Fig 1.
Workflow to identify diagnostic markers of C. reticulata/C. maxima differentiation from GBS reads.
Table 1.
Polymorphisms mined from GBS data on 55 citrus varieties along the nine chromosomes.
Table 2.
Polymorphisms (SNPs and Indels) mined from GBS data on 11 mandarin and 6 pummelo varieties along the nine chromosomes; intra horticultural group diversity.
Table 3.
Polymorphisms (SNPs and Indels) mined from GBS data on 11 mandarin and 6 pummelo varieties along the nine chromosomes; global diversity and inter-horticultural group differentiation.
Fig 2.
NJ tree analysis of the representatives of pummelos and mandarins.
Fig 3.
Distribution of heterozygosity computed from average values of successive windows of 100 polymorphisms along the genome.
(the frequency y represent the proportion of genome fragments (windows) with Ho between x and x + 0.05).
Fig 4.
Identification of interspecific introgressions in accessions representative of ancestral taxa: Example of the “Ponkan” variety for chromosome II.
A: observed heterozygosity (gray), similarity with centroids of mandarins (red) and pummelos (blue); windows of 20 markers (GST1>0.5) B: proportion of C. reticulata/C. maxima diagnostic polymorphisms in homozygosity for C. reticulata (red), for C. maxima (blue) and interspecific heterozygosity (purple). C: deduced phylogenomic structure of Ponkan mandarin chromosome II (red: C. reticulata homozygosity; blue: C. maxima homozygosity; purple: C. maxima/C. reticulata heterozygosity).
Fig 5.
Distribution along the genome of diagnostic polymorphisms (red), whole set of polymorphisms (blue), and genes (green); relative frequency by successive windows of 1 Mb for each chromosome.
Table 4.
Distribution of diagnostic polymorphisms among the nine chromosomes.
Fig 6.
Factorial analysis from the dissimilarity table for 54 varieties, 30,943 markers.
Fig 7.
Overall proportion of C. maxima and C. reticulata admixture estimated from diagnostic polymorphisms for the 55 varieties.
Red: C. reticulata; blue: C. maxima.
Fig 8.
Comparison of “phylogenomic karyotypes” inferred from GBS data (A) and WGS data (B; from Wu et al. data (15)] for the “Ponkan” mandarin, the “Chandler” pummelo, the haploid clementine used to establish the citrus reference sequence, the diploid “Nules” clementine, the “Washington Navel” sweet orange and the sour orange.
Red: C. reticulata homozygosity; blue: C. maxima homozygosity; purple: C. reticulata/C. maxima heterozygosity; grey: undetermined.
Fig 9.
“Phylogenomic karyotypes” of the citrus accessions used as a reference for C. maxima and C. reticulata ancestral taxa.
Red: C. reticulata homozygosity; blue: C. maxima homozygosity; purple: C. reticulata/C. maxima heterozygosity; grey: undetermined.
Fig 10.
“Phylogenomic karyotypes” of 38 citrus varieties derived from the C.reticulata/C. maxima gene pools.
Red: C. reticulata homozygosity; blue: C. maxima homozygosity; purple: C. reticulata/C. maxima heterozygosity; grey: undetermined.