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Chromosomal organization, as well as the linear order of genes in cp DNA, vary little in angiosperms [23, 24].

Chloroplast DNA ranges between 120 and 160 kb in size in most plants, with each chloroplast containing multiple copies of a circular chromosome composed of four regions: Large Single Copy (LSC), Small Single Copy (SSC), and two copies of an Inverted Repeat (IRa and IRb) [23].

The k-mer size on CLC Bio assembler was set to 25 bp and the coverage cutoff to 1000X.

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These relationships were maintained when molecular and morphological data were combined. decumbens in a strongly supported clade [5], while U. Analyses of plastid genomes traditionally involve laborious isolation of chloroplasts, extraction and purification of plastid DNA, followed by sequencing and assembly [8,9,10].

Graphic representations of the annotated plastid genomes were obtained with OGDraw [46].

Complete chloroplast genomes from nine species in tribe Paniceae were compared regarding their levels of sequence conservation, using the Multi-LAGAN alignment program [47] included in m VISTA [48, 49], with default parameters. humidicola was used as a reference for these alignments.

Assembly Length Fraction and Similarity parameters were set to 0.5 and 0.8, respectively.

Mismatch, deletion and insertion cost parameters were set to 2, 3 and 3, respectively.

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