Giant tortoise genomes provide insights into longevity and age-related disease

Quesada, Vı́ctor; Freitas‐Rodríguez, Sandra; Miller, Joshua M.; Pérez-Silva, José G; Jiang, Zi Feng; Tapia, Washington; Santiago‐Fernández, Olaya; Campos-Iglesias, Diana; Kuderna, Lukas F. K.; Quinzin, Maud C.; Álvarez, Marina Rodríguez; Carrero, Dido; Beheregaray, Luciano B.; Gibbs, James P.; Chiari, Ylenia; Glaberman, Scott; Ciofi, Claudio; Araujo‐Voces, Miguel; Mayoral, Pablo; Arango, Javier R.; Tamargo‐Gómez, Isaac; Roiz‐Valle, David; Pascual-Torner, Maria; Evans, Benjamin R.; Edwards, Danielle L.; Garrick, Ryan C.; Russello, Michael A.; Poulakakis, Nikos; Gaughran, Stephen J.; Rueda, Danny; Bretones, Gabriel; Marquès-Bonet, Tomàs; White, Kevin P.; Caccone, Adalgisa; López-Otı́n, Carlos

doi:10.1038/s41559-018-0733-x

Cited by 87 publications

(89 citation statements)

References 67 publications

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“…We also annotated perforin genes in the genomes of 43 species of sauria ( Figure 1, green boxes). The results showed widely different evolutionary patterns, as suggested by previous studies [10,12]. Fortunately, the improved genomic assemblies for many of these species have allowed a more detailed view of perforin-1 evolution.…”

Section: Sauriasupporting

confidence: 59%

Frequent birth-and-death events throughout perforin-1 evolution

Araujo‐Voces

Quesada

2020

Preprint

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Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

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Section: Sauriasupporting

confidence: 59%

Frequent birth-and-death events throughout perforin-1 evolution

Araujo‐Voces

Quesada

2020

Preprint

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“…Long-lived species, such as myotis bats and parrots, also evolved mechanisms of telomere maintenance throughout lifespan (Foley et al, 2018;Wirthlin et al, 2018). The long-lived giant tortoise has unique variants in the DNA repair gene X-ray repair cross complementing 6 (XRCC6) (Quesada et al, 2019). Accordingly, DNA repair mechanisms are enhanced in several long-lived species.…”

Section: Aging and Longevity Through The Lens Of Evolutionmentioning

confidence: 99%

The Genetics of Aging: A Vertebrate Perspective

Singh

Demmitt

Nath

et al. 2019

Cell

194

162

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Aging negatively impacts vitality and health. Many genetic pathways that regulate aging were discovered in invertebrates. However, the genetics of aging is more complex in vertebrates because of their specialized systems. This Review discusses advances in the genetic regulation of aging in vertebrates from work in mice, humans, and organisms with exceptional lifespans. We highlight challenges for the future, including sex-dependent differences in lifespan and the interplay between genes and environment. We also discuss how the identification of reliable biomarkers of age and development of new vertebrate models can be leveraged for personalized interventions to counter aging and age-related diseases.

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“…The reference “genome” used for alignment of nuclear capture loci consisted of 140‐bp‐long target sequences, as well as 100 bp of flanking sequence on either end obtained from a draft genome of Chelonoidis abingdonii (Quesada et al., in preparation). Sequences were processed using the BAM pipeline in PALEOMIX (version 1.2.6, Schubert et al., ), which employs other standard bioinformatic tools alongside native scripts to support the pipeline.…”

Section: Methodsmentioning

confidence: 99%

Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head‐starting in a Galapagos giant tortoise

Jensen

Edwards

Garrick

et al. 2018

Evolutionary Applications

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Population genetic theory related to the consequences of rapid population decline is well‐developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long‐term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome‐wide single nucleotide polymorphism data from prebottleneck historical (c.1906) and postbottleneck contemporary (c.2014) samples of Pinzón giant tortoises (Chelonoidis duncanensis; n = 25 and 149 individuals, respectively) endemic to a single island in the Galapagos. Pinzón giant tortoises had a historically large population size that was reduced to just 150–200 individuals in the mid 20th century. Since then, Pinzón's tortoise population has recovered through an ex situ head‐start programme in which eggs or pre‐emergent individuals were collected from natural nests on the island, reared ex situ in captivity until they were 4–5 years old and subsequently repatriated. We found that the extent and distribution of genetic variation in the historical and contemporary samples were very similar, with the latter group not exhibiting the characteristic genetic patterns of recent population decline. No population structure was detected either spatially or temporally. We estimated an effective population size (N e) of 58 (95% CI = 50–69) for the postbottleneck population; no prebottleneck N e point estimate was attainable (95% CI = 39–infinity) likely due to the sample size being lower than the true N e. Overall, the historical sample provided a valuable benchmark for evaluating the head‐start captive breeding programme, revealing high retention of genetic variation and no skew in representation despite the documented bottleneck event. Moreover, this work demonstrates the effectiveness of head‐starting in rescuing the Pinzón giant tortoise from almost certain extinction.

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Giant tortoise genomes provide insights into longevity and age-related disease

Cited by 87 publications

References 67 publications

Frequent birth-and-death events throughout perforin-1 evolution

Frequent birth-and-death events throughout perforin-1 evolution

The Genetics of Aging: A Vertebrate Perspective

Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head‐starting in a Galapagos giant tortoise

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