Sequence_alignments_cp_treegourd

The sequence alignments are shown using the nexus format. This file was applied to estimate chloroplast diversity analysis and construct the haplotype network, performed respectively in DNAsp and POPART softwares. The labels of the samples correspond to the Sequencing_codes in the passport (Table S1)

Genotypes of treegourd in Amazonia

This file was applied to run Structure analyses. The first column shows the labels of the samples which correspond to the Collection_codes in the passport (Table S1). The other columns indicate the 8 nuclear SSR loci analysed. The lines indicate the genotypes. Missing data was indicated as -9

Commandlines

Biinformatic command lines to obtain final VC

replace95bam_and_ref

replace95bam_and_re

De novo assembly Chloroplast of Cenchrus americanus

The software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Zea may

RAM63_reverse_500k

RAM63_reverse_500

De novo assembly Chloroplast of Dioscorea rotundata

The software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Dioscorea elephantipes (EF380353.1

De novo assembly Chloroplast of Digitaria excilis

The software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Pennisetum glaucu

Fastq-files2

Sequence in .fastq file format as listed in S1 Table

Fastq-files1

Sequence in .fastq file format as listed in S1 Table