Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data (original) (raw)

• Ekblom, R. & Wolf, J. B. A field guide to whole-genome sequencing, assembly and annotation. Evolut. Appl. 7, 1026–1042 (2014).
  Article Google Scholar
• Deschamps, S. et al. A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping. Nat. Commun. 9, 4844 (2018).
• Belser, C. et al. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat. Plants 4, 879–887 (2018).
  Article CAS PubMed Google Scholar
• Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
  CAS PubMed PubMed Central Google Scholar
• Zhang, J. et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat. Genet. 50, 1565–1573 (2018).
• Bickhart, D. M. et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat. Genet. 49, 643–650 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Reyes-Chin-Wo, S. et al. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat. Commun. 8, 14953 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Dekker, J. The three ‘C’ s of chromosome conformation capture: controls, controls, controls. Nat. Methods 3, 17–21 (2006).
  Article CAS PubMed Google Scholar
• van Berkum, N. L. et al. Hi-C: a method to study the three-dimensional architecture of genomes. J. Vis. Exp. https://doi.org/10.3791/1869 (2010).
• Zhang, L. et al. RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis. Nat. Commun. 8, 2264 (2017).
  Article PubMed PubMed Central Google Scholar
• Jarvis, D. E. et al. The genome of Chenopodium quinoa. Nature 542, 307–312 (2017).
  Article CAS PubMed Google Scholar
• Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Putnam, N. H. et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26, 342–350 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Ghurye, J., Pop, M., Koren, S., Bickhart, D. & Chin, C. S. Scaffolding of long read assemblies using long range contact information. BMC Genom. 18, 527 (2017).
  Article Google Scholar
• Schmitt, A. D., Hu, M. & Ren, B. Genome-wide mapping and analysis of chromosome architecture. Nat. Rev. Mol. Cell Biol. 17, 743–755 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Wood, T. E. et al. The frequency of polyploid speciation in vascular plants. Proc. Natl Acad. Sci. USA 106, 13875–13879 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Ming, R. & Man Wai, C. Assembling allopolyploid genomes: no longer formidable. Genome Biol. 16, 27 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Paterson, A. H. et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492, 423–427 (2012).
  Article CAS PubMed Google Scholar
• Li, F. et al. Genome sequence of the cultivated cotton Gossypium arboreum. Nat. Genet. 46, 567–572 (2014).
  Article CAS PubMed Google Scholar
• Zhang, T. et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat. Biotechnol. 33, 531–537 (2015).
  Article CAS PubMed Google Scholar
• Sierro, N. et al. The tobacco genome sequence and its comparison with those of tomato and potato. Nat. Commun. 5, 3833 (2014).
  Article CAS PubMed Google Scholar
• Sierro, N. et al. Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol. 14, R60 (2013).
  Article PubMed PubMed Central Google Scholar
• Bertioli, D. J. et al. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat. Genet. 48, 438–446 (2016).
  Article CAS PubMed Google Scholar
• Zhuang, W. et al. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nat. Genet. 51, 865–876 (2019).
• Chapman, J. A. et al. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol. 16, 26 (2015).
  Article PubMed PubMed Central Google Scholar
• The Potato Genome Sequencing,. et al. Genome sequence and analysis of the tuber crop potato. Nature 475, 189–195 (2011).
• Yang, J. et al. Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nat. Plants 3, 696–703 (2017).
• Kronenberg, Z. N. et al. FALCON-Phase: integrating PacBio and Hi-C data for phased diploid genomes. Preprint at https://doi.org/10.1101/327064 (2018).
• Chin, C. S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, Q. et al. N(6)-Methyladenine DNA methylation in japonica and indica rice genomes and Its association with gene expression, plant development, and stress responses. Mol. Plant 11, 1492–1508 (2018).
  Article CAS PubMed Google Scholar
• Schneeberger, K. et al. Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc. Natl Acad. Sci. USA 108, 10249–10254 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Xie, T. et al. De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana. Mol. Plant 8, 489–492 (2015).
  Article CAS PubMed Google Scholar
• Ferhat et al. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 24, 999–1011 (2014).
  Article Google Scholar
• Bastian, M., Heymann, S. & Jacomy, M. Gephi: an open source software for exploring and manipulating networks. In International AAAI Conference on Weblogs and Social Media 361–362 (AAAI, 2009).
• Tang, H. Disentangling a polyploid genome. Nat. Plants 3, 688–689 (2017).
  Article PubMed Google Scholar
• Wang, J. et al. Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics 11, 261 (2010).
  Article PubMed PubMed Central Google Scholar
• Zhang, J. et al. Recent polyploidization events in three Saccharum founding species. Plant Biotechnol. J. 17, 264–274 (2019).
  Article CAS PubMed Google Scholar
• Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Marie-Nelly, H. et al. High-quality genome (re)assembly using chromosomal contact data. Nat. Commun. 5, 5695 (2014).
• Irvine, J. E. Saccharum species as horticultural classes. Theor. Appl. Genet. 98, 186–194 (1999).
  Article Google Scholar
• Fávero, A. P., Simpson, C. E., Valls, J. F. M. & Vello, N. A. Study of the evolution of cultivated peanut through crossability studies among Arachis ipaensis, A. duranensis, and A. hypogaea. Crop Sci. 46, 1546–1552 (2006).
• Bertioli, D. J. et al. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat. Genet. 51, 877–884 (2019).
• Koren, S. et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat. Biotechnol. 36, 1174–1182 (2018).
• Wang, M. et al. Evolutionary dynamics of 3D genome architecture following polyploidization in cotton. Nat. Plants 4, 90–97 (2018).
  Article CAS PubMed Google Scholar
• Tang, H. et al. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol. 16, 3 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
  Article PubMed PubMed Central Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
  Article CAS PubMed PubMed Central Google Scholar