ArticleAnnals of botany2019
Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus.
Article in Annals of botany, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution.Plant biotechnology journal · 2026Article
- Comparative Genetic Diversity and Population Structure of WildPlants (Basel, Switzerland) · 2026Article
- Genotyping-by-Sequencing Reveals Marker-Based Genome Stability in Tetraploid Clementines for Triploid Breeding.Plants (Basel, Switzerland) · 2026Article
- Pollen performance under controlled temperatures and chromosome stability of diploid and tetraploid citrus.BMC plant biology · 2025Article
- Low-density SNP marker sets for genetic variation analysis and variety identification in cultivated citrus.BMC plant biology · 2025Article
- Comparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within theFrontiers in plant science · 2024Article
- Biological effects of bergamot and its potential therapeutic use as an anti-inflammatory, antioxidant, and anticancer agent.Pharmaceutical biology · 2023Review
- Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks.Plants (Basel, Switzerland) · 2023Article
- Genotyping by Sequencing for SNP-Based Linkage Analysis and the Development of KASPar Markers for Male Sterility and Polyembryony in Citrus.Plants (Basel, Switzerland) · 2023Article
- ConservingPlants (Basel, Switzerland) · 2023Article
- Article
- GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics.Database : the journal of biological databases and curation · 2022Article
- When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships.Molecular ecology resources · 2022Article
- Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas.Frontiers in plant science · 2022Article
- Insight into resistance to 'Frontiers in plant science · 2022Article
- Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica).Plant methods · 2021Article
- Citrus Genetic Transformation: An Overview of the Current Strategies and Insights on the New Emerging Technologies.Frontiers in plant science · 2021Review
- Specific Physiological and Anatomical Traits Associated With Polyploidy and Better Detoxification Processes Contribute to Improved Huanglongbing Tolerance of the Persian Lime Compared With the Mexican Lime.Frontiers in plant science · 2021Article
- Article
- Preferential Disomic Segregation andFrontiers in plant science · 2020Article
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9 authors.
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Abstract
BACKGROUND AND
aimsReticulate evolution, coupled with reproductive features limiting further interspecific recombinations, results in admixed mosaics of large genomic fragments from the ancestral taxa. Whole-genome sequencing (WGS) data are powerful tools to decipher such complex genomes but still too costly to be used for large populations. The aim of this work was to develop an approach to infer phylogenomic structures in diploid, triploid and tetraploid individuals from sequencing data in reduced genome complexity libraries. The approach was applied to the cultivated Citrus gene pool resulting from reticulate evolution involving four ancestral taxa, C. maxima, C. medica, C. micrantha and C. reticulata.
methodsA genotyping by sequencing library was established with the restriction enzyme ApeKI applying one base (A) selection. Diagnostic single nucleotide polymorphisms (DSNPs) for the four ancestral taxa were mined in 29 representative varieties. A generic pipeline based on a maximum likelihood analysis of the number of read data was established to infer ancestral contributions along the genome of diploid, triploid and tetraploid individuals. The pipeline was applied to 48 diploid, four triploid and one tetraploid citrus accessions. KEY
resultsAmong 43 598 mined SNPs, we identified a set of 15 946 DSNPs covering the whole genome with a distribution similar to that of gene sequences. The set efficiently inferred the phylogenomic karyotype of the 53 analysed accessions, providing patterns for common accessions very close to that previously established using WGS data. The complex phylogenomic karyotypes of 21 cultivated citrus, including bergamot, triploid and tetraploid limes, were revealed for the first time.
conclusionsThe pipeline, available online, efficiently inferred the phylogenomic structures of diploid, triploid and tetraploid citrus. It will be useful for any species whose reproductive behaviour resulted in an interspecific mosaic of large genomic fragments. It can also be used for the first generations of interspecific breeding schemes.
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