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Novel insights into karyotype evolution and whole genome duplications in legumes

https://doi.org/10.1101/099044
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Polyploidy and Genome Evolution
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Phytochemical dictionary of the leguminosae
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The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
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Genome sequence of the palaeopolyploid soybean
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The Medicago genome provides insight into the evolution of rhizobial symbioses
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Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
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Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement
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A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms
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Genome sequence of mungbean and insights into evolution within Vigna species
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Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species
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Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
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Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
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SiZer for Exploration of Structures in Curves
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Placing Paleopolyploidy in Relation to Taxon Divergence: A Phylogenetic Analysis in Legumes Using 39 Gene Families
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Evolutionary Rates Analysis of Leguminosae Implicates a Rapid Diversification of Lineages during the Tertiary
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Hive plots--rational approach to visualizing networks
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DAGchainer: a tool for mining segmental genome duplications and synteny
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Clustal W and Clustal X version 2.0
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Genome Structure of the Legume, Lotus japonicus
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MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes
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PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
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LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes
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T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks
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The EMBL-EBI bioinformatics web and programmatic tools framework
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Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps
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Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1101/gr.109744.110openalex-snapshot
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
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Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
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A Medaka Gene Map: The Trace of Ancestral Vertebrate Proto-Chromosomes Revealed by Comparative Gene Mapping
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Comparative genome analyses of Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A. thaliana
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Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids
inferredcites →https://doi.org/10.1105/tpc.021345openalex-snapshot
Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes[W]
inferredcites →https://doi.org/10.1105/tpc.160710openalex-snapshot
Two Genomes Are Better Than One: Widespread Paleopolyploidy in Plants and Evolutionary Effects
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An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III
inferredcites →https://doi.org/10.1111/j.1469-8137.2007.02039.xopenalex-snapshot
The Medicago truncatula reference accession A17 has an aberrant chromosomal configuration
inferredcites →https://doi.org/10.1111/j.1755-0998.2011.03002.xopenalex-snapshot
Comparison of random and SSR‐enriched shotgun pyrosequencing for microsatellite discovery and single multiplex PCR optimization inAcacia harpophyllaF. Muell. Ex Benth
inferredcites →https://doi.org/10.1111/pbi.12371openalex-snapshot
A SNP ‐based consensus genetic map for synteny‐based trait targeting in faba bean (Vicia faba L.)
inferredcites →https://doi.org/10.1111/tpj.12173openalex-snapshot
A draft genome sequence of the pulse crop chickpea ( C icer arietinum L.)
inferredcites →https://doi.org/10.1126/science.1128691openalex-snapshot
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
inferredcites →https://doi.org/10.1139/g04-047openalex-snapshot
Mining EST databases to resolve evolutionary events in major crop species
inferredcites →https://doi.org/10.1145/2016741.2016785openalex-snapshot
The CIPRES science gateway
inferredcites →https://doi.org/10.1146/annurev-arplant-042110-103754openalex-snapshot
Genome-Enabled Insights into Legume Biology
inferredcites →https://doi.org/10.1146/annurev-ecolsys-102710-145119openalex-snapshot
The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates
inferredcites →https://doi.org/10.1186/1471-2105-10-192openalex-snapshot
OrthoClusterDB: an online platform for synteny blocks
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-12-102openalex-snapshot
Screening synteny blocks in pairwise genome comparisons through integer programming
inferredcites →https://doi.org/10.1186/1471-2156-13-15openalex-snapshot
A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts
inferredcites →https://doi.org/10.1186/1471-2164-10-45openalex-snapshot
An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes.
inferredcites →https://doi.org/10.1186/1471-2164-12-101openalex-snapshot
Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa
inferredcites →https://doi.org/10.1186/1471-2164-12-342openalex-snapshot
Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing
inferredcites →https://doi.org/10.1186/1471-2164-13-726openalex-snapshot
Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data
inferredcites →https://doi.org/10.1186/1471-2164-14-192openalex-snapshot
Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil
inferredcites →https://doi.org/10.1186/1471-2164-15-238openalex-snapshot
High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species
inferredcites →https://doi.org/10.1186/1471-2164-15-312openalex-snapshot
An improved genome release (version Mt4.0) for the model legume Medicago truncatula
inferredcites →https://doi.org/10.1186/s12864-015-1291-0openalex-snapshot
Species-specific duplications driving the recent expansion of NBS-LRR genes in five Rosaceae species
inferredcites →https://doi.org/10.1371/journal.pone.0011630openalex-snapshot
Polyploidy Did Not Predate the Evolution of Nodulation in All Legumes
inferredcites →https://doi.org/10.1534/g3.111.000349openalex-snapshot
Translational Genomics in Legumes Allowed Placing In Silico 5460 Unigenes on the Pea Functional Map and Identified Candidate Genes in Pisum sativum L.
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Comparative Genetic Mapping and Discovery of Linkage Disequilibrium Across Linkage Groups in White Clover (Trifolium repensL.)
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SiZer for Exploration of Structures in Curves
inferredcites →https://doi.org/10.3389/fpls.2014.00676openalex-snapshot
Genetic mapping of legume orthologs reveals high conservation of synteny between lentil species and the sequenced genomes of Medicago and chickpea
inferredcites →https://doi.org/10.3732/ajb.0800079openalex-snapshot
Polyploidy and angiosperm diversification
inferredcites →https://doi.org/10.3732/ajb.1200380openalex-snapshot
Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early‐branching lineages
inferredcites →https://doi.org/10.3835/plantgenome2011.06.0019openalex-snapshot
Cowpea-Soybean Synteny Clarified through an Improved Genetic Map

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s00606-020-01691-7openalex-snapshot
Interfamilial relationships in order Fabales: new insights from the nuclear regions sqd1 and 26S rDNA
inferred← citeshttps://doi.org/10.1007/s40415-018-0449-9openalex-snapshot
Cytomolecular analysis of species in the Peltophorum clade (Caesalpinioideae, Leguminosae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108281openalex-snapshot
Plastid-Nuclear Coevolution of Ribosomal Protein Genes in Papilionoid Legumes
inferred← citeshttps://doi.org/10.1093/sysbio/syaa041openalex-snapshot
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event
inferred← citeshttps://doi.org/10.1371/journal.pgen.1009249openalex-snapshot
Lotus japonicus karrikin receptors display divergent ligand-binding specificities and organ-dependent redundancy
inferred← citeshttps://doi.org/10.1590/1678-4685-gmb-2018-0250openalex-snapshot
Low cytomolecular diversification in the genus Stylosanthes Sw. (Papilionoideae, Leguminosae)
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