Expanding the Triangle of U: Comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits

Annals of Botany, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 24, 2024

Abstract Background and Aims The Brassiceae tribe encompasses many economically important crops exhibits high intra- interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 Mya), differential lineage diversification genomic changes contributed to an array of divergence in morphology, biochemistry physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied because it displays photosynthetic rates high-light conditions. Our aim was elucidate evolution that gave rise genome H. its high-photosynthesis Methods We reconstructed chromosome-level assembly for (Nijmegen, v.2.0) using nanopore chromosome conformation capture (Hi-C) technologies, with 409 Mb size N50 52 (a 10× improvement over previously published scaffold-level v.1.0 assembly). updated annotation were subsequently used investigate WGT history comparative phylogenomic framework from ancestral blocks related diploidized crops. Key Results (x = 7) shares extensive collinearity Raphanus sativus 9). These two share some commonalities Brassica rapa oleracea (A genome, x 10 C 9, respectively) other similarities nigra (B 8). Phylogenetic analysis revealed R. form monophyletic clade between A/C B genomes. postulate genomes are results hybridization or introgression types. might explain discrepancy observed studies regarding phylogenetic placement relationship ‘triangle U’ species. Expression retained gene copies sub-genome expression divergence, probably attributable neo- sub-functionalization. Finally, we highlight genes associated physio-biochemical–anatomical adaptive incana, which likely facilitate traits under light. Conclusions improved assembly, presented this work will be valuable resource future research unravel genetic basis ability maintain efficiency conditions thereby improve photosynthesis enhanced agricultural production.

Language: Английский

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Comprehensive analysis of the oligopeptide transporter gene family in maize: Genome-wide identification, structural characterization, and stress-responsive expression

South African Journal of Botany, Journal Year: 2024, Volume and Issue: 175, P. 560 - 573

Published: Nov. 2, 2024

Language: Английский

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Pairing omics to decode the diversity of plant specialized metabolism

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102657 - 102657

Published: Nov. 10, 2024

Plants have evolved complex bouquets of specialized natural products that are utilized in medicine, agriculture, and industry. Untargeted product discovery has benefitted from growing plant omics data resources. Yet, genome complexity limits the identification curation biosynthetic pathways via single omics. Pairing multi-omics types within experiments provides multiple layers evidence for pathway mining. The extraction paired biological information facilitates connecting genes to transcripts metabolites, especially when captured across time points, conditions chemotypes. Experimental design requires specific adaptations enable effective paired-omics analysis. Ultimately, metadata standards required support integration unpaired public datasets accelerate collaborative efforts research community.

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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Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of paralogs from target enrichment data

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

Published: July 2, 2024

Abstract Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large scale phylogenomic studies often exclude polyploids hybrids due to challenges in assessing paralog status targeted loci incorporating them into tree reconstruction methods. Using a target enrichment dataset 1081 from 452 samples Brassicaceae tribe Arabideae, including many hybrid high ploidy taxa, we developed novel approach disentangle evolutionary history this phylogenetically taxonomically challenging clade. Our extends beyond commonly used gene tree-species reconciliation techniques by using phylogenetic placement, method adopted metagenomics, paralogous sequences diploid tree. We call Paralog PhyloGenomics (PPG), show how it allows simultaneous assessment origins ancient recent autopolyploids, detection nested polyploidization events. Additionally, demonstrate synonymous substitution rates provide further evidence mode polyploidization, specifically distinguish between allo- autopolyploidization, identify hybridization events involving ghost lineage. will be valuable addition methods available study polyploids.

Language: Английский

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Phylogenomics of a genus of "Great Speciators" reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems

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

Published: Aug. 29, 2024

The flora and fauna of island systems, especially those in the Indo-Pacific, are renowned for their high diversification rates outsized contribution to development evolutionary theories. total diversity geographic radiations many Indo-Pacific is often incompletely sampled phylogenetic studies due difficulty obtaining single endemic forms across Pacific relatively poor performance degraded DNA when using museum specimens inference relationships. New methods production analysis genome-wide datasets sourced from facilitating insights into complex histories these influential faunas. Here, we leverage whole genome resequencing (20X average coverage) extensive sampling all taxonomic within Todiramphus kingfishers, a rapid radiation largely "Great Speciators." We find that do not outright resolve relationships this clade: four types molecular markers (UCEs, BUSCOs, SNPs, mtDNA) tree building did well-supported concordant species-level topology. then uncover evidence widespread incomplete lineage sorting both ancient contemporary gene flow demonstrate how factors contribute conflicting histories. Our complete allowed us further identify novel case mitochondrial capture between two allopatric species, suggesting potential historical (but since lost) hybrid zone as islands were successively colonized. Taken together, results highlight increased genomic taxon can reveal patterns radiations.

Language: Английский

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Identification and Extraction of Biomarker Information

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Language: Английский

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Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species

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

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