Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

Current Biology, Journal Year: 2023, Volume and Issue: 33(19), P. 4052 - 4068.e6

Published: Sept. 1, 2023

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of are incompletely sampled often contain poorly supported branches. Here, we present complete Brassicaceae genus-level phylogenies to date (Brassicaceae Tree Life or BrassiToL) based on nuclear (1,081 genes, 319 349 genera; 57 58 tribes) plastome (60 265 all data. We found cytonuclear discordance between two, which likely result rampant hybridization among closely more distantly related lineages. To evaluate impact such phylogeny reconstruction, performed five different gene sampling routines, increasingly removed putatively paralog genes. Our cleaned subset 297 genes revealed high support for tribes, whereas main lineages (supertribes) was moderate. Calibration 20 clock-like suggests late Eocene Oligocene origin family. Finally, our results strongly recently published new classification, dividing into two subfamilies (one with supertribes), together representing tribes. This includes described re-established including Arabidopsideae, monogeneric tribe accommodating without any close relatives. With worldwide community thousands researchers working diverse members, will be an indispensable tool studies biodiversity biology.

Language: Английский

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The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(5), P. 1334 - 1359

Published: Jan. 24, 2023

Abstract Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as model to study C4 photosynthesis due its evolutionary proximity C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with total length 740 Mb, an N50 42 Mb 30,933 well-supported gene models. The previously released genomes relatives in Cleomaceae Brassicaceae make excellent for studying role evolution transition from photosynthesis. Our analyses revealed that relative Tarenaya hassleriana shared whole-genome duplication event (Gg-α), then addition third (Th-α, +1×) took place T. but not gynandra. Analysis syntenic copy number photosynthesis-related families indicates generally retained more duplicated copies these genes than C3T. hassleriana, might have under positive selection pressure. Both single-gene were found contribute expansion aforementioned Collectively, this enhances our understanding polyploidy history, retention, well their impact on Cleomaceae.

Language: Английский

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Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: March 22, 2024

Abstract Background Eriophyoid mites (Eriophyoidea) are among the largest groups in Acariformes; they strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to limited number available morphological characters—some them homoplastic. Nevertheless, sequenced date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving phylogenetic relationships. Results Here, we and compared complete mt genomes 153 mite species, 54 patterns rearranged orders relative that hypothetical ancestor arthropods. shared derived clusters support monophyly as a whole monophylies six clades within Eriophyoidea. These monophyletic their relationships were largely supported trees inferred from genome sequences well. Our molecular dating results Eriophyoidea originated Triassic diversified Cretaceous, coinciding with diversification angiosperms. Conclusions This study reveals multiple synapomorphies (i.e. clusters) at different levels family, subfamily or tribe level) species. We demonstrated use unveiling underlines origin these co-diversification

Language: Английский

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Genome-wide exploration: evolution, structural characterization, molecular docking, molecular dynamics simulations and expression analysis of sugar transporter (ST) gene family in potato (Solanum tuberosum)

Computational Biology and Chemistry, Journal Year: 2025, Volume and Issue: 117, P. 108402 - 108402

Published: March 1, 2025

Language: Английский

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SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(7)

Published: April 10, 2025

Abstract With the explosive growth of whole-genome datasets, accurate detection orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods identifying face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable robust approach, based on Orthology Index (OI), to effectively identify Our evaluation across large-scale empirical dataset diverse polyploidization events demonstrated high reliability robustness OI method. Simulation-based benchmarks further validated accuracy our method, showing its superior performance against existing wide range scenarios. Additionally, explored broad applications plant genomes, including inference polyploidy, identification reticulation, phylogenomics. conclusion, offers robust, interpretable, approach synteny, facilitating more efficient analyses genomics.

Language: Английский

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The trichome pattern diversity of Cardamine shares genetic mechanisms with Arabidopsis but differs in environmental drivers

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: unknown

Published: April 12, 2024

Abstract Natural variation in trichome pattern (amount and distribution) is prominent among populations of many angiosperms. However, the degree parallelism genetic mechanisms underlying this diversity its environmental drivers different species remain unclear. To address these questions, we analyzed genomic bases leaf Cardamine hirsuta, a relative Arabidopsis (Arabidopsis thaliana). We characterized 123 wild accessions for their diversity, patterns at temperatures, adjustments. Nucleotide diversities biogeographical distribution models identified two major lineages with distinct demographic adaptive histories. Additionally, C. hirsuta showed substantial plasticity to temperature. Trichome amount correlated positively spring precipitation but negatively temperature, which opposite climatic A. thaliana. Contrastingly, analysis glabrous indicated that, like thaliana, glabrousness caused by null mutations ChGLABRA1 (ChGL1). Phenotypic genome-wide association studies (GWAS) further ChGL1 haplogroup associated low density expression. Therefore, series partial loss-of-function alleles accounts parallel evolution Finally, GWAS also detected other candidate genes (e.g. ChETC3, ChCLE17) that might affect pattern. Accordingly, trait thaliana shows partially conserved likely involved adaptation environments.

Language: Английский

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Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae

Plant Communications, Journal Year: 2024, Volume and Issue: 5(7), P. 100878 - 100878

Published: March 11, 2024

Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this have not been fully characterized, especially upon uplift Tibetan Plateau, which was followed by increasing aridity in Asian interior, intensifying monsoons Eastern Asia, significantly fluctuating daily temperatures. Here, we reveal architecture that accompanied analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) Tetracme quadricornis (Hesperodae; E), together with representing all major clades basal Aethionemeae. We reconstructed ancestral core karyotype (CBK) containing 9 pseudochromosomes 65 conserved syntenic blocks identified 9702 genes Brassicaceae. detected pervasive conflicting phylogenomic signals widespread ancient hybridization events, correlate well divergence successive Brassicaceae-specific expansion class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, encodes enzymes essential regulatory roles flowering time embryo development. The TPS1s were mainly randomly amplified, expression divergence. Our results provide fresh insights into historical coupled evolution offer potential model broad-scale studies adaptive radiation under ever-changing environment.

Language: Английский

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OrthoRefine: automated enhancement of prior ortholog identification via synteny

BMC Bioinformatics, Journal Year: 2024, Volume and Issue: 25(1)

Published: April 25, 2024

Abstract Background Identifying orthologs continues to be an early and imperative step in genome analysis but remains a challenging problem. While synteny (conservation of gene order) has previously been used independently combination with other methods identify orthologs, applying ortholog identification yet automated user-friendly manner. This desire for automation ease-of-use led us develop OrthoRefine, standalone program that uses refine identification. Results We developed OrthoRefine improve the detection orthologous genes by implementing look-around window approach detect synteny. tested tandem OrthoFinder, one most software recent years. evaluated improvements provided several bacterial eukaryotic dataset. efficiently eliminates paralogs from groups detected OrthoFinder. Using increased specificity functional identification; additionally, BLAST e-value, phylogenetics, operon occurrence further supported using A comparison sizes suggested smaller (eight genes) were generally suitable identifying via However, larger windows (30 performed better datasets containing less closely related genomes. typical run ~ 10 genomes can completed few minutes on regular desktop PC. Conclusion is simple-to-use, tool automates application detection. particularly efficient eliminating delineated standard methods.

Language: Английский

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SYNY: a pipeline to investigate and visualize collinearity between genomes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 13, 2024

Investigating collinearity between chromosomes is often used in comparative genomics to help identify gene orthologs, pinpoint genes that might have been overlooked as part of annotation processes and/or perform various evolutionary inferences. Collinear segments, also known syntenic blocks, can be inferred from sequence alignments the identification arrayed same order and relative orientations investigated genomes. To these analyses assess their outcomes, we built a simple pipeline called SYNY (for synteny) implements two distinct approaches produces different visualizations. The was with ease use mind runs on modest hardware. written Perl Python available GitHub (https://github.com/PombertLab/SYNY) under permissive MIT license.

Language: Английский

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Expanding the Triangle of U: The genome assembly ofHirschfeldia incanaprovides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 18, 2024

ABSTRACT The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event ( Br-α , ∼15.9 million years ago), different lineages species underwent differential chromosomal rearrangements (diploidization) leading to diverse patterns of gene retention loss (fractionation). Lineage diversification genomic changes contributed an array divergence in morphology, biochemistry, physiology underlying photosynthesis-related traits. C 3 Hirschfeldia incana is studied as it displays photosynthetic rates under high-light conditions. We present improved chromosome-level genome assembly for H. (Nijmegen, v2.0) using nanopore chromosome conformation capture (Hi-C) technologies, with 409Mb size N50 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). updated annotation allowed investigate WGT history comparative phylogenomic framework from ancestral blocks related diploidized crops. (x=7) shares extensive collinearity Raphanus sativus (x=9). These two share some commonalities Brassica rapa B. oleracea (A genome, x=10 x=9, respectively) other similarities nigra (B x=8). Phylogenetic analysis revealed that R. form monophyletic clade between A/C B genomes. postulate genomes are results reciprocal hybridization combinations types. Our might explain discrepancy observed studies regarding phylogenetic placement relation “Triangle U” species. Expression retained copies sub-genome expression divergence, likely due neo- or sub-functionalization. Finally, we highlighted genes associated physio-biochemical-anatomical adaptive which facilitate its high-photosynthesis traits light.

Language: Английский

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