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.
abstract: OBJECTIVE
  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.
  
  
  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.
authors.affiliation: Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada (Valencia), Spain.
authors.forename: Andres
authors.initials: A
authors.lastname: Garcia-Lor
authors.forename: Franck
authors.initials: F
authors.lastname: Curk
authors.forename: Hager
authors.initials: H
authors.lastname: Snoussi-Trifa
authors.forename: Raphael
authors.initials: R
authors.lastname: Morillon
authors.forename: Gema
authors.initials: G
authors.lastname: Ancillo
authors.forename: François
authors.initials: F
authors.lastname: Luro
authors.forename: Luis
authors.initials: L
authors.lastname: Navarro
authors.forename: Patrick
authors.initials: P
authors.lastname: Ollitrault
mesh_terms: D000383:Agriculture; D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics*; D002957:Citrus / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D006239:Haplotypes / Q000235:genetics; D006824:Hybridization, Genetic; D054643:INDEL Mutation / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D025341:Principal Component Analysis; D014197:Trees / Q000235:genetics*