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Forage grasses belonging to four species of Urochloa (previously included in Brachiaria) represent 85% of planted pastures in Brazil , extending over 115 Mha . ruziziensis has grown due to its recent use in crop-livestock integrated systems, which could restore 18 Mha of degraded pastures in the next few years . Inclusion of species in either Brachiaria or Urochloa has changed over time , and many research groups - forage breeders in particular - still refer to them as Brachiaria. Chloroplast SSRs usually show polymorphism, and are generally composed of poly-A or poly-T sequences of approximately 20 bp [33,34,35]. Genomic libraries were prepared according to manufacturer’s instructions (Illumina, San Diego, CA, USA).
humidicola are the main species used as forages, interest in U. humidicola are predominantly polyploid and apomictic, U. The genus includes 110 species, and it is the largest of subtribe Melinidinae . Chloroplast microsatellites or SSRs (Simple Sequence Repeats) can be useful tools for the conservation and use of plant genetic resources.
Predicted coding regions were manually adjusted for their start and stop codons, after inspection and comparison with available chloroplast genomes in tribe Paniceae.
Corrections were made using Sequin ( and Artemis .
Examples in recent literature include species of bamboo , coconut palm  and the Lolium-Festuca complex .
Complete chloroplast genomes from nine species in tribe Paniceae were compared regarding their levels of sequence conservation, using the Multi-LAGAN alignment program  included in m VISTA [48, 49], with default parameters. humidicola was used as a reference for these alignments. oligobrachiata , a pattern that in part has not been confirmed in phylogenies based on molecular data. Structural and sequence variations in chloroplasts include single-nucleotide polymorphisms (SNPs), insertion-deletions (In Dels), as well as microsatellites. Use of cp DNA in phylogenetic analyses is also favored by the abundance of cp DNA after DNA extraction from leaf tissue [29, 30], by its usually maternal inheritance , and by the absence of recombination .Kumar S, Filipski A, Swarna V, Walker A, & Hedges SB. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Proceedings of the National Academy of Sciences 1842-18847. Philosophical Transactions of the Royal Society of London B 377-1483.