Background: Structural descriptions of complete genomes have elucidated evolutionary processes in angiosperms. In Cactaceae (Caryophyllales), a high structural diversity of the chloroplast genome has been identified within and among genera. In this study, we assembled the first mitochondrial genome (mtDNA) for the short-globose cactus Mammillaria huitzilopochtli. For comparative purposes, we used the published genomes of 19 different angiosperms and the gymnosperm Cycas taitungensis as an external group for phylogenetic issues. Results: The mtDNA of M. huitzilopochtli was assembled into one linear chromosome of 2,052,004 bp, in which 65 genes were annotated. These genes account for 57,606 bp including 34 protein-coding genes (PCGs), 27 tRNAs, and three rRNAs. In the non-coding sequences, repeats were abundant, with a total of 4,550 (179,215 bp). In addition, five complete genes (psaC and four tRNAs) of chloroplast origin were documented. Negative selection was estimated for most (23) of the PCGs. The phylogenetic tree showed a topology consistent with previous analyses based on the chloroplast genome. Conclusions: The number and type of genes contained in the mtDNA of M. huitzilopochtli were similar to those reported in 19 other angiosperm species, regardless of their phylogenetic relationships. Although other Caryophyllids exhibit strong differences in structural arrangement and total size of mtDNA, these differences do not result in an increase in the typical number and types of genes found in M. huitzilopochtli. We concluded that the total size of mtDNA in angiosperms increases by the lengthening of the non-coding sequences rather than a significant gain of coding genes.

The complete sequence of chloroplast genome (cpDNA) has been documented for single large columnar species of Cactaceae, lacking inverted repeats (IRs). We sequenced cpDNA for seven species of the short-globose cacti of Mammillaria and de novo assembly revealed three novel structures in land plants. These structures have a large single copy (LSC) that is 2.5 to 10 times larger than the small single copy (SSC), and two IRs that contain strong differences in length and gene composition. Structure 1 is distinguished by short IRs of <1 kb composed by rpl23-trnI-CAU-ycf2; with a total length of 110,189 bp and 113 genes. In structure 2, each IR is approximately 7.2 kb and is composed of 11 genes and one Intergenic Spacer-(psbK-trnQ)-trnQ-UUG-rps16-trnK-UUU-matK-trnK-UUU-psbA-trnH-GUG-rpl2-rpl23-trnI-CAU-ycf2; with a total size of 116,175 bp and 120 genes. Structure 3 has divergent IRs of approximately 14.1 kb, where IRA is composed of 20 genes: psbA-trnH-GUG-rpl23-trnI-CAU-ycf2-ndhB-rps7-rps12-trnV-GAC-rrn16-ycf68-trnI-GAU-trnA-AGC-rrn23-rrn4.5-rrn5-trnR-ACG-trnN-GUU-ndhF-rpl32; and IRB is identical to the IRA, but lacks rpl23. This structure has 131 genes and, by pseudogenization, it is shown to have the shortest cpDNA, of just 107,343 bp. Our findings show that Mammillaria bears an unusual structural diversity of cpDNA, which supports the elucidation of the evolutionary processes involved in cacti lineages.

The Military Macaw (Ara militaris) is a globally threatened species with a fragmented distribution, and assessing the genetics of populations could help identify conservation units. Nine microsatellites were used to analyze 86 samples in seven localities along the Sierra Madre Occidental, the Sierra Madre del Sur, and the Sierra Madre Oriental in Mexico. Results showed that the Military Macaw has moderate levels of genetic diversity, similar to that found in other macaw species in Latin America. This species shows a high genetic structure; we find a genetic break between localities separated by the Central Plateau and the Trans-Mexican Volcanic Belt, which serve as geographic barriers. However, the locations within each genetic group are not genetically differentiated. It was observed that three locations of the Military Macaw have excess homozygotes, which could indicate a small effective size of the population and in combination with genetic isolation could increase the risk of extinction of the species. We propose two genetic groups for the species, the first comprising localities in the Sierra Madre Occidental and the Sierra Madre del Sur, and the second comprising localities of the Sierra Madre Oriental. According to the genetic differentiation, which was significant between the physiographic regions, and the unique allelic richness shown in this study, these two groups should be considered as independent conservation units. We strongly recommend the conservation and restoration of the natural habitats of the Military Macaw to maintain and increase the size of its population and recover and expand its original geographical distribution.

Habitat characterization and modeling of the potential distribution of the Military Macaw (Ara militaris) in Mexico