Genetic and genomic architecture in eight strains of the laboratory opossum Monodelphis domestica
| Autor: | Chao Zhang, Ana C Leandro, Wenqi Cao, Richard P. Metz, Xu Wang, Xiao Xiong, John L. VandeBerg, Paul B. Samollow |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
AcademicSubjects/SCI01140
AcademicSubjects/SCI00010 Population Biology QH426-470 AcademicSubjects/SCI01180 Monodelphis domestica Nucleotide diversity Inbred strain Metatheria Genetics Animals Humans education Molecular Biology Phylogeny Genetics (clinical) Investigation Comparative genomics Genetic diversity education.field_of_study Genome Strain (biology) population structure Genomics marsupial genetic diversity biology.organism_classification Genetic architecture Monodelphis Evolutionary biology AcademicSubjects/SCI00960 SNP discovery Laboratories |
| Zdroj: | G3: Genes, Genomes, Genetics, Vol 12, Iss 1 (2021) G3: Genes|Genomes|Genetics |
| ISSN: | 2160-1836 |
| DOI: | 10.1093/g3journal/jkab389 |
| Popis: | The gray short-tailed opossum (Monodelphis domestica) is an established laboratory-bred marsupial model for biomedical research. It is a critical species for comparative genomics research, providing the pivotal phylogenetic outgroup for studies of derived vs ancestral states of genomic/epigenomic characteristics for eutherian mammal lineages. To characterize the current genetic profile of this laboratory marsupial, we examined 79 individuals from eight established laboratory strains. Double digest restriction site-associated DNA sequencing and whole-genome resequencing experiments were performed to investigate the genetic architecture in these strains. A total of 66,640 high-quality single nucleotide polymorphisms (SNPs) were identified. We analyzed SNP density, average heterozygosity, nucleotide diversity, and population differentiation parameter Fst within and between the eight strains. Principal component and population structure analysis clearly resolve the strains at the level of their ancestral founder populations, and the genetic architecture of these strains correctly reflects their breeding history. We confirmed the successful establishment of the first inbred laboratory opossum strain LSD (inbreeding coefficient F > 0.99) and a nearly inbred strain FD2M1 (0.98 |
| Databáze: | OpenAIRE |
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