Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data
| Autor: | Xie Wang, Xiao Sen Guo, Xiu Juan Yang, Huan Liu, Jacob Njaramba-Ngatia, Hai Meng Li, Yu Lin, Hua Bing Guo, Tian Ming Lan, Ren Gui Li, Sunil Kumar-Sahu, Karsten Kristiansen, Yan Chun Xu, Wenhao Xu |
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| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
0301 basic medicine lcsh:QH426-470 Computer science species identification Morphology (biology) Computational biology DNA Mitochondrial 010603 evolutionary biology 01 natural sciences Article DNA sequencing Mammoths 03 medical and health sciences Mapping algorithm Genetics Animals Humans Species identification Horses BLAST ancient DNA Genetics (clinical) computer.programming_language Genome Goats Basic Local Alignment Search Tool High-Throughput Nucleotide Sequencing Paleontology Ruminants humanities lcsh:Genetics 030104 developmental biology Ancient DNA next-generation sequencing Identification (biology) Perl computer Algorithms |
| Zdroj: | Genes Volume 10 Issue 7 Lan, T M, Lin, Y, Njaramba-Ngatia, J, Guo, X S, Li, R G, Li, H M, Kumar-Sahu, S, Wang, X, Yang, X J, Guo, H B, Xu, W H, Kristiansen, K, Liu, H & Xu, Y C 2019, ' Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data ', Genes, vol. 10, no. 7, 509 . https://doi.org/10.3390/genes10070509 Genes, Vol 10, Iss 7, p 509 (2019) |
| ISSN: | 2073-4425 |
| Popis: | The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub. |
| Databáze: | OpenAIRE |
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