ArticleGenome biology and evolution2023
Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae.
Article in Genome biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 42 citations in OpenAlex.
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- Systematic mass-spectrometry-guided metabolic fingerprinting elucidates diversity of specialized metabolites across the Brassicaceae.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- 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 · 2026Article
- The Brassicaceae then and now: advancements in the past three decades, a review.Annals of botany · 2026Review
- Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family.Annals of botany · 2026Article
- Murbeckiella is dead, long live Oreophyton: origin and systematics of tribe Oreophytoneae (Brassicaceae).Annals of botany · 2026Article
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- Diverse reference genomes detect variants in the US winter wheat.The plant genome · 2026Article
- Genomic-Driven Identification of Conserved Biosynthetic Gene Clusters inMetabolites · 2026Article
- Genome-wide bioinformatics analysis of the MATE gene family for abiotic stress tolerance in sunflower (Helianthus annuus L.).PloS one · 2026Article
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- Genomic advances in orphan and underutilized Brassicaceae crops and their wild relatives.Frontiers in plant science · 2026Review
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana.Plant biotechnology journal · 2025Article
- SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.Nucleic acids research · 2025Article
- The trichome pattern diversity of Cardamine shares genetic mechanisms with Arabidopsis but differs in environmental drivers.Plant physiology · 2024Article
- Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae.Plant communications · 2024Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large genomic data sets are becoming the new normal in phylogenetic research, but the identification of true orthologous genes and the exclusion of problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with ortholog detection through genomic synteny in a data set of 11 representative diploid Brassicaceae whole-genome sequences spanning the entire phylogenetic space. Then, we evaluated the resulting gene sets regarding gene number, functional annotation, and gene and species tree resolution. Finally, we used the syntenic gene sets for comparative genomics and ancestral genome analysis. The use of synteny resulted in considerably more orthologs and also allowed us to reliably identify paralogs. Surprisingly, we did not detect notable differences between species trees reconstructed from syntenic orthologs when compared with other gene sets, including the Angiosperms353 set and a Brassicaceae-specific target enrichment gene set. However, the synteny data set comprised a multitude of gene functions, strongly suggesting that this method of marker selection for phylogenomics is suitable for studies that value downstream gene function analysis, gene interaction, and network studies. Finally, we present the first ancestral genome reconstruction for the Core Brassicaceae which predating the Brassicaceae lineage diversification ∼25 million years ago.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.