De novo assembly and annotation of the singing mouse genome
Abstract Background Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be il...
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09678-7 |
| _version_ | 1797577958501646336 |
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| author | Samantha K. Smith Paul W. Frazel Alireza Khodadadi-Jamayran Paul Zappile Christian Marier Mariam Okhovat Stuart Brown Michael A. Long Adriana Heguy Steven M. Phelps |
| author_facet | Samantha K. Smith Paul W. Frazel Alireza Khodadadi-Jamayran Paul Zappile Christian Marier Mariam Okhovat Stuart Brown Michael A. Long Adriana Heguy Steven M. Phelps |
| author_sort | Samantha K. Smith |
| collection | DOAJ |
| description | Abstract Background Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston’s singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions. Results Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types. Conclusions These resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses. |
| first_indexed | 2024-03-10T22:15:27Z |
| format | Article |
| id | doaj.art-798eb7a09956465eb3041f88f28ffb5e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:27Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-798eb7a09956465eb3041f88f28ffb5e2023-11-19T12:27:38ZengBMCBMC Genomics1471-21642023-09-0124111210.1186/s12864-023-09678-7De novo assembly and annotation of the singing mouse genomeSamantha K. Smith0Paul W. Frazel1Alireza Khodadadi-Jamayran2Paul Zappile3Christian Marier4Mariam Okhovat5Stuart Brown6Michael A. Long7Adriana Heguy8Steven M. Phelps9Department of Integrative Biology, University of Texas at AustinDepartment of Neuroscience and Physiology, New York University Grossman School of MedicineApplied Bioinformatics Laboratory, New York University Grossman School of MedicineGenome Technology Center, New York University Grossman School of MedicineGenome Technology Center, New York University Grossman School of MedicineDepartment of Integrative Biology, University of Texas at AustinNYU Center for Health Informatics and Bioinformatics, New York University Grossman School of MedicineDepartment of Neuroscience and Physiology, New York University Grossman School of MedicineGenome Technology Center, New York University Grossman School of MedicineDepartment of Integrative Biology, University of Texas at AustinAbstract Background Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston’s singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions. Results Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types. Conclusions These resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.https://doi.org/10.1186/s12864-023-09678-7GenomeRodentsVocal communicationSocial cognition |
| spellingShingle | Samantha K. Smith Paul W. Frazel Alireza Khodadadi-Jamayran Paul Zappile Christian Marier Mariam Okhovat Stuart Brown Michael A. Long Adriana Heguy Steven M. Phelps De novo assembly and annotation of the singing mouse genome BMC Genomics Genome Rodents Vocal communication Social cognition |
| title | De novo assembly and annotation of the singing mouse genome |
| title_full | De novo assembly and annotation of the singing mouse genome |
| title_fullStr | De novo assembly and annotation of the singing mouse genome |
| title_full_unstemmed | De novo assembly and annotation of the singing mouse genome |
| title_short | De novo assembly and annotation of the singing mouse genome |
| title_sort | de novo assembly and annotation of the singing mouse genome |
| topic | Genome Rodents Vocal communication Social cognition |
| url | https://doi.org/10.1186/s12864-023-09678-7 |
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