PMC

Part of the NJ tree from . Numbers at the nodes are NJ Jackknife support values. Cluster I contains Solanum tarderemotum and Solanum florulentum. In cluster II are Solanum retroflexum and Solanum hirsutum. Cluster III is composed of individuals of Solanum umalilaense

Phylogeny of sect. Lycopersicon. (a) A maximum-likelihood phylogeny from all accessions excluding those with >10% admixture according to STRUCTURE. The species groups are delineated by black lines and labeled. Node labels give bootstrap support. (b) Coalescent phylogeny with all accessions excluding the early diverging “Hirsutum” group. Taxon abbreviations: Solanum arcanum (S.arc), Solanum chmielewskii (S.chm), Solanum corneliomulleri (S.cor), Solanum chilense (S.chi), Solanum galapagense (S.gal), Solanum huaylasense (S.hua), Solanum habrochaites (S.hab), Solanum lycopersicoides (S.lyc), Solanum neorickii (S.neo), Solanum ochranthum (S.och), Solanum pennellii (S.pen), Solanum peruvianum (S.per), Solanum pimpinellifolium (S.pim).

Cladogram of the miR482/2118 genes in the Solanaceae. The consensus Bayesian phylogeny of 67 miR482/2118 genes in seven miR482/2118 orthologous groups (distinguished by the different background colors). Bayesian posterior probabilities are indicated at the branches. Ghr, Gossypium hirsutum (outgroup); Sly, Solanum lycopersicum; Spi, Solanum pimpinellifolium; Spe, Solanum peruvianum; Sco, Solanum corneliomulleri; Sch, Solanum chilense; Soc, Solanum ochranthum; Slc, Solanum lycopersicoides; Stu, Solanum tuberosum; Sme, Solanum melongena; Can, Capsicum annum; Ppe, Physalis peruviana; Nta, Nicotiana tabacum; Nbe, Nicotiana benthamiana; Nsy, Nicotiana sylvestris. Bootstrap values greater than 50 are shown.

Sequence alignment, tertiary structure model and phylogenetic analysis of SpCBF1. a Amino acid sequences alignment. Sequences used for alignment are derived from Solanum tuberosum (StCBF1, ACB45096.1), Solanum commersonii (ScCBF1, ACJ26751.1), Solanum habrochaites (ShCBF1, ACB45087.1), Solanum lycopersicum (SlCBF1, AAS77820.1) Lycopersicon hirsutum (LhCBF1, BAE17131.1), Capsicum annuum (CaCBF1, AAR88363.1), Populus trichocarpa (PtCBF1, ABO48363.1), Arabidopsis thaliana (AtCBF3, ABV27138.1), Arabidopsis thaliana (AtCBF1, AAV80413.1), Arabidopsis thaliana (AtCBF2, AAV80415.1). Boxes indicate conserved regions of CBFs. b Tertiary structure model of SpCBF1. c Phylogenetic analysis. Sequences were aligned by CLUSTALX and analyzed using the MEGA 4.1. Construction was carried out by the parsimony method with 1000 bootstrap replicates and a consensus tree was generated. Database accession numbers are as follows: Solanum pinnatisectum (SpCBF1), Solanum tuberosum (StCBF1, ACB45096.1), Solanum lycopersicum (SlCBF1, AAS77820.1; SlCBF2, AAS77821.1), Solanum commersonii (ScCBF1, ACB45093.1; ScCBF2, ACB45094.1; ScCBF3, ACB45092.1), Solanum habrochaites (ShCBF1, ACB45087.1; ShCBF2, ACB45088.1; ShCBF3, ACB45078.1), Capsicum annuum (CaCBF1, AAR88363.1), Populus trichocarpa (PtCBF1, ABO48363.1), Manihot esculenta (MeCBF1, AFB83707.1), Morus alba var. multicaulis (MamCBF1, AFQ59977.1), Arabidopsis thaliana (AtCBF1, AAV80413.1; AtCBF2, AAV80415.1; AtCBF3, ABV27149.1), Nicotiana tabacum (NtCBF2, ACE73694.1; NtCBF3, ACE73695.1), Betula pendula (BpeCBF1, ADZ23479.1), Betula platyphylla (BplCBF1, ADZ23479.1), Malus domestica (MdCBF1, AAZ20446.1), Camellia sinensis (CsCBF1, AFN93974.1), Gossypium hirsutum (GhCBF1, ABD65473.1), Bruguiera gymnorhiza (BgCBF1, AFU81298.1), Oryza sativa Japonica Grou (OsCBF, NP_001056909.1), Lolium perenne (LpCBF, BAF36838.1), Avena sativa (AsCBF, CAJ21276.1), Aegilops biuncialis (AbCBF2, CBX87016.1)