Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

Abstract

Black raspberry (Rubus occidentalis L.) is a niche fruit crop valued for its flavor and potential health benefits. The improvement of fruit and cane characteristics via molecular breeding technologies has been hindered by the lack of a high-quality reference genome. The recently released draft genome for black raspberry (ORUS 4115-3) lacks assembly of scaffolds to chromosome scale. We used high-throughput chromatin conformation capture (Hi-C) and Proximity-Guided Assembly (PGA) to cluster and order 9650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes. The seven pseudo-chromosomes cover ~97.2% of the total contig length (~223.8 Mb). Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic map. Centromeric regions were inferred from recombination frequencies of genetic markers, alignment of 303 bp centromeric sequence with the PGA, and heat map showing the physical contact matrix over the entire genome. We demonstrate a high degree of synteny between each of the seven chromosomes of black raspberry and a high-quality reference genome for strawberry (Fragaria vesca L.) assembled using only PacBio long-read sequences. We conclude that PGA is a cost-effective and rapid method of generating chromosome-scale assemblies from Illumina short-read sequencing data.

References

[1] Shulaev, V. et al. The genome of woodland strawberry (Fragaria vesca) . Nat. Genet. 43, 109-116 (2011).

[2] Verde, I. et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution . Nat. Genet. 45, 487-494 (2013).

[3] Daccord, N. et al. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat. Genet. 49, 1099-1106 (2017).

[4] Tang, H. et al. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol. 16, 3 (2015).

[5] 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).

[6] Peichel C. L., Sullivan S. T., Liachko I., & White M. A. Improvement of the threespine stickleback (Gasterosteus aculeatus) genome using a Hi-C-based proximity-guided assembly method . bioRxiv 068528 (2016). J Hered. 108, 693-700 (2017).

[7] Belton, J.-M. et al. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58, 268-276 (2012).

[8] Marie-Nelly, H. et al. High-quality genome (re) assembly using chromosomal contact data. Nat. Commun. 5, 5695 (2014).

[9] Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).

[10] Velasco, R. et al. The genome of the domesticated apple (Malus×domestica Borkh.) . Nat. Genet. 42, 833-839 (2010).

[11] Verde, I. et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution . Nat. Genet. 45, 487-494 (2013).

[12] Foucher, F. et al. Towards the rose genome sequence and its use in research and breeding 167-175 (International Society for Horticultural Science (ISHS), Leuven, Belgium, 2015).

[13] Chagné, D. et al. The draft genome sequence of European Pear (Pyrus communis L. ‘Bartlett’) . PLoS ONE 9, e92644 (2014).

[14] Wu, J. et al. The genome of the pear (Pyrus bretschneideri Rehd.) . Genome Res. 23, 396-408 (2013).

[15] Zhang, Q. et al. The genome of Prunus mume . Nat. Commun. 3, 1318 (2012).

[16] VanBuren, R. et al. The genome of black raspberry (Rubus occidentalis) . Plant J. 87, 535-547 (2016).

[17] Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).

[18] Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).

[19] Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119-1125 (2013).

[20] Kuhn, R. M., Haussler, D. & Kent, W. J. The UCSC genome browser and associated tools. Brief Bioinformatics 14, 144-161 (2013).

[21] Wu, T. D. & Watanabe, C. K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859-1875 (2005).

[22] Lyons, E., Pedersen, B., Kane, J. & Freeling, M. The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. Trop. Plant Biol. 1, 181-190 (2008).

[23] Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).

[24] Naranjo, C. A., Poggio, L. & Brandham, P. E. A practical method of chromosome classification on the basis of centromere position. Genetica 62, 51-53 (1983).

[25] Edger, P. P. et al. Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity . GigaScience (2017).

[26] Dekker, J., Marti-Renom, M. A. & Mirny, L. A . Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 14, 390-403 (2013).

[27] Kaplan, N. & Dekker, J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat. Biotechnol. 31, 1143-1147 (2013).

[28] Yu, A. et al. Comparison of human genetic and sequence-based physical maps. Nature 409, 951-953 (2001).

[29] Petes, T. D. Meiotic recombination hot spots and cold spots. Nat. Rev. Genet. 2, 360 (2001).

[30] Chen, M. et al. An integrated physical and genetic map of the rice genome. Plant Cell 14, 537-545 (2002).

[31] DeWan, A. T., Parrado, A. R., Matise, T. C. & Leal, S. M. The map problem: a comparison of genetic and sequence-based physical maps. Am. J. Hum. Genet. 70, 101-107 (2002).

[32] Lee, W. K. et al. Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps. Theor. Appl. Genet. 126, 1103-1119 (2013).

[33] Bustamante, F. O., Aliyeva-Schnorr, L., Fuchs, J., Beier, S. & Houben, A. Correlating the genetic and physical map of barley chromosome 3H revealed limitations of the FISH-based mapping of nearby single-copy probes caused by the dynamic structure of metaphase chromosomes. Cytogenet. Genome Res. 152, 90-96 (2017).

[34] Talbert, P. B. & Henikoff, S. Centromeres convert but don’t cross. PLoS Biol. 8, e1000326 (2010).

[35] Heslop-Harrison, J. P. & Schwarzacher, T. Nucleosomes and centromeric DNA packaging. Proc. Natl Acad. Sci. USA 110, 19974-19975 (2013).

[36] Henikoff, S., Ahmad, K . & Malik, H. S. The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293, 1098-1102 (2001).

[37] Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R. & Flavell, R. A. Interchromosomal associations between alternatively expressed loci. Nature 435, 637 (2005).

[38] Jung, S. et al. GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. BMC Bioinformatics 5, 130 (2004).