A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species
Background and Aims: Despite differences in morphology, the genera representing ‘true citrus fruit trees’ are sexually compatible, and their phylogenetic relationships remain unclear. Most of the important commercial ‘species’ of Citrus are believed to be of interspecific origin. By studying polymo...
| Main Authors: | , , , , , , , |
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| Format: | article |
| Language: | Inglés |
| Published: |
2017
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| Online Access: | http://hdl.handle.net/20.500.11939/5246 https://academic.oup.com/aob/article/111/1/1/181653 |
| _version_ | 1855032248054579200 |
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| author | García-Lor, Andrés Curk, Franck Snoussi-Trifa, Hager Morillon, Raphael Ancillo, Gema Luro, Francois Navarro, Luis Ollitrault, Patrick |
| author_browse | Ancillo, Gema Curk, Franck García-Lor, Andrés Luro, Francois Morillon, Raphael Navarro, Luis Ollitrault, Patrick Snoussi-Trifa, Hager |
| author_facet | García-Lor, Andrés Curk, Franck Snoussi-Trifa, Hager Morillon, Raphael Ancillo, Gema Luro, Francois Navarro, Luis Ollitrault, Patrick |
| author_sort | García-Lor, Andrés |
| collection | ReDivia |
| description | Background and Aims:
Despite differences in morphology, the genera representing ‘true citrus fruit trees’ are sexually compatible, and their phylogenetic relationships remain unclear. Most of the important commercial ‘species’ of Citrus are believed to be of interspecific origin. By studying polymorphisms of 27 nuclear genes, the average molecular differentiation between species was estimated and some phylogenetic relationships between ‘true citrus fruit trees’ were clarified.
Methods:
Sanger sequencing of PCR-amplified fragments from 18 genes involved in metabolite biosynthesis pathways and nine putative genes for salt tolerance was performed for 45 genotypes of Citrus and relatives of Citrus to mine single nucleotide polymorphisms (SNPs) and indel polymorphisms. Fifty nuclear simple sequence repeats (SSRs) were also analysed.
Key Results:
A total of 16 238 kb of DNA was sequenced for each genotype, and 1097 single nucleotide polymorphisms (SNPs) and 50 indels were identified. These polymorphisms were more valuable than SSRs for inter-taxon differentiation. Nuclear phylogenetic analysis revealed that Citrus reticulata and Fortunella form a cluster that is differentiated from the clade that includes three other basic taxa of cultivated citrus (C. maxima, C. medica and C. micrantha). These results confirm the taxonomic subdivision between the subgenera Metacitrus and Archicitrus. A few genes displayed positive selection patterns within or between species, but most of them displayed neutral patterns. The phylogenetic inheritance patterns of the analysed genes were inferred for commercial Citrus spp.
Conclusions:
Numerous molecular polymorphisms (SNPs and indels), which are potentially useful for the analysis of interspecific genetic structures, have been identified. The nuclear phylogenetic network for Citrus and its sexually compatible relatives was consistent with the geographical origins of these genera. The positive selection observed for a few genes will help further works to analyse the molecular basis of the variability of the associated traits. This study presents new insights into the origin of C. sinensis. |
| format | article |
| id | ReDivia5246 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | ReDivia52462025-04-25T14:45:45Z A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species García-Lor, Andrés Curk, Franck Snoussi-Trifa, Hager Morillon, Raphael Ancillo, Gema Luro, Francois Navarro, Luis Ollitrault, Patrick Background and Aims: Despite differences in morphology, the genera representing ‘true citrus fruit trees’ are sexually compatible, and their phylogenetic relationships remain unclear. Most of the important commercial ‘species’ of Citrus are believed to be of interspecific origin. By studying polymorphisms of 27 nuclear genes, the average molecular differentiation between species was estimated and some phylogenetic relationships between ‘true citrus fruit trees’ were clarified. Methods: Sanger sequencing of PCR-amplified fragments from 18 genes involved in metabolite biosynthesis pathways and nine putative genes for salt tolerance was performed for 45 genotypes of Citrus and relatives of Citrus to mine single nucleotide polymorphisms (SNPs) and indel polymorphisms. Fifty nuclear simple sequence repeats (SSRs) were also analysed. Key Results: A total of 16 238 kb of DNA was sequenced for each genotype, and 1097 single nucleotide polymorphisms (SNPs) and 50 indels were identified. These polymorphisms were more valuable than SSRs for inter-taxon differentiation. Nuclear phylogenetic analysis revealed that Citrus reticulata and Fortunella form a cluster that is differentiated from the clade that includes three other basic taxa of cultivated citrus (C. maxima, C. medica and C. micrantha). These results confirm the taxonomic subdivision between the subgenera Metacitrus and Archicitrus. A few genes displayed positive selection patterns within or between species, but most of them displayed neutral patterns. The phylogenetic inheritance patterns of the analysed genes were inferred for commercial Citrus spp. Conclusions: Numerous molecular polymorphisms (SNPs and indels), which are potentially useful for the analysis of interspecific genetic structures, have been identified. The nuclear phylogenetic network for Citrus and its sexually compatible relatives was consistent with the geographical origins of these genera. The positive selection observed for a few genes will help further works to analyse the molecular basis of the variability of the associated traits. This study presents new insights into the origin of C. sinensis. 2017-06-01T10:11:58Z 2017-06-01T10:11:58Z 2013 JAN article Garcia-Lor, A., Curk, F., Snoussi-Trifa, Hager, Morillon, R., Ancillo, G., Luro, Francois, Navarro, L., Ollitrault, P. (2013). A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae), and the origin of cultivated species. Annals of Botany, 111(1), 1-19. 0305-7364 http://hdl.handle.net/20.500.11939/5246 10.1093/aob/mcs227 https://academic.oup.com/aob/article/111/1/1/181653 en openAccess Impreso |
| spellingShingle | García-Lor, Andrés Curk, Franck Snoussi-Trifa, Hager Morillon, Raphael Ancillo, Gema Luro, Francois Navarro, Luis Ollitrault, Patrick A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species |
| title | A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species |
| title_full | A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species |
| title_fullStr | A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species |
| title_full_unstemmed | A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species |
| title_short | A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species |
| title_sort | nuclear phylogenetic analysis snps indels and ssrs deliver new insights into the relationships in the true citrus fruit trees group citrinae rutaceae and the origin of cultivated species |
| url | http://hdl.handle.net/20.500.11939/5246 https://academic.oup.com/aob/article/111/1/1/181653 |
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