Investigation of ancestral alleles in the Bovinae subfamily
Abstract Background In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced...
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| Format: | Article |
| Language: | English |
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BMC
2021-02-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07412-9 |
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| author | Maulana M. Naji Yuri T. Utsunomiya Johann Sölkner Benjamin D. Rosen Gábor Mészáros |
| author_facet | Maulana M. Naji Yuri T. Utsunomiya Johann Sölkner Benjamin D. Rosen Gábor Mészáros |
| author_sort | Maulana M. Naji |
| collection | DOAJ |
| description | Abstract Background In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study. Results Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~ 32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu. Conclusions Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience. |
| first_indexed | 2024-12-17T05:44:48Z |
| format | Article |
| id | doaj.art-68e3b30a9ed74b6b9b227a578c0d1a2a |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-17T05:44:48Z |
| publishDate | 2021-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-68e3b30a9ed74b6b9b227a578c0d1a2a2022-12-21T22:01:21ZengBMCBMC Genomics1471-21642021-02-0122111210.1186/s12864-021-07412-9Investigation of ancestral alleles in the Bovinae subfamilyMaulana M. Naji0Yuri T. Utsunomiya1Johann Sölkner2Benjamin D. Rosen3Gábor Mészáros4University of Natural Resources and Life Sciences (BOKU)São Paulo State University (Unesp), School of Veterinary Medicine, Department of Production and Animal HealthUniversity of Natural Resources and Life Sciences (BOKU)Agricultural Research Service USDAUniversity of Natural Resources and Life Sciences (BOKU)Abstract Background In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study. Results Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~ 32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu. Conclusions Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.https://doi.org/10.1186/s12864-021-07412-9Ancestral alleleBovinaeGene ontologyWhole genome sequences |
| spellingShingle | Maulana M. Naji Yuri T. Utsunomiya Johann Sölkner Benjamin D. Rosen Gábor Mészáros Investigation of ancestral alleles in the Bovinae subfamily BMC Genomics Ancestral allele Bovinae Gene ontology Whole genome sequences |
| title | Investigation of ancestral alleles in the Bovinae subfamily |
| title_full | Investigation of ancestral alleles in the Bovinae subfamily |
| title_fullStr | Investigation of ancestral alleles in the Bovinae subfamily |
| title_full_unstemmed | Investigation of ancestral alleles in the Bovinae subfamily |
| title_short | Investigation of ancestral alleles in the Bovinae subfamily |
| title_sort | investigation of ancestral alleles in the bovinae subfamily |
| topic | Ancestral allele Bovinae Gene ontology Whole genome sequences |
| url | https://doi.org/10.1186/s12864-021-07412-9 |
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