Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus
Background and Aims: Reticulate 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. Methods : A 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 Results: Among 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. Conclusions: The 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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Subjects: | F30 - Génétique et amélioration des plantes, Citrus, lime, génotype, pool de gènes, phylogénie, amélioration génétique, caryotype, évolution, http://aims.fao.org/aos/agrovoc/c_1637, http://aims.fao.org/aos/agrovoc/c_4341, http://aims.fao.org/aos/agrovoc/c_3225, http://aims.fao.org/aos/agrovoc/c_3212, http://aims.fao.org/aos/agrovoc/c_13325, http://aims.fao.org/aos/agrovoc/c_49902, http://aims.fao.org/aos/agrovoc/c_32486, http://aims.fao.org/aos/agrovoc/c_2745, http://aims.fao.org/aos/agrovoc/c_1907, http://aims.fao.org/aos/agrovoc/c_3081, |
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dig-cirad-fr-5921882024-01-29T01:53:18Z http://agritrop.cirad.fr/592188/ http://agritrop.cirad.fr/592188/ Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus. Ahmed Dalel, Comte Aurore, Curk Franck, Costantino Gilles, Luro François, Dereeper Alexis, Mournet Pierre, Froelicher Yann, Ollitrault Patrick. 2019. Annals of Botany, 123 (7) : 1231-1251.https://doi.org/10.1093/aob/mcz029 <https://doi.org/10.1093/aob/mcz029> Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus Ahmed, Dalel Comte, Aurore Curk, Franck Costantino, Gilles Luro, François Dereeper, Alexis Mournet, Pierre Froelicher, Yann Ollitrault, Patrick eng 2019 Annals of Botany F30 - Génétique et amélioration des plantes Citrus lime génotype pool de gènes phylogénie amélioration génétique caryotype évolution http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_4341 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_32486 http://aims.fao.org/aos/agrovoc/c_2745 Corse France http://aims.fao.org/aos/agrovoc/c_1907 http://aims.fao.org/aos/agrovoc/c_3081 Background and Aims: Reticulate 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. Methods : A 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 Results: Among 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. Conclusions: The 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/592188/7/mcz029.pdf text Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1093/aob/mcz029 10.1093/aob/mcz029 info:eu-repo/semantics/altIdentifier/doi/10.1093/aob/mcz029 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1093/aob/mcz029 |
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F30 - Génétique et amélioration des plantes Citrus lime génotype pool de gènes phylogénie amélioration génétique caryotype évolution http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_4341 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_32486 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_1907 http://aims.fao.org/aos/agrovoc/c_3081 F30 - Génétique et amélioration des plantes Citrus lime génotype pool de gènes phylogénie amélioration génétique caryotype évolution http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_4341 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_32486 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_1907 http://aims.fao.org/aos/agrovoc/c_3081 |
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F30 - Génétique et amélioration des plantes Citrus lime génotype pool de gènes phylogénie amélioration génétique caryotype évolution http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_4341 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_32486 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_1907 http://aims.fao.org/aos/agrovoc/c_3081 F30 - Génétique et amélioration des plantes Citrus lime génotype pool de gènes phylogénie amélioration génétique caryotype évolution http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_4341 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_32486 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_1907 http://aims.fao.org/aos/agrovoc/c_3081 Ahmed, Dalel Comte, Aurore Curk, Franck Costantino, Gilles Luro, François Dereeper, Alexis Mournet, Pierre Froelicher, Yann Ollitrault, Patrick Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus |
description |
Background and Aims: Reticulate 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. Methods : A 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 Results: Among 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. Conclusions: The 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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes Citrus lime génotype pool de gènes phylogénie amélioration génétique caryotype évolution http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_4341 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_49902 http://aims.fao.org/aos/agrovoc/c_32486 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_1907 http://aims.fao.org/aos/agrovoc/c_3081 |
author |
Ahmed, Dalel Comte, Aurore Curk, Franck Costantino, Gilles Luro, François Dereeper, Alexis Mournet, Pierre Froelicher, Yann Ollitrault, Patrick |
author_facet |
Ahmed, Dalel Comte, Aurore Curk, Franck Costantino, Gilles Luro, François Dereeper, Alexis Mournet, Pierre Froelicher, Yann Ollitrault, Patrick |
author_sort |
Ahmed, Dalel |
title |
Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus |
title_short |
Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus |
title_full |
Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus |
title_fullStr |
Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus |
title_full_unstemmed |
Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus |
title_sort |
genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus |
url |
http://agritrop.cirad.fr/592188/ http://agritrop.cirad.fr/592188/7/mcz029.pdf |
work_keys_str_mv |
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_version_ |
1792499715144679424 |