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Flack N, Drown M, Walls C, Pratte J, McLain A, Faulk C. Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genom Bioinform 2023; 5:lqad033. [PMID: 37025970 PMCID: PMC10071556 DOI: 10.1093/nargab/lqad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/10/2023] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
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Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Melissa Drown
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Carrie Walls
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jay Pratte
- Bloomington Parks and Recreation, Miller Park Zoo, Bloomington, IL 61701, USA
| | - Adam McLain
- Department of Biology and Chemistry, SUNY Polytechnic Institute, Utica, NY 13502, USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
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Ochoa A, Onorato DP, Roelke-Parker ME, Culver M, Fitak RR. Give and Take: Effects of Genetic Admixture on Mutation Load in Endangered Florida Panthers. J Hered 2022; 113:491-499. [PMID: 35930593 DOI: 10.1093/jhered/esac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e., proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e., non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida x Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.
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Affiliation(s)
- Alexander Ochoa
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
| | - David P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL
| | - Melody E Roelke-Parker
- Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD
| | - Melanie Culver
- U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, and School of Natural Resources and the Environment, University of Arizona, Tucson, AZ
| | - Robert R Fitak
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
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Lok S, Lau TNH, Trost B, Tong AHY, Wintle RF, Engstrom MD, Stacy E, Waits LP, Scrafford M, Scherer SW. Chromosomal-level reference genome assembly of the North American wolverine ( Gulo gulo luscus): a resource for conservation genomics. G3 GENES|GENOMES|GENETICS 2022; 12:6604289. [PMID: 35674384 PMCID: PMC9339297 DOI: 10.1093/g3journal/jkac138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/19/2022] [Indexed: 11/21/2022]
Abstract
We report a chromosomal-level genome assembly of a male North American wolverine (Gulo gulo luscus) from the Kugluktuk region of Nunavut, Canada. The genome was assembled directly from long-reads, comprising: 758 contigs with a contig N50 of 36.6 Mb; contig L50 of 20; base count of 2.39 Gb; and a near complete representation (99.98%) of the BUSCO 5.2.2 set of 9,226 genes. A presumptive chromosomal-level assembly was generated by scaffolding against two chromosomal-level Mustelidae reference genomes, the ermine and the Eurasian river otter, to derive a final scaffold N50 of 144.0 Mb and a scaffold L50 of 7. We annotated a comprehensive set of genes that have been associated with models of aggressive behavior, a trait which the wolverine is purported to have in the popular literature. To support an integrated, genomics-based wildlife management strategy at a time of environmental disruption from climate change, we annotated the principal genes of the innate immune system to provide a resource to study the wolverine’s susceptibility to new infectious and parasitic diseases. As a resource, we annotated genes involved in the modality of infection by the coronaviruses, an important class of viral pathogens of growing concern as shown by the recent spillover infections by severe acute respiratory syndrome coronavirus-2 to naïve wildlife. Tabulation of heterozygous single nucleotide variants in our specimen revealed a heterozygosity level of 0.065%, indicating a relatively diverse genetic pool that would serve as a baseline for the genomics-based conservation of the wolverine, a rare cold-adapted carnivore now under threat.
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Affiliation(s)
- Si Lok
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Timothy N H Lau
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Amy H Y Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , ON M5S 3E1, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Mark D Engstrom
- Department of Natural History, Royal Ontario Museum , Toronto, ON M5S 2C6, Canada
| | - Elise Stacy
- Environmental Science Program, University of Idaho , Moscow, ID 83844, USA
- Wildlife Conservation Society, Arctic Beringia , Fairbanks, AK 99709, USA
| | - Lisette P Waits
- Department of Fish and Wildlife, University of Idaho , Moscow, ID 83844, USA
| | - Matthew Scrafford
- Wildlife Conservation Society Canada , Thunder Bay, ON P7A 4K9, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- McLaughlin Centre, University of Toronto , Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto , ON M5S 1A8, Canada
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Ramirez JL, Lescroart J, Figueiró HV, Torres-Florez JP, Villela PMS, Coutinho LL, Freitas PD, Johnson WE, Antunes A, Galetti PM, Eizirik E. Genomic signatures of divergent ecological strategies in a recent radiation of Neotropical wild cats. Mol Biol Evol 2022; 39:6594307. [PMID: 35639983 PMCID: PMC9189605 DOI: 10.1093/molbev/msac117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here we use whole genome sequences of five species from the genus Leopardus, a recently diversified Neotropical lineage with species bearing distinctive morphological, ecological and behavioral features, to investigate genome-wide diversity, comparative demographic history and signatures of positive selection. Our results show that divergent ecological strategies are reflected in genomic features, e.g. a generalist species shows historically larger effective population size and higher heterozygosity than habitat specialists. The demographic history of these cats seems to have been jointly driven by climate fluctuations and habitat specialization, with different ecological adaptations leading to distinct trajectories. Finally, a gene involved in vertebrate retinal neurogenesis (POU4F2) was found to be under positive selection in the margay, a cat with notoriously large eyes that are likely associated with its nocturnal and arboreal specializations.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Peru
| | - Jonas Lescroart
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Henrique V Figueiró
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, USA
| | - Juan Pablo Torres-Florez
- Instituto Chico Mendes de Conservação da Biodiversidade/Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos (ICMBio/CMA), Santos, Brazil
| | | | - Luiz L Coutinho
- Centro de Genômica Funcional, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Patricia D Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil.,INCT-EECBio, Goiânia, GO, Brazil
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