VCF2Networks: applying genotype networks to single-nucleotide variants data

Summary: A wealth of large-scale genome sequencing projects opens the doors to new approaches to study the relationship between genotype and phenotype. One such opportunity is the possibility to apply genotype networks analysis to population genetics data. Genotype networks are a representation of the set of genotypes associated with a single phenotype, and they allow one to estimate properties such as the robustness of the phenotype to mutations, and the ability of its associated genotypes to evolve new adaptations. So far, though, genotype networks analysis has rarely been applied to population genetics data. To help fill this gap, here we present VCF2Networks, a tool to determine and study genotype network structure from single-nucleotide variant data. Availability and implementation: VCF2Networks is available at https://bitbucket.org/dalloliogm/vcf2networks. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Mitochondrial and nuclear genes from the extinct Balearic bovid Myotragus balearicus

Myotragus balearicus és un bòvid extingit de les Illes Balears Orientals o Gimnèsies (Mallorca, Menorca i illots que les envolten). Myotragus presenta nombroses novetats evolutives que enfosqueixen el seu emplaçament taxonòmic dintre dels Caprinae. A un projecte desenvolupat els darrers anys hem analitzat diferents mostres d'ossos de Myotragus i hem recuperat el gen cytb mtDNA complet, una seqüència del gen 12S mtDNA, una seqüència de la regió D-Ioop, i una seqüència d'un gen nuclear multi-còpia (el rDNA 28 S), emprant tècniques de DNA antic. Diferents controls experimentals, incloent-hi un laboratori dedicat, obtenció independent de rèpliques, solapament de fragments, extraccions múltiples i clonatge de productes PCR, donen suport a l'autenticitat de les seqüències. Els arbres filogenètics nous situen consistentment Myotragus a una posició basal al clade Ouis-Budorcas. Emperò, alguns gèneres de Caprinae, tals com Otearnnos i Amnotragus, presenten posicions inestables a tots els arbres. La branca llarga observada a Myotragus correspon a una taxa evolutiva elevada a aquesta línia que podria estar associada a la seva petita mida corporal. A més, la recuperació de gens nuclears per primera vegada d'una espècie extingida de la Mediterrània obre noves possibilitats de recerca sobre els trets genòmics i fenotípics.Myotragus balearicus was an extinct endemic bovid from some of the Balearic Islands (Mallorca and Menorca). Myotragus had many evolutionary novelties that obscure its phylogenetic placement among the extant Caprinae. In a project developed during the last years, we have analyzed several Myotragus fossil bones, and have retrieved the complete mtDNA cyt b gene (1143 bp in length), a sequence from the mtDNA 12S gene, a sequence from the D-Ioop region, and a sequence from a multi-copy nuclear gene (the 28 S rDNA), using ancient DNA techniques. Different experimental controls, including a dedicated laboratory, independent replication, overlapping fragments, multiple extractions and cloning of PCR products, support the authenticity of the sequences. The new phylogenetic trees consistently place Myotragus in a position basal to the Ouis-Budorcas clade. However, some Caprinae species, such as Oreamnos and Ammotragus, show unstable positions in all trees, attributable to a quick initial radiation of the Caprinae lineages. Moreover, the retrieval of nuclear genes for first time from an extinct species from the Mediterranean area opens new possibilities of research on comparative genomics and genetic bases of phenotypic traits

Comparative analysis of cancer genes in the human and chimpanzee genomes

BACKGROUND: Cancer is a major medical problem in modern societies. However, the incidence of this disease in non-human primates is very low. To study whether genetic differences between human and chimpanzee could contribute to their distinct cancer susceptibility, we have examined in the chimpanzee genome the orthologous genes of a set of 333 human cancer genes. RESULTS: This analysis has revealed that all examined human cancer genes are present in chimpanzee, contain intact open reading frames and show a high degree of conservation between both species. However, detailed analysis of this set of genes has shown some differences in genes of special relevance for human cancer. Thus, the chimpanzee gene encoding p53 contains a Pro residue at codon 72, while this codon is polymorphic in humans and can code for Arg or Pro, generating isoforms with different ability to induce apoptosis or interact with p73. Moreover, sequencing of the BRCA1 gene has shown an 8 Kb deletion in the chimpanzee sequence that prematurely truncates the co-regulated NBR2 gene. CONCLUSION: These data suggest that small differences in cancer genes, as those found in tumor suppressor genes, might influence the differences in cancer susceptibility between human and chimpanzee. Nevertheless, further analysis will be required to determine the exact contribution of the genetic changes identified in this study to the different cancer incidence in non-human primates

Nuclear gene indicates coat-color polymorphism in mammoths

By amplifying the melanocortin type 1 receptor from the woolly mammoth, we can report the complete nucleotide sequence of a nuclear-encoded gene from an extinct species. We found two alleles and show that one allele produces a functional protein whereas the other one encodes a protein with strongly reduced activity. This finding suggests that mammoths may have been polymorphic in coat color, with both dark- and light-haired individuals co-occurring