Abstract
In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500–1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of Mammillaria. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was M. solisioides (256), whereas M. pectinifera contained the highest amount of SSRs (84). In contrast, M. zephyranthoides contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.
Highlights
The analysis of DNA variation is critical when studying biological patterns in evolutionary biology, conservation and molecular ecology
We focused on studying complete chloroplast genomes, since the comparative genomics perspective allows for a better identification of deep structural changes and punctual mutation changes that may provide insight into evolutionary processes
After analyzing the complete chloroplast genomes of seven Mammillaria species, we estimated the different levels of molecular variation among the repeated sequences (RSs), short sequence repeats (SSRs) and divergent DNA sequences in the different levels ofthe molecular among the RSs, SSRs Mammillaria and divergent
Summary
The analysis of DNA variation is critical when studying biological patterns in evolutionary biology, conservation and molecular ecology. The comparison of complete sequences of chloroplast DNA (cpDNA) has enabled the interpretation of its evolutionary history [1] by tracking variations in genes related to the contemporary cyanobacteria. Genes are not randomly arranged in the circular molecule of cpDNA contained in each chloroplast. On the contrary, they are often located in a relatively conserved position that can be associated to each taxonomic group. The information used for evolutionary studies varies depending on the type of plant
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