Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications

Abstract

Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.

How complete are “complete” genome assemblies?—An avian perspective

“… Assembly metrics from Table S1 of Kapusta and Suh (), except for galGal4 (Hillier et al., ), hooded crow (Weissensteiner et al., ) and Anna's hummingbird + zebra finch PacBio (present study). …”

“…As of July 5, 2017, B10K has generated 334 genome assemblies of representatives from nearly all avian families (http://b10k.genomics.cn/). In parallel to these quantity‐focused efforts, others aim to improve the quality of already existing genome assemblies (chicken, Anna's hummingbird, zebra finch, hooded crow; Korlach et al., ; Warren et al., ; Weissensteiner et al., ).…”

“…Thanks to the combination of all these techniques (including Sanger read lengths longer than those in short‐read sequencing), these genome assemblies have lower amounts of missing DNA than the aforementioned short‐read assemblies, but nevertheless contain tens of thousands of gaps between scaffolds (Table ). With the recent release of the first avian genome assemblies using the Pacific Biosciences long‐read sequencing platform (chicken, zebra finch, Anna's hummingbird and hooded crow), the sequence resolution of GC‐rich and repeat‐rich regions has been strongly improved (Korlach et al., ; Warren et al., ; Weissensteiner et al., ). Among these four birds with now available long‐read assemblies (Table ), the chicken long‐read genome assembly (version galGal5) is the most complete and facilitates a direct comparison to the previous chicken Sanger genome (version galGal4).…”

New advances in sequence assembly

“…With the emergence of long sequencing reads has come a renewed interest in repetitive sequences, which can be properly analyzed for the first time. This includes detailed analysis of highly repetitive satellite sequence in flies (Khosta et al 2017) and birds (Weissensteiner et al 2017), paving the way for functional studies in areas of the genome not previously accessible. Long-read assembly is even revealing new variation in the human genome, and Huddleston et al (2017) highlights the importance of long-read sequencing and haplotype resolution for accurate structural variant detection.…”

Beyond speciation genes: an overview of genome stability in evolution and speciation

“…The resulting fluorescent molecule can be imaged and used to anchor and assemble contigs and scaffolds [e.g. 69]. …”