Complete mitochondrial genomes of the Spondias tuberosa Arr. Cam and Spondias mombin L. reveal highly repetitive DNA sequences.

Mitogenomes in plants are well-known as exhibiting high diversity in genome size architecture and repetitive DNA sequences. In this research study, we report on the complete mitochondrial genomes of S. tuberosa and S. mombin using Illumina paired-end and mate-pair end reads. These genomes were obtained by a combination of methods of de novo assembly and contig extension. The mitogenomes of S. tuberosa and S. mombin showed 779,106 bp and 685,788 bp in length, with a total of 35 genes. Genome comparisons showed many rearrangements that were mediated by repetitive DNA, and also high incorporation of DNA from chloroplast. In summary, we demonstrate: (1) first complete mitochondrial genomes for the genus Spondias; (2) the synteny between S. tuberosa and S. mombin showed rearrangements, mediated by repetitive DNA; (3) that gene content in Spondias mitogenomes is highly conserved; and (4) the high incorporation DNA from chloroplast genome, (5) the mitogenome size is due intergenic spacers and (6) the non-tandem repeats contributes for giant intergenic spacers.

Genome survey and development of 18 microsatellite markers to assess genetic diversity in Spondias tuberosa Arruda Câmara (Anacardiaceae) and cross-amplification in congeneric species.

Spondias tuberosa Arr. Cam belongs to the Anacardiaceae family, an economically important family of plants whose fruits are consumed by humans and animals. The aim of this study was to develop microsatellite markers using sequences from high-throughput sequencing and a magnetic bead enrichment method. The sequences were used to obtain contigs with a minimum of 500 nucleotides using Ray software and the mining of the simple sequence repeats (SSR) was performed with Phobos software, while the primers were designed by Primer3. We developed 18 polymorphic nuclear microsatellite markers and successfully cross-amplified them to three Spondias species. In S. tuberosa, the alleles ranged from 2 to 5 for each locus and Hardy-Weinberg equilibrium was found for 16 loci, with an expected and observed heterozygosity at 0.095-0.755 and 0.1-0.75, respectively. Cross-transferability was obtained for all loci in S. bahiensis, S. dulcis and S. purpurea. We concluded that the microsatellite markers developed in this study are useful in genetic population and conservation studies, as well as for investigating the hybrid origins of Spondias species.