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.
References
Ai, H., Fang, X., Yang, B., Huang, Z., Chen, H., Mao, L., Zhang, F., Zhang, L., Cui, L., He, W., et al. (2015). Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47, 217–225.
Arumemi, F., Bayles, I., Paul, J., and Milcarek, C. (2013). Shared and discrete interacting partners of ELL1 and ELL2 by yeast two-hybrid assay. ABB 04, 774–780.
Blanco, E., Parra, G., and Guigo, R. (2007). Using geneid to identify genes. Curr Protoc Bioinformatics Chapter 4, Unit 4.3.
Burge, C.B., and Karlin, S. (1998). Finding the genes in genomic DNA. Curr Opin Struct Biol 8, 346–354.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: architecture and applications. BMC BioInf 10, 421.
Casper, J., Zweig, A.S., Villarreal, C., Tyner, C., Speir, M.L., Rosenbloom, K.R., Raney, B.J., Lee, C.M., Lee, B.T., Karolchik, D., et al. (2017) OUP accepted manuscript. Nucleic Acids Res.
Christopoulos, A., Ligoudistianou, C., Bethanis, P., and Gazouli, M. (2018). Successful use of adipose-derived mesenchymal stem cells to correct a male breast affected by Poland Syndrome: a case report. J Surg Case Rep 2018(7), rjy151.
Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., and Ren, B. (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380.
Doerks, T., Copley, R.R., Schultz, J., Ponting, C.P., and Bork, P. (2002). Systematic identification of novel protein domain families associated with nuclear functions. Genome Res 12, 47–56.
Dong, P., Tu, X., Chu, P.Y., Lü, P., Zhu, N., Grierson, D., Du, B., Li, P., and Zhong, S. (2017). 3D chromatin architecture of large plant genomes determined by local A/B compartments. Mol Plant 10, 1497–1509.
Durand, N.C., Shamim, M.S., Machol, I., Rao, S.S.P., Huntley, M.H., Lander, E.S., and Aiden, E.L. (2016). Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst 3, 95–98.
Fang, X., Mou, Y., Huang, Z., Li, Y., Han, L., Zhang, Y., Feng, Y., Chen, Y., Jiang, X., Zhao, W., et al. (2012). The sequence and analysis of a Chinese pig genome. Gigascience 1, 16.
Frantz, L.A.F., Schraiber, J.G., Madsen, O., Megens, H.J., Cagan, A., Bosse, M., Paudel, Y., Crooijmans, R.P.M.A., Larson, G., and Groenen, M.A.M. (2015). Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes. Nat Genet 47, 1141–1148.
Frazee, A.C., Pertea, G., Jaffe, A.E., Langmead, B., Salzberg, S.L., and Leek, J.T. (2015). Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol 33, 243–246.
Golicz, A.A., Bayer, P.E., Barker, G.C., Edger, P.P., Kim, H.R., Martinez, P. A., Chan, C.K.K., Severn-Ellis, A., McCombie, W.R., Parkin, I.A.P., et al. (2016). The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7, 13390.
Gordon, S.P., Contreras-Moreira, B., Woods, D.P., Des Marais, D.L., Burgess, D., Shu, S., Stritt, C., Roulin, A.C., Schackwitz, W., Tyler, L., et al. (2017). Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nat Commun 8, 2184.
Groenen, M.A.M., Archibald, A.L., Uenishi, H., Tuggle, C.K., Takeuchi, Y., Rothschild, M.F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H.J., et al. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393–398.
Guirao-Rico, S., Ramirez, O., Ojeda, A., Amills, M., and Ramos-Onsins, S. E. (2018). Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations. Heredity 120, 63–76.
Hirsch, C.N., Foerster, J.M., Johnson, J.M., Sekhon, R.S., Muttoni, G., Vaillancourt, B., Peñagaricano, F., Lindquist, E., Pedraza, M.A., Barry, K., et al. (2014). Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26, 121–135.
Jeong, H., Song, K.D., Seo, M., Caetano-Anollés, K., Kim, J., Kwak, W., Oh, J.D., Kim, E.S., Jeong, D.K., Cho, S., et al. (2015). Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing. BMC Genet 16, 104.
Kent, W.J. (2002). BLAT—The BLAST-like alignment tool. Genome Res 12, 656–664.
Kim, D., Langmead, B., and Salzberg, S.L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357–360.
Knight, P.A., and Ruiz, D. (2013). A fast algorithm for matrix balancing. IMA J Numer Anal 33, 1029–1047.
Kumar, S., Stecher, G., and Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33, 1870–1874.
Larson, G., Dobney, K., Albarella, U., Fang, M., Matisoo-Smith, E., Robins, J., Lowden, S., Finlayson, H., Brand, T., Willerslev, E., et al. (2005). Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307, 1618–1621.
Leung, D., Jung, I., Rajagopal, N., Schmitt, A., Selvaraj, S., Lee, A.Y., Yen, C.A., Lin, S., Lin, Y., Qiu, Y., et al. (2015). Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature 518, 350–354.
Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079.
Li, M., Chen, L., Tian, S., Lin, Y., Tang, Q., Zhou, X., Li, D., Yeung, C.K.L., Che, T., Jin, L., et al. (2017). Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies. Genome Res 27, 865–874.
Li, M., Tian, S., Jin, L., Zhou, G., Li, Y., Zhang, Y., Wang, T., Yeung, C.K.L., Chen, L., Ma, J., et al. (2013). Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet 45, 1431–1438.
Li, R., Li, Y., Zheng, H., Luo, R., Zhu, H., Li, Q., Qian, W., Ren, Y., Tian, G., Li, J., et al. (2010). Building the sequence map of the human pan-genome. Nat Biotechnol 28, 57–63.
Li, Y., Zhou, G., Ma, J., Jiang, W., Jin, L., Zhang, Z., Guo, Y., Zhang, J., Sui, Y., Zheng, L., et al. (2014). De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32, 1045–1052.
Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293.
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20, 1297–1303.
Monat, C., Pera, B., Ndjiondjop, M.N., Sow, M., Tranchant-Dubreuil, C., Bastianelli, L., Ghesquière, A., and Sabot, F. (2016). de novo assemblies of three Oryza glaberrima accessions provide first insights about pan-genome of African rices. Genome Biol Evol evw253.
Morgulis, A., Gertz, E.M., Schäffer, A.A., and Agarwala, R. (2006). WindowMasker: window-based masker for sequenced genomes. Bioinformatics 22, 134–141.
Neafsey, D.E., Waterhouse, R.M., Abai, M.R., Aganezov, S.S., Alekseyev, M.A., Allen, J.E., Amon, J., Arcà, B., Arensburger, P., Artemov, G., et al. (2015). Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes. Science 347, 1258522–43.
Pertea, M., Pertea, G.M., Antonescu, C.M., Chang, T.C., Mendell, J.T., and Salzberg, S.L. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33, 290–295.
Rao, S.S.P., Huntley, M.H., Durand, N.C., Stamenova, E.K., Bochkov, I.D., Robinson, J.T., Sanborn, A.L., Machol, I., Omer, A.D., Lander, E.S., et al. (2014). A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680.
Ron, G., Globerson, Y., Moran, D., and Kaplan, T. (2017). Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains. Nat Commun 8, 2237.
Schatz, M.C., Maron, L.G., Stein, J.C., Hernandez Wences, A., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., et al. (2014). Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 15, 506.
Shen, W., Le, S., Li, Y., and Hu, F. (2016). SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962.
Sherman, R.M., Forman, J., Antonescu, V., Puiu, D., Daya, M., Rafaels, N., Boorgula, M.P., Chavan, S., Vergara, C., Ortega, V.E., et al. (2019). Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nat Genet 51, 30–35.
Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., and Morgenstern, B. (2006). AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34, W435–W439.
Sun, C., Hu, Z., Zheng, T., Lu, K., Zhao, Y., Wang, W., Shi, J., Wang, C., Lu, J., Zhang, D., et al. (2017). RPAN: rice pan-genome browser for ∼3000 rice genomes. Nucleic Acids Res 45, 597–605.
Uyama, T., Ichi, I., Kono, N., Inoue, A., Tsuboi, K., Jin, X.H., Araki, N., Aoki, J., Arai, H., and Ueda, N. (2012). Regulation of peroxisomal lipid metabolism by catalytic activity of tumor suppressor H-rev107. J Biol Chem 287, 2706–2718.
Vaccari, C.M., Romanini, M.V., Musante, I., Tassano, E., Gimelli, S., Divizia, M.T., Torre, M., Morovic, C.G., Lerone, M., Ravazzolo, R., et al. (2014). De novo deletion of chromosome 11q12.3 in monozygotic twins affected by Poland Syndrome. BMC Med Genet 15, 63.
Wang, X., Zheng, Z., Cai, Y., Chen, T., Li, C., Fu, W., and Jiang, Y. (2017). CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations. GigaScience 6.
Wong, K.H.Y., Levy-Sakin, M., and Kwok, P.Y. (2018). De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations. Nat Commun 9, 3040.
Xiao, S., Xie, D., Cao, X., Yu, P., Xing, X., Chen, C.C., Musselman, M., Xie, M., West, F.D., Lewin, H.A., et al. (2012). Comparative epigenomic annotation of regulatory DNA. Cell 149, 1381–1392.
Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., Kong, L., Gao, G., Li, C.Y., and Wei, L. (2011). KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39, W316–W322.
Yan, G., Zhang, G., Fang, X., Zhang, Y., Li, C., Ling, F., Cooper, D.N., Li, Q., Li, Y., van Gool, A.J., et al. (2011). Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol 29, 1019–1023.
Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B. E., Nussbaum, C., Myers, R.M., Brown, M., Li, W., et al. (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biol 9, R137.
Zhao, Q., Feng, Q., Lu, H., Li, Y., Wang, A., Tian, Q., Zhan, Q., Lu, Y., Zhang, L., Huang, T., et al. (2018). Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat Genet 50, 278–284.
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