Polymorphic microsatellite loci and partial mitogenome for the Chestnut-bellied Seed-finch Sporophila angolensis (Aves, Passeriformes) using next generation sequencing

Mitochondrion genomes of seven species of the endangered genus Sporophila (Passeriformes: Thraupidae)

We announce the mitochondrial genomes of seven species of the genus Sporophila (S. bouvreuil, S. iberaensis, S. melanogaster, S. minuta, S. nigrorufa, S. pileata, and S. ruficollis) which were validated by comparative genomic and phylogenetic analysis with related species. The mitochondrial genomes of seven passerines of the genus Sporophila were assembled (three complete and four nearly complete genomes) and were validated by reconstructing phylogenetic relations within Thraupidae. The complete mitogenomes ranged from 16,781 bp in S. ruficollis to 16,791 bp in S. minuta. We identified a conserved genome composition within all mitogenomes with 13 protein-coding genes, 22 tRNAs and two rRNAs. We observed a bias in the nucleotide composition and six mutational hotspots in Sporophila mitogenomes. Our mitogenome-based phylogenetic tree has S. minuta, S. maximiliani and S. nigricollis as sister species of the remaining species in the genus. We present new mitogenome sequences for seven Sporophila species, providing new genomic resources that may be useful for research on the evolution, comparative genetics, and conservation of this threatened group.

New set of microsatellite markers for the Great-billed Seed-finch (Sporophila maximiliani - Passeriformes: Thraupidae): tools for inspection and conservation

The Thraupidae family is one of the most wanted by bird breeders in Brazil because it is represented by its diverse, colorful and melodious singers. The Great-billed Seed-finch, Sporophila maximiliani, is the only representative of the genus Sporophila considered critically endangered in Brazil. Due to the demands of environmental agencies and of conservation programs, there is a need to increase the number of molecular markers available for the genus and specially for S. maximiliani. Therefore, this work aimed to provide a new set of microsatellite markers for S. maximiliani in order to help bird breeders and environmental agencies on fulfilling its demands as well as contributing with extra genetics tools for conservation programs of the S. maximiliani. Of the 30 markers developed, 25 successfully amplified, and 22 were polymorphic. Annealing temperature varied from 52 to 64 °C, number of alleles from 2 to 13, and the medium allele richness was 7.25 and medium expected, observed heterozygosity and PIC were, respectively, 0.812, 0.661 and 0.752. The probability of identity estimate was 8.54 × 10^-27 and all the other probabilities of non-exclusion (sib-identity, parent pair and first-parent) were < 0.001, indicating that this set of microsatellite markers have high genetic variability and high power of individual genetic differentiation for S. maximiliani. Therefore, this work increases the options of molecular markers to be used on inspection for environmental agencies and for conservation programs on analyzing genetic variability and population studies for S. maximiliani.