De Novo Assembly and Annotation from Parental and F-1 Puma Genomes of the Florida Panther Genetic Restoration Program
AffiliationUniv Arizona, Sch Nat Resources & Environm
KeywordsGene family expansion/contraction
MetadataShow full item record
PublisherGENETICS SOCIETY AMERICA
CitationOchoa, A., Onorato, D. P., Fitak, R. R., Roelke-Parker, M. E., & Culver, M. (2019). De Novo Assembly and Annotation from Parental and F1 Puma Genomes of the Florida Panther Genetic Restoration Program. G3: Genes, Genomes, Genetics, 9(11), 3531-3536.
JournalG3-GENES GENOMES GENETICS
RightsCopyright © 2019 Ochoa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at email@example.com.
AbstractIn the mid-1990s, the population size of Florida panthers became so small that many individuals manifested traits associated with inbreeding depression (e.g., heart defects, cryptorchidism, high pathogen-parasite load). To mitigate these effects, pumas from Texas were introduced into South Florida to augment genetic variation in Florida panthers. In this study, we report a de novo puma genome assembly and annotation after resequencing 10 individual genomes from partial Florida-Texas-F1 trios. The final genome assembly consisted of ∼2.6 Gb and 20,561 functionally annotated protein-coding genes. Foremost, expanded gene families were associated with neuronal and embryological development, whereas contracted gene families were associated with olfactory receptors. Despite the latter, we characterized 17 positively selected genes related to the refinement of multiple sensory perceptions, most notably to visual capabilities. Furthermore, genes under positive selection were enriched for the targeting of proteins to the endoplasmic reticulum, degradation of mRNAs, and transcription of viral genomes. Nearly half (48.5%) of ∼6.2 million SNPs analyzed in the total sample set contained putative unique Texas alleles. Most of these alleles were likely inherited to subsequent F1 Florida panthers, as these individuals manifested a threefold increase in observed heterozygosity with respect to their immediate, canonical Florida panther predecessors. Demographic simulations were consistent with a recent colonization event in North America by a small number of founders from South America during the last glacial period. In conclusion, we provide an extensive set of genomic resources for pumas and elucidate the genomic effects of genetic rescue on this iconic conservation success story.
NoteOpen access journal
VersionFinal published version
SponsorsWilliam A. Calder III Memorial Scholarship from the Department of Ecology and Evolutionary Biology of the University of Arizona; Consejo Nacional de Ciencia y Tecnologia (CONACyT); National Science Foundation-Integrative Graduate Education and Research Traineeship scholarships
- Evolutionary and Functional Mitogenomics Associated With the Genetic Restoration of the Florida Panther.
- Authors: Ochoa A, Onorato DP, Fitak RR, Roelke-Parker ME, Culver M
- Issue date: 2017 Jun 1
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- Intentional genetic introgression influences survival of adults and subadults in a small, inbred felid population.
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- Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.
- Authors: Saremi NF, Supple MA, Byrne A, Cahill JA, Coutinho LL, Dalén L, Figueiró HV, Johnson WE, Milne HJ, O'Brien SJ, O'Connell B, Onorato DP, Riley SPD, Sikich JA, Stahler DR, Villela PMS, Vollmers C, Wayne RK, Eizirik E, Corbett-Detig RB, Green RE, Wilmers CC, Shapiro B
- Issue date: 2019 Oct 18