Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Ahmed, Dalel, Comte, Aurore, Curk, Franck, Costantino, Gilles, Luro, François, Dereeper, Alexis, Mournet, Pierre, Froelicher, Yann, Ollitrault, Patrick
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612944/
https://www.ncbi.nlm.nih.gov/pubmed/30924905
http://dx.doi.org/10.1093/aob/mcz029
_version_ 1783432966510215168
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
collection PubMed
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 Online
Article
Text
id pubmed-6612944
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-66129442019-07-12 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 Ann Bot Original Articles 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. Oxford University Press 2019-07 2019-03-29 /pmc/articles/PMC6612944/ /pubmed/30924905 http://dx.doi.org/10.1093/aob/mcz029 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of the Annals of Botany Company. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Articles
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
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_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_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_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
topic Original Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612944/
https://www.ncbi.nlm.nih.gov/pubmed/30924905
http://dx.doi.org/10.1093/aob/mcz029
work_keys_str_mv AT ahmeddalel genotypingbysequencingcanrevealthecomplexmosaicgenomesingenepoolsresultingfromreticulateevolutionacasestudyindiploidandpolyploidcitrus
AT comteaurore genotypingbysequencingcanrevealthecomplexmosaicgenomesingenepoolsresultingfromreticulateevolutionacasestudyindiploidandpolyploidcitrus
AT curkfranck genotypingbysequencingcanrevealthecomplexmosaicgenomesingenepoolsresultingfromreticulateevolutionacasestudyindiploidandpolyploidcitrus
AT costantinogilles genotypingbysequencingcanrevealthecomplexmosaicgenomesingenepoolsresultingfromreticulateevolutionacasestudyindiploidandpolyploidcitrus
AT lurofrancois genotypingbysequencingcanrevealthecomplexmosaicgenomesingenepoolsresultingfromreticulateevolutionacasestudyindiploidandpolyploidcitrus
AT dereeperalexis genotypingbysequencingcanrevealthecomplexmosaicgenomesingenepoolsresultingfromreticulateevolutionacasestudyindiploidandpolyploidcitrus
AT mournetpierre genotypingbysequencingcanrevealthecomplexmosaicgenomesingenepoolsresultingfromreticulateevolutionacasestudyindiploidandpolyploidcitrus
AT froelicheryann genotypingbysequencingcanrevealthecomplexmosaicgenomesingenepoolsresultingfromreticulateevolutionacasestudyindiploidandpolyploidcitrus
AT ollitraultpatrick genotypingbysequencingcanrevealthecomplexmosaicgenomesingenepoolsresultingfromreticulateevolutionacasestudyindiploidandpolyploidcitrus