Cross-species utility of the Mouse Diversity Genotyping Array in assaying single nucleotide polymorphisms

In the study of genetic diversity in non-model species there is a notable lack of the low-cost, high resolution tools that are readily available for model organisms. Genotyping microarray technology for model organisms is well-developed, affordable, and potentially adaptable for cross-species hybridization. The Mouse Diversity Genotyping Array (MDGA), a single nucleotide polymorphism (SNP) genotyping tool designed for M. musculus, was tested as a tool to survey genomic diversity of wild species for inter-order, inter-family, inter-genus, and intra-genus comparisons. Application of the MDGA cross-species provides genetic distance information that reflects known taxonomic relationships reported previously between non-model species, but there is an underestimation of genetic diversity for non-Mus samples. The number and types of samples included in sets genotyped together must be considered in cross-species hybridization. The number of loci with heterozygous genotypes mapped to published genome sequences indicates potential for cross-species MDGA utility

Development and application of RNA-seq bioinformatic tools to explore non-model organisms in ageing research

Im Rahmen dieser Arbeit habe ich eine Software entwickelt, die alle notwendigen Schritte vollzieht um von Sequenzierungsdaten zu Transkriptkatalogen zu gelangen. Dazu werden sowohl öffentlich verfügbare als auch selbst angefertigte Programme effizient miteinander verbunden, um die Transkriptomassemblierung und -annotation vorzunehmen, sowie Schwachstellen der Assemblierung auszubessern. Die Wettbewerbsfähigkeit von FRAMA im Vergleich zu genombasierten Verfahren wurde durch Anwendung auf Sequenzierungsdaten des Nacktmulls demonstriert. Der Nacktmull rückt immer stärker in den Fokus der Alternsforschung, durch seine außergewöhnlich Lebensspanne von >30 Jahren in Gefangenschaft, die von einer extremen Widerstandskraft gegen altersbedingten Zerfall und einer lebenslangen Fruchtbarkeit begleitet wird. In Anbetracht seiner eusozialen Lebensweise, ist eine lebenslange Fruchtbarkeit bemerkenswert, denn in einer Kolonie trägt ein einzelnes Weibchen die metabolische Last der Fortpflanzung und wird dabei mindestens genauso alt wie ihre fortpflanzungsinaktiven Geschwister. Als Teil dieser Arbeit habe ich mit Hilfe von Genexpressionsanalysen und basierend auf dem zuvor angefertigten Transkriptkatalog, fortpflanzungaktive und -inaktive Nacktmulle verglichen. Weiterhin habe ich FRAMA auf Sequenzierungsdaten von Saisonfischen der Gattung Nothobranchius angewandt. Diese Gattung zeigt, vermutlich in Anpassung an die kurze Verfügbarkeit von Wasser in ihrem Habitat, eine sehr kurze Lebensspanne und umfasst eines der kurzlebigstes bekannten Wirbeltiere. Die Transkriptkataloge dienten als Grundlage zur Analyse positiver Selektion um genetische Determinanten kurzer Lebensspannen zu identifizieren. Beide Analysen haben interessante Genkandidaten in Bezug zur Alterung aufgedeckt und sowohl Einblicke in die sexuelle Reifung von Nacktmullen als auch der Evolution kurzer Lebenspannen in Saisonfischen gegebe

A bioinformatics analysis of contributors to false discovery for a mouse genotyping array

Microarray experiments employing massively-parallel hybridization are valuable for the study of genetic variation, however, errors during hybridization and limitations of single-species design must be considered for use within and across species. The Mouse Diversity Genotyping Array (MDGA) is a low cost, high-resolution microarray with probes that bind to target DNA for variant detection. Errors associated with probe design and incomplete protein removal from target DNA lead to false discovery and thus necessitate examination of probe suitability and target DNA availability. Bioinformatics methods were used to carry out confirmation of probe annotations, assessment of DNA accessibility for hybridization to probes, and prediction of the theoretical ability of MDGA probes to hybridize cross-species to naked mole-rat genomic DNA. The results are a filtered probe list demonstrated to reduce false discovery, a suggested approach to assess biases arising from protein-bound DNA, and predictions for cross-species application of the MDGA to naked mole-rat samples

Growing old, yet staying young: The role of telomeres in bats' exceptional longevity

Understanding aging is a grand challenge in biology. Exceptionally long-lived animals have mechanisms that underpin extreme longevity. Telomeres are protective nucleotide repeats on chromosome tips that shorten with cell division, potentially limiting life span. Bats are the longest-lived mammals for their size, but it is unknown whether their telomeres shorten. Using >60 years of cumulative mark-recapture field data, we show that telomeres shorten with age inRhinolophus ferrumequinumandMiniopterus schreibersii, but not in the bat genus with greatest longevity,Myotis. As in humans, telomerase is not expressed inMyotis myotisblood or fibroblasts. Selection tests on telomere maintenance genes show thatATMandSETX, which repair and prevent DNA damage, potentially mediate telomere dynamics inMyotisbats. Twenty-one telomere maintenance genes are differentially expressed inMyotis, of which 14 are enriched for DNA repair, and 5 for alternative telomere-lengthening mechanisms. We demonstrate how telomeres, telomerase, and DNA repair genes have contributed to the evolution of exceptional longevity inMyotisbats, advancing our understanding of healthy aging

Positive Selektion in langlebigen Nagern und kurzlebigen Fischen: eine bioinformatische Suche nach der genetischen Basis des Alterns

Zahlreiche Geschichten und Legenden, angefangen von den frühen Hochkulturen bis hinein in die moderne Populärliteratur, zeugen von dem Wunsch der Menschen das Altern zu verlangsamen. Viele Forscher gehen davon aus, dass genau dies notwendig sein wird, um den seit einigen Jahrzehnten anhaltenden Trend steigender Lebenserwartungen auch in Zukunft fortsetzen zu können und halten es für wahrscheinlich, dass ein verbessertes Verständnis des Alternsprozesses uns dahin führen wird. Um zu einem solchen Verständnis beizutragen, habe ich in dieser Arbeit mit bioinformatischen Mitteln nach der genetischen Basis natürlicherweise Weise vorhandener Unterschiede in der Lebenserwartung verschiedener Spezies gefahndet. Ich bediente mich dabei der Methode der genomweiten Suche nach positiv selektierten Genen (PSGs), die auf dem Vergleich der proteinkodierenden Sequenzen verschiedener Spezies beruht. Dazu habe ich verschiedene Software-Werkzeuge entwickelt und diese in dem Programm PosiGene zusammengefasst. PosiGene ist das erste öffentliche verfügbare Programm, das es ermöglicht PSGs genomweit auf beliebigen, vom Nutzer ausgewählten evolutionären Zweigen zu detektieren. Das erlaubt es allgemein also über die in dieser Arbeit im Fokus stehende Alternsforschung hinaus nach der genetischen Basis speziesspezifischer, phänotypischer Merkmale zu suchen. Die Offenlegung des Quellcodes in GitHub und die Bereitstellung einer installationslos, direkt nach dem Herunterladen einsatzfähigen Software ermöglicht eine breite Anwendung sowie eine kollektive Weiterentwicklung des Programmpakets zum Nutzen der wissenschaftlichen Gemeinschaft (Manuskript I). Konkret untersuchte ich mittels PosiGene zum einen die Verkürzung von Lebensspannen auf evolutionären Zweigen der Prachtgrundkärpflinge (Nothobranchius). Diese zählen mit Lebenserwartungen von z.T. nur sechs Monaten zu den kurzlebigsten Wirbeltierarten überhaupt. Zum anderen untersuchte ich die Verlängerung von Lebensspannen auf Zweigen der Nagetierfamilie der Sandgräber (Bathyergidae), deren Vertreter mit bis zu 30 Jahren um ein Vielfaches älter werden als die meisten anderen Nagetiere. ..

Human Ageing Genomic Resources:updates on key databases in ageing research

Ageing is a complex and multifactorial process. For two decades, the Human Ageing Genomic Resources (HAGR) have aided researchers in the study of various aspects of ageing and its manipulation. Here, we present the key features and recent enhancements of these resources, focusing on its six main databases. One database, GenAge, focuses on genes related to ageing, featuring 307 genes linked to human ageing and 2205 genes associated with longevity and ageing in model organisms. AnAge focuses on ageing, longevity, and life-history across animal species, containing data on 4645 species. DrugAge includes information about 1097 longevity drugs and compounds in model organisms such as mice, rats, flies, worms and yeast. GenDR provides a list of 214 genes associated with the life-extending benefits of dietary restriction in model organisms. CellAge contains a catalogue of 866 genes associated with cellular senescence. The LongevityMap serves as a repository for genetic variants associated with human longevity, encompassing 3144 variants pertaining to 884 genes. Additionally, HAGR provides various tools as well as gene expression signatures of ageing, dietary restriction, and replicative senescence based on meta-analyses. Our databases are integrated, regularly updated, and manually curated by experts. HAGR is freely available online (https://genomics.senescence.info/).</p

What Lies Beneath? Molecular Evolution During the Radiation of Caecilian Amphibians

Background: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. Results: A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. Conclusions: The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates

Human Ageing Genomic Resources:updates on key databases in ageing research

Ageing is a complex and multifactorial process. For two decades, the Human Ageing Genomic Resources (HAGR) have aided researchers in the study of various aspects of ageing and its manipulation. Here, we present the key features and recent enhancements of these resources, focusing on its six main databases. One database, GenAge, focuses on genes related to ageing, featuring 307 genes linked to human ageing and 2205 genes associated with longevity and ageing in model organisms. AnAge focuses on ageing, longevity, and life-history across animal species, containing data on 4645 species. DrugAge includes information about 1097 longevity drugs and compounds in model organisms such as mice, rats, flies, worms and yeast. GenDR provides a list of 214 genes associated with the life-extending benefits of dietary restriction in model organisms. CellAge contains a catalogue of 866 genes associated with cellular senescence. The LongevityMap serves as a repository for genetic variants associated with human longevity, encompassing 3144 variants pertaining to 884 genes. Additionally, HAGR provides various tools as well as gene expression signatures of ageing, dietary restriction, and replicative senescence based on meta-analyses. Our databases are integrated, regularly updated, and manually curated by experts. HAGR is freely available online (https://genomics.senescence.info/).</p

Comparative genomics approaches to study species divergence in ageing

Life, ageing and death have been concepts known to man since time immemorial. To this day, human beings have been fascinated by death and focused on stipulating what occurs after the life ends. In comparison, little attention has been given to ageing, which all experience daily and many take for granted. It is only the recent scientific movement that enabled mankind to shift its attention to studying ageing through the field of biology and gerontology. The observation that different species show different ageing phenotypes has intrigued many biologists. Comparative biologists, who study genetic, anatomy and behaviour of different species in order to understand the diversity of life, have been trying to explain the different ageing phenotypes through their divergence in their anatomy, natural habitat and behaviour. And since the expansion of the field of genetics, comparative biologists have been employing genomics to study differences in ageing phenotypes at the genome level. In the last few years, the number of species with their genome sequenced has increased at an impressive rate. However, the number of studies exploiting this wealth of data to study specific phenotypes has remained surprisingly small. Here, we present our work on comparative genomics to study species differences in ageing, that is, why many species age at different rates. We describe three projects which helped us 1) find a correlation between amino acid usage in mitochondrial proteins and maximal lifespan, 2) detect patterns of selection associated with longevity increases in proteins during mammalian evolution, and 3) compare the genes expression level in two closely related mammalian organisms, the naked mole-rat and the wild-type mouse. These projects led to several insights about ageing in mammals. We argue that the lack of detection of proteins with anti-oxidant properties in our analyses, coupled with a similar absence observed in other mammalian studies, suggest that contrary to some lower organisms, reactive oxygen species (ROS) may have a lesser impact on ageing in mammals. However, we found evidence that mammalian species may regulate ROS levels through the optimisation of pathways involved, for instance, in the actin cytoskeleton and lipid peroxidation, as well as through the optimisation of amino acid usage in mitochondrial proteins. Additionally, we discovered that genes involved in two pathways, namely lipid metabolism genes and proteasome-related genes, were associated to ageing in both the protein evolution project and the genes expression analysis, suggesting that these two pathways may be important regulators of mammalian ageing. We also discovered a few interesting genes. For instance, the DNA damage-binding protein 1, DBB1, which has a strong selection pattern related to longevity evolution in mammals. Additionally, we found that alpha-2-macroblobulin, A2M, is over-expressed at more than few hundreds fold in the long-lived naked mole-rat and has previously been associated to ageing. All in all, we present work that is interesting not only because of the original approaches taken to study mammalian ageing, but also because of the significance of the biological implications obtained. We hope to convince the readers that some of the discoveries made are good candidates for further studies by giving ideas of possible follow up experiments