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Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance.Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in ].The BEP-PACMAD group was constrained as monophyletic during MCMC analysis.Each MCMC run had a chain length of 100,000,000 iterations, with sampling every 10,000 steps.The Kmer Freq and Error Correction routines were run with default parameters (seed length = 17, quality cutoff = 5).Illumina sequencing adapters and low quality reads were eliminated using the CLC trimmer function (default limit = 0.05) (CLC Genomics Workbench 4.1 software, CLC Bio, Aarhus, Denmark).
Bootstrapping was stopped automatically with the auto MRE Majority Rule Criterion, and was followed by ML optimization steps. 3.2.3 , with two independent runs and four chains.
This data was then used to investigate phylogenetic relationships between these species based on complete cp DNA sequences, to estimate their times of divergence and to describe polymorphic cp DNA regions which will be useful for genetic analysis of cv. Genomic libraries were prepared according to manufacturer’s instructions (Illumina, San Diego, CA, USA).
In summary, DNA fragments were obtained by nebulization, and their 3′ ends were added an adenine, to which adapter fragments were ligated.
These regions included 77 protein-coding genes, 31 t RNAs, and 4 r RNAs.
Eleven protein-coding genes and seven t RNAs contained introns.