive mode identified as critical to these patterns, the symmetry of meiosis during sporogenesis overlooked potential cause difference in chromosome numbers. most megasporogenesis is asymmetric, meaning one four meiotic products survives become egg. Comparatively, symmetric and all survive. important because asymmetric enables drive associated genomic changes, while cannot lead drive. Meiotic deviation from Mendelian inheritance where genetic elements are preferentially inherited by surviving egg cell, can profoundly impact (and genome) size, structure, number. Here we review how impacts number evolution lack plants their genomes, explore future approaches understand role on across land plants.

Language: Английский

Citations

0
BolANT3 Positively Regulates Indolic Glucosinolate Accumulation by Transcriptionally Activating BolCYP83B1 in Cabbage DOI Open Access

Chengtai Yan,

Wenjing Yang,

Xuemei Yan

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(7), P. 3415 - 3415

Published: April 5, 2025

Indolic glucosinolates are a group of plant secondary metabolites found in Brassica vegetables, and their breakdown products could act as important anti-cancer defense compounds against biotic stresses. Transcriptional regulation plays key role modulating the biosynthesis indolic model Arabidopsis, but little is known about transcriptional regulatory landscape these vegetables. In this study, we selected functionally validated biosynthetic gene BolCYP83B1 from glucosinolate pathway cabbage. Through yeast one-hybrid assay, systemically screened identified upstream regulators cabbage with BolANTs top candidates for further functional validation. Two homologs BolANTs, BolANT1 BolANT3, were confirmed to bind promoter via both assay an LUC assay. The overexpression BolANT3 significantly increased accumulation glucosinolates, while virus-induced silencing (VIGS) reduced Our work provides valuable insights into mechanisms

Language: Английский

Citations

0
Celebrating the American Society of Plant Biologists centennial anniversary: A compendium of review articles in plant biology DOI Creative Commons
Nancy A. Eckardt, Blake C. Meyers, Yunde Zhao

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(5), P. 1183 - 1185

Published: March 11, 2024

to fill a gap in the rapidly progressing areas of

Language: Английский

Citations

2
Tangled webs and spider‐flowers: Phylogenomics, biogeography, and seed morphology inform the evolutionary history of Cleomaceae DOI Creative Commons
Theresa Saunders, Isabel Larridon, William J. Baker

et al.

American Journal of Botany, Journal Year: 2024, Volume and Issue: 111(9)

Published: Aug. 29, 2024

Abstract Premise Cleomaceae is an important model clade for studies of evolutionary processes including genome evolution, floral form diversification, and photosynthetic pathway evolution. Diversification divergence patterns in remain tangled as research has been restricted by its worldwide distribution, limited genetic sampling species coverage, a lack definitive fossil calibration points. Methods We used target sequence capture the Angiosperms353 probe set to perform phylogenetic study Cleomaceae. estimated times biogeographic analyses explore origin diversification family. Seed morphology across extant taxa was documented with multifocal image‐stacking techniques morphological characters were extracted, analyzed, compared records. Results recovered well‐supported resolved tree generic relationships that includes 236 (~86%) species. identified 11 principal clades confidently placed Cleomella sister rest Our suggested Brassicaceae diverged ~56 mya, began diversify ~53 mya Palearctic Africa. Multiple transatlantic disjunct distributions identified. Seeds imaged from 218 (~80%) family all known Conclusions results represent most comprehensive date. disjunctions proposed explanations these patterns, likely either long‐distance dispersals or contractions latitudinal caused climate change over geological timescales. found seed varied considerably but mostly mirrored relationships.

Language: Английский

Citations

1
Celebrating the American Society of Plant Biologists centennial anniversary: A compendium of review articles in plant biology DOI Creative Commons
Nancy A. Eckardt, Blake C. Meyers, Yunde Zhao

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(1), P. 1 - 3

Published: March 28, 2024

Language: Английский

Citations

0
Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species DOI Creative Commons
Irene T. Liao, Karen E. Sears, Lena C. Hileman

et al.

Applications in Plant Sciences, Journal Year: 2024, Volume and Issue: 13(1)

Published: Dec. 25, 2024

Abstract Premise Orthology inference is crucial for comparative genomics, and multiple algorithms have been developed to identify putative orthologs downstream analyses. Despite the abundance of proposed solutions, including publicly available benchmarks, it difficult assess which tool most suitable plant species, commonly complex genomic histories. Methods We explored performance four orthology algorithms—OrthoFinder, SonicParanoid, Broccoli, OrthNet—on eight Brassicaceae genomes in two groups: one group comprising only diploids another set diploids, mesopolyploids, recent hexaploid genome. Results The composition orthogroups reflected species' ploidy histories, with diploid having a higher proportion identical orthogroups. While + had lower compositions, average degree similarity between was not different from set. Discussion Three Broccoli—are helpful initial predictions. produced using OrthNet were generally outliers but could still provide detailed information about gene colinearity. With our dataset, slight discrepancies found across algorithms, necessitating additional analyses such as tree fine‐tune results.

Language: Английский

Citations

0