Table 1.
Variation in repeat length among genomic globe artichoke perfect and imperfect SSRs.
Fig 1.
Perfect SSRs in the globe artichoke genome.
(A) The frequency of repeat classes (class I >30 nt, class II 20–30 nt, class III <20 nt. (B) The distribution of motif type within each class. (C) The relative frequency of motifs.
Fig 2.
The distribution of the major repeat types in the globe artichoke genome.
Table 2.
The chromosome-by-chromosome distribution of perfect, compound and imperfect SSRs.
Fig 3.
The intra-chromosomal distribution of SSRs.
(A) The comparison of perfect SSR number/density. (B) The frequency of mono- to hexanucleotide motifs in the 17 linkage groups of globe artichoke.
Fig 4.
The distribution of SSRs along each of the 17 globe artichoke linkage groups.
The orange trend line tracks gene density, and the boxed black trend line the density of perfect SSRs.
Fig 5.
Circos diagram depicting the chromosome-scale SSR distribution (perfect).
In green, from outside to inside: all SSRs, SSRs formed by mono-, di-, tri-, tetra-, penta- and hexanucleotides. In red: gene density. In blue: repeat density.
Table 3.
Variation in repeat length among genic globe artichoke perfect and imperfect SSRs.
Fig 6.
Functional analysis (gene ontology) of the set of globe artichoke genes containing SSRs.
(A) GO categorization. The blue bars indicate input genes, while the green bars indicate background genes. (B) REVIGO summary of “biological process”, “molecular function” and “cellular component” enriched terms. The bubble size is proportional to the log10 (p value) of enrichment analyses and its color is also a function of log10(p value) of enrichment analyses (blue: low, -red: high p value). The x and y axes reflect semantic similarity according to the REVIGO algorithm (similar GO terms appear close together).
Fig 7.
Work flow for the CyMSatDB user.
Fig 8.
A worked example of an SSR search and primer design using CyMSatDB.
(A) Settings given for chromosome selection and SSR search. (B) The SSR output and settings given for the design of primers. (C) Suggested primers and the downloading of the result.
Table 4.
A comparative survey of perfect SSRs across 15 plant species.
Fig 9.
The representation of different SSR motifs across 15 plant genomes.