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Phylogenomic synteny analysis tracks conserved ancient polyploid-derived triplicated genomic blocks across Asteraceae genomes

https://doi.org/10.1101/2025.01.08.631874

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae

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A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae

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Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants

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syntenet: an R/Bioconductor package for the inference and analysis of synteny networks

inferredcites →https://doi.org/10.1093/bioinformatics/btae272openalex-snapshot

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btq110openalex-snapshot

DensiTree: making sense of sets of phylogenetic trees

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DRIMM-Synteny: decomposing genomes into evolutionary conserved segments

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Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

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STAR: ultrafast universal RNA-seq aligner

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TPMCalculator: one-step software to quantify mRNA abundance of genomic features

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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

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Asteraceae as a model system for evolutionary studies: from fossils to genomes

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PKAD: a database of experimentally measured pKa values of ionizable groups in proteins

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Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae

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Anomalous capitulum structure and monoecy may confer flexibility in sex allocation and life history evolution in the Ifloga lineage of paper daisies (Compositae: Gnaphalieae)

inferredcites →https://doi.org/10.3732/ajb.1100256openalex-snapshot

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inferredcites →https://doi.org/10.3732/ajb.1600113openalex-snapshot

Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

inferredcites →https://doi.org/10.3732/apps.1300085openalex-snapshot

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae

inferredcites →https://doi.org/10.53875/capitulum.01.2.04openalex-snapshot

Understanding capitulum development: Gerbera hybrida inflorescence meristem as an experimental system

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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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