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. 2019 Oct 11;9(12):3933–3941. doi: 10.1534/g3.119.400529

Figure 2.

Figure 2

A) Maximum Likelihood (ML) phylogenetic tree constructed based on six CT loci (nuclear genes) extracted from the S. chilense LA3111 sample sequenced in this study (in bold; marked with gray rectangle) and previously sequenced S. peruvianum and S. chilense samples. For the samples from whole genome data, sequences were aligned to the S. pennellii reference genome and the sequence data for the CT loci was extracted. Single-gene alignments were concatenated; the resulting super alignment was used as in input for RaxML to construct the ML tree (1000 bootstrap replicates). The branch length is shown as expected number of substitutions per site and bootstrap values are reported on each tree node. S. ochranthum was used as an outgroup. The sequence IDs containing chil and peru represent Sanger sequences from S. chilense and S. peruvianum individuals, respectively, followed by the accession/ individual number. The sequences with IDs containing SRR- and ERR-numbers followed by the accession number were extracted from previously generated whole genome data. B) Phylogeny constructed based on chloroplast SNP data extracted from S. chilense LA3111 (in bold and marked with gray rectangle) and previously sequenced S. peruvianum whole genome sequence data. Chloroplast sequences were aligned to the S. pennellii reference genome. The tree was built using resulting alignments and PhyML (GTR, NNI, BioNJ, 1000 bootstrap replicates). The branch length is shown as expected number of substitutions per site and bootstrap values are reported on each tree node. aSequences of individuals with IDs containing SRR1572692, SRR1572693, SRR1572694, SRR1572695 and SRR1572696 were obtained from Lin et al. (2014). bSequences with IDs containing ERR418084, ERR418094, ERR418097 and ERR418098 originate from 100 Tomato Genome Sequencing Consortium (2014). Individual SRR1572696 was reported as S. chilense in the main text of the paper (ref) and as S. peruvianum in the supplementary, which contain all original data. The original classification of the sequences with IDs ERR418097 and ERR418098 as S. chilense has been later withdrawn from the CGN database.