Table 1.
General statistics obtained for S. lycopersicoides genome assembly using ABySS.
Fig 1.
Circular view of the S. lycopersicoides genome assembly used for sequence variation mining.
The outermost to the innermost rings represent the 12 representative pseudomolecules, contigs (≥500 bp), transposable elements, SSRs, and indels and SNPs. Color keys for the transposable elements and SSRs indicate the density of the repeats. The more intense the color, the more repetitive sequences in the pseudomolecule position. The indel and SNP density was determined based on sequence alignments between S. lycopersicoides and tomato. All tracks show binned data with a window size of 1 Mb.
Fig 2.
Distribution of the different (A) SSR motifs and (B) SSR lengths throughout the draft assembly of S. lycopersicoides based on GMATA data.
Table 2.
SSRs mined from assembled Solanum lycopersicoides genome using GMATA software.
Table 3.
Summary of primer pairs designed by Primer3 of GMATA based on the SSRs mined.
Table 4.
Target amplification and cross-species transferability of S. lycopersicoides-specific SSR and indel markers.
Fig 3.
Chromosome distribution of S. lycopersicoides-specific SSR and indel markers.
Map position of all the markers is based on their position in tomato chromosomes. Red markers are SSRs and blue markers are indels. Red triangle = centromere.
Fig 4.
Cross-species amplification of S. lycopersicoides-specific markers in other members of Solanaceae.
One SSR and one indel marker for each chromosome were used to amplify targets in tomato, silverleaf nightshade, eggplant and pepper. SLM = SSR marker, SLYD = indel marker, 1 = S. lycopersicoides, 2 = tomato, 3 = silverleaf nightshade, 4 = eggplant, 5 = pepper, L = 100 bp-ladder.