Reconstructing protein-coding sequences from ancient DNA
- Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.
| Author details: | Michael HofreiterORCiDGND, Stefanie HartmannORCiDGND |
|---|---|
| DOI: | https://doi.org/10.1016/bs.mie.2020.05.008 |
| ISBN: | 978-0-12-821157-1 |
| ISSN: | 0076-6879 |
| Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/32828254 |
| Title of parent work (English): | Odorant binding and chemosensory proteins |
| Publisher: | Academic Press, an imprint of Elsevier |
| Place of publishing: | Cambridge, MA. |
| Publication type: | Article |
| Language: | English |
| Date of first publication: | 2020/06/19 |
| Publication year: | 2020 |
| Release date: | 2023/02/03 |
| Tag: | SRAssembler; ancient DNA; genome assembly; mapping; paleogenomics; re-sequencing; reference sequence; targeted assembly |
| Volume: | 642 |
| Number of pages: | 13 |
| First page: | 21 |
| Last Page: | 33 |
| Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie |
| DDC classification: | 5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie |
| Peer review: | Referiert |
