Abstract
Pigs were domesticated independently in the Near East and China, indicating that a single reference genome from one individual is unable to represent the full spectrum of divergent sequences in pigs worldwide. Therefore, 12 de novo pig assemblies from Eurasia were compared in this study to identify the missing sequences from the reference genome. As a result, 72.5 Mb of non-redundant sequences (∼3% of the genome) were found to be absent from the reference genome (Sscrofa11.1) and were defined as pan-sequences. Of the pan-sequences, 9.0 Mb were dominant in Chinese pigs, in contrast with their low frequency in European pigs. One sequence dominant in Chinese pigs contained the complete genic region of the tazarotene-induced gene 3 (TIG3) gene which is involved in fatty acid metabolism. Using flanking sequences and Hi-C based methods, 27.7% of the sequences could be anchored to the reference genome. The supplementation of these sequences could contribute to the accurate interpretation of the 3D chromatin structure. A web-based pan-genome database was further provided to serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research.
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Data availability
The sequencing reads of each sequencing library have been deposited at NCBI for Hi-C data (Project ID: PRJNA482496). The assembly of the pig pan-genome and subsequent analysis results are available from our PIGPAN website (http://animal.nwsuaf.edu.cn/code/index.php/pan-Pig). All other data supporting the findings of this study are available in the article and its supplementary information files are available from the corresponding author on request.
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (31822052 and 31572381) to Y.J and the Science & Technology Support Program of Sichuan (2016NYZ0042 and 2017NZDZX0002) to M.Z.L. We thank the High Performance Computing platform of Northwest A&F University for their assistance with the computing.
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Tian, X., Li, R., Fu, W. et al. Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data. Sci. China Life Sci. 63, 750–763 (2020). https://doi.org/10.1007/s11427-019-9551-7
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DOI: https://doi.org/10.1007/s11427-019-9551-7