An updated classification of the Brassicaceae (Cruciferae)

PhytoKeys, Journal Year: 2023, Volume and Issue: 220, P. 127 - 144

Published: March 6, 2023

Based on recent achievements in phylogenetic studies of the Brassicaceae, a novel infrafamilial classification is proposed that includes major improvements at subfamilial and supertribal levels. Herein, family subdivided into two subfamilies, Aethionemoideae (subfam. nov.) Brassicoideae. The Brassicoideae, with 57 58 tribes are further partitioned five supertribes, including previously recognized Brassicodae newly established Arabodae, Camelinodae, Heliophilodae, Hesperodae. Additional tribus-level contributions include descriptions Arabidopsideae, Asperuginoideae, Hemilophieae, Schrenkielleae, resurrection Chamireae Subularieae. Further detailed comments 17 need clarifications provided.

Language: Английский

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Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(3)

Published: Feb. 24, 2023

Large genomic data sets are becoming the new normal in phylogenetic research, but identification of true orthologous genes and exclusion problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with through synteny a set 11 representative diploid Brassicaceae whole-genome sequences spanning entire space. Then, evaluated resulting gene regarding number, functional annotation, species tree resolution. Finally, syntenic for comparative genomics ancestral genome analysis. The use resulted considerably more orthologs also allowed us to reliably identify paralogs. Surprisingly, did not detect notable differences between trees reconstructed from other sets, including Angiosperms353 Brassicaceae-specific enrichment set. However, comprised multitude functions, strongly suggesting that this method marker selection phylogenomics suitable studies value downstream function analysis, interaction, network studies. present first reconstruction Core which predating lineage diversification ∼25 million years ago.

Language: Английский

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Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 197, P. 108093 - 108093

Published: May 11, 2024

Language: Английский

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Net diversification rates of the woody plant genus Petalidium (Acanthaceae) are highest in the ancient and arid Namib Desert

Frontiers in Ecology and Evolution, Journal Year: 2023, Volume and Issue: 11

Published: May 15, 2023

At present, tropical arid biomes house less woody plant species diversity than moist biomes, which could be due to lower rates of evolutionary diversification in the recent or distant past. Here, we study Petalidium (Acanthaceae), a genus 36 shrubs found Namib Desert southwest Africa, and surrounding areas. We generated new, nearly fully sampled temporally calibrated phylogeny for using RADseq SNP data secondary calibrations. then investigated variation net rate across phylogeny, ancestral climatic niche lineages link between two. find that conditions are linked with increased genus. Despite its great age, clearly hosts young radiations. This apparent contradiction can explained by scenario high turnover, this case potentially caused alternating hyper-arid relatively mesic phases. Hyper-arid phases result mortality extinction species, leading ecological opportunity during Taken together, our results contribute growing body literature shows evidence elevated Quaternary globe.

Language: Английский

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Molecular phylogeny and phylogeography reveal recent divergence in the Iberis simplex DC. (Brassicaceae) species complex

TURKISH JOURNAL OF BOTANY, Journal Year: 2022, Volume and Issue: 46(6), P. 567 - 582

Published: Jan. 1, 2022

According to the current taxonomic delimitation, Mediterranean genus Iberis comprises about 30 species. Among them, taxonomy and species delimitation of simplex its morphologically close relatives (I. attica, I. carica, gypsicola, halophila, spruneri), described here as complex, are controversial several different names used for members this complex. Past phylogenetic studies did not include complex we present first comprehensive phylogeographic study based on nuclear ITS chloroplast trnL-F regions delimit boundaries contribute knowledge Anatolian biogeography. Our analyses clearly showed a monophyletic origin polytomic relationships within clade, recent divergence starting from ca. 0.65 million years ago. Finally, population expansion (as driver rapid radiation) which is possibly associated with climatic oscillations during Pleistocene was supported by multiple tests mismatch distribution analyses.

Language: Английский

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The meso‐octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora

The Plant Journal, Journal Year: 2023, Volume and Issue: 116(2), P. 446 - 466

Published: July 10, 2023

Although the South African Cape flora is one of most remarkable biodiversity hotspots, its high diversity has not been associated with polyploidy. Here, we report chromosome-scale genome assembly an ephemeral cruciferous species Heliophila variabilis (~334 Mb, n = 11) adapted to semiarid biomes. Two pairs differently fractionated subgenomes suggest allo-octoploid origin at least 12 million years ago. The ancestral octoploid (2n 8x ~60) probably originated through hybridization between two allotetraploids 4x ~30) formed by distant, intertribal, hybridization. Rediploidization was marked extensive reorganization parental subgenomes, downsizing, and speciation events in genus Heliophila. We found evidence for loss-of-function changes genes leaf development early flowering, over-retention sub/neofunctionalization involved pathogen response chemical defense. genomic resources H. will help elucidate role polyploidization diploidization plant adaptation hot arid environments flora. sequenced represents first a meso-octoploid representative mustard family.

Language: Английский

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Pollen morphology of some genera selected tribe Alysseae (Brassicaceae)

Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, Journal Year: 2023, Volume and Issue: 157(4), P. 792 - 811

Published: April 12, 2023

The tribe Alysseae (Brassicaceae) contains the genera Brachypus, Clastopus, Fibigia, Irania, Physoptychis, and Straussiella. Little is known about pollen morphology in these taxa. In this study, from 11 species one variety representing some of were examined using light microscopy (LM) scanning electron (SEM). size smallest Brachypus tabriziana (30.23 µm), conversely, largest Irania umbellata (47.17 µm) Clastopus vestitus (46.60 Alysseae. deviated I. multicaulis was distinct having perprolate, ornamentation reticulate, thickest exine, polar axis length. previously placed Fibigia genus order to determine significance features as taxonomic characters. addition, our results indicated that differs related Physoptychis Straussiella, conforms separation three genera. These support research phylogenetic studies Based on above evidence, new combinations such kermanshahensis, B. khoshyelaqensis, proposed.

Language: Английский

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The evolution of the hypotetraploid Catolobus pendulus genome – the poorly known sister species of Capsella

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: May 8, 2023

The establishment of Arabidopsis as the most important plant model has also brought other crucifer species into spotlight comparative research. While genus Capsella become a prominent system, its closest relative been overlooked. unispecific Catolobus is native to temperate Eurasian woodlands, from eastern Europe Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability pendulus throughout range. Unexpectedly, all populations were hypotetraploid (2 n = 30, ~330 Mb). Comparative cytogenomic analysis revealed that arose by whole-genome duplication in diploid resembling Ancestral Crucifer Karyotype (ACK, 8). In contrast much younger allotetraploid genomes, presumably autotetraploid 32) early after / divergence. Since origin, tetraploid undergone chromosomal rediploidization, including reduction number 2 32 30. Diploidization occurred through end-to-end fusion rearrangements affecting total six 16 ancestral chromosomes. cytotype expanded toward present range, accompanied some longitudinal differentiation. sister relationship between allows studies genomes contrasting ages different degrees diploidization.

Language: Английский

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Distributional ecology of Noccaea vesicaria in relation to the Anatolian Diagonal

TURKISH JOURNAL OF BOTANY, Journal Year: 2023, Volume and Issue: 47(4), P. 267 - 277

Published: Jan. 1, 2023

Anatolia is located at the intersection of three world's 36 biodiversity hotspots (the Caucasus, Irano-Anatolian, and Mediterranean Basin hotspots) has about 10,000 plant species, over 3000 which are endemic. Among many reasons for astonishing Anatolia, one that stands out Anatolian Diagonal. Although Diagonal long been recognized as a biogeographical boundary between Central Eastern its exact functioning still not well understood. Thus, in this study, our aims were 1) to assess environmental barrier function Noccaea vesicaria, living on east it; 2) evaluate climate-driven range shifts (contractions or expansions), especially through Quaternary glacial-interglacial cycles; 3) contribute long-standing debate causes floral break west Accordingly, we used an ecological niche modeling approach with presence records bioclimatic data. Under present conditions, areas more suitable conditions observed, throughout Diagonal, therefore largely matching geographical distribution N. vesicaria. However, high suitability also observed Taurus Mountains Pontic Mountains. by itself cannot explain vesicaria absence it, past contracted during warmer time periods expanded colder periods, suggesting respectively, least around Highlands. There may be two why does occur Diagonal: dispersal and/or biotic interactions (e.g., competition facilitation). Biotic (likely positive interaction facilitation) have played significant role shaping because it seems highly associated Highlands steppe order Festuco oreophilae-Veronicetalia orientalis Hamzaoğlu whose extend Anatolia.

Language: Английский

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Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Sept. 7, 2022

Abstract Large genomic datasets are becoming the new normal for any facet of phylogenetic research, but identification true orthologous genes and exclusion problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with through synteny in a dataset eleven representative diploid Brassicaceae whole genome sequences spanning entire space. We then evaluated resulting gene sets regarding number, functional annotation, species tree resolution. Finally, syntenic comparative genomics ancestral analysis. The use resulted considerably more orthologs also allowed us to reliably identify paralogs. Surprisingly, did not detect notable differences between trees reconstructed from other sets, including Angiosperm353 set specific enrichment set. However, comprised multitude functions, strongly suggesting that this method marker selection phylogenomics suitable studies value downstream function analysis, interaction network studies. present first reconstruction Core predating lineage diversification ∼25 million years ago.

Language: Английский

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