Dynamic turnover of centromeres drives karyotype evolution in Drosophila

Bracewell, Ryan; Chatla, Kamalakar; Nalley, Matthew J.; Bachtrog, Doris

doi:10.1101/733527

Cited by 15 publications

(30 citation statements)

References 131 publications

(133 reference statements)

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“…BUSCO results suggest our final scaffolded genome assembly is of high quality and 181 95.7% of BUSCOs were found complete (Table 1). We found the BUSCO statistics to be slightly 182 lower than our other high-quality obscura group assemblies which average 98.7% complete 183 (Bracewell et al 2019). To investigate this reduction, we looked for missing BUSCOs in a 184 9 species with a similar karyotype and higher score (D. athabasca) and found that 49% of missing 185 BUSCOs (20 of 41 total) were in pericentromeric regions.…”

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confidence: 86%

“…Therefore, residual genome assembly 186 and polishing issues of highly repetitive pericentromeric regions are likely the main contributor 187 to the slightly lower scores of D. bifasciata. Figure S3) and was also the most frequently encountered TE in 199 D. athabasca, which also has large metacentric chromosomes (Bracewell et al 2019).…”

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confidence: 92%

“…Muller A was metacentric prior to the fusion, that could explain the presence of ancestral Muller 55 A genes on the long arm of the fused A-D chromosome (denoted XR in D. pseudoobscura) 56 (Mahajan et al 2018, Bracewell et al 2019) (hereafter referred to as Muller A-AD). Third, the 57 putative Muller C-D fusion is only present in some species of the obscura subgroup, suggesting it 58 occurred recently.…”

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confidence: 99%

“…At each step of assembly and polishing we assessed genome completeness using BUSCO v3 94 (Simão et al 2015) and the odb9 eukaryota database. Repetitive element identification and genome masking 113 We first used REPdenovo (Chu et al 2016) to identify novel repeats from our single-end Hi-C 114 Illumina sequencing data (above) using parameters described in detail in Bracewell et al (2019). best hit searches between proteins from our annotations of each species (Bracewell et al 2019).…”

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confidence: 99%

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Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

Bracewell

Tran

Chatla

et al. 2019

Preprint

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7The Drosophila obscura species group is one of the most studied clades of Drosophila and 8 harbors multiple distinct karyotypes. Here we present a de novo genome assembly and 9 annotation of D. bifasciata, a species which represents an important subgroup for which no high-10 quality chromosome-level genome assembly currently exists. We combined long-read 11 sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly 12 approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. 13Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our 14 assembly contains each chromosome in a single scaffold, including the highly repetitive 15 pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We 16 annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca 17 orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are 18 conserved between these species. Importantly, Muller A (X chromosome) was found to be 19 metacentric in D. bifasciata and the pericentromeric region appears homologous to the 20 pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis 21 subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D 22 and created the large neo-X (Muller A-AD) chromosome ~15 MYA. We also confirm the fusion 23 2 of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere 24 fusion. 25 26 INTRODUCTION 27 Recent advances in DNA sequencing technology have dramatically improved the quality and 28 quantity of genome assemblies in both model and non-model species. Long-read sequencing 29 technologies (e.g., PacBio and Nanopore) combined with long-range scaffolding information 30 generated through chromatin conformation capture methods such as Hi-C (Lieberman-Aiden et 31 al. 2009) or Chicago (Putnam et al. 2016) can produce assemblies of unprecedented length and 32 accuracy. However, there are still relatively few assemblies that traverse through megabase-long 33 stretches of highly repetitive sequence, thereby limiting our understanding of the evolution of 34 pericentromere/heterochromatic regions of the genome and the genes, satellites, and transposable 35 elements that inhabit them (Chang et al. 2019, Miga 2019). 36 Drosophila has been at the forefront of genetics and genomics research for over a century 37 and new chromosome-level assemblies are now becoming available for several non-model 38 species (Mahajan et al. 2018, Miller et al. 2018, Bracewell et al. 2019, Karageorgiou et al. 2019, 39 Mai et al. 2019). Recent comparative genomic analysis in the Drosophila obscura group has 40 revealed extensive karyotype evolution and turnover of centromeric satellites that alters 41 chromosome morphology (Bracewell et al. 2019) (Figure 1). Unfortunately, our understanding of 42 karyotype and genome evolution is currently limited because no high-q...

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confidence: 86%

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confidence: 92%

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confidence: 99%

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confidence: 99%

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Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

Bracewell

Tran

Chatla

et al. 2019

Preprint

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“…On an evolutionary timescale, tandem repeats change rapidly and are among the first sequence classes to diversify in emerging species (Charlesworth et al, 1994, Oliver et al, 2013, Zhang et al, 2015, McCann et al, 2018, Bracewell et al, 2019. Accumulation of mutations (single nucleotide changes, indels) leads to the emergence of new satDNAs variants, which may spread and displace existing variants and often form homogenised arrays (Plohl et al, 2012, Garrido-Ramos, 2015.…”

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confidence: 99%

Satellite DNA landscapes after allotetraploidisation of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

Heitkam

Weber

Walter

et al. 2019

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Key words: Chenopodium quinoa, polyploidy, tandem repeat, satellite DNA, 5S rDNA, fluorescent in situ hybridisation (FISH), single molecule real-time (SMRT) reads Word count: 7,901 (total without abstract, references and figure legends), divided into 754 (introduction), 3,578 (results), 2,181 (discussion), 1,164 (experimental procedures) SUMMARY If two related plant species hybridise, their genomes are combined within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co-evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn-over sequence class in eukaryotes, aiming to trace its emergence, amplification and loss during plant speciation and allopolyploidisation. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n=4x=36 chromosomes. Quinoa originated by hybridisation of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3 to 6.3 million years.Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterised seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic and fluorescent in situ hybridisation. As C. pallidicaule harbours a unique satDNA profile, we are able to exclude it as quinoa's parental species. Using quinoa long reads and scaffolds, we detected only limited evidence of interlocus homogenisation of satDNA after allopolyploidisation, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidisation, and may provide sequence targets for the identification of quinoa's progenitors.

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The Theory and Applications of Measuring Broad-Range and Chromosome-Wide Recombination Rate from Allele Frequency Decay around a Selected Locus

Wei

Bachtrog

2020

Molecular Biology and Evolution

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Recombination is the exchange of genetic material between homologous chromosomes via physical crossovers. High throughput sequencing approaches detect crossovers genome-wide to produce recombination rate maps but are difficult to scale as they require large numbers of recombinants individually sequenced. We present a simple and scalable pooled-sequencing approach to experimentally infer near chromosome-wide recombination rates by taking advantage of non-Mendelian allele frequency generated from a fitness differential at a locus under selection. As more crossovers decouple the selected locus from distal loci, the distorted allele frequency attenuates distally towards Mendelian and can be used to estimate the genetic distance. Here, we use marker selection to generate distorted allele frequency and theoretically derive the mathematical relationships between allele frequency attenuation, genetic distance, and recombination rate in marker selected pools. We implemented nonlinear curve fitting methods that robustly estimate the allele frequency decay from batch sequencing of pooled individuals, and derive chromosome-wide genetic distance and recombination rates. Empirically, we show that marker selected pools closely recapitulate genetic distances inferred from scoring recombinants. Using this method, we generated novel recombination rate maps of three wild derived strains of Drosophila melanogaster, which strongly correlate with previous measurements. Moreover, we show that this approach can be extended to estimate chromosome-wide crossover interference with reciprocal marker selection and discuss how it can be applied in the absence of visible markers. Altogether, we find that our method is a simple and cost-effective approach to generate chromosome-wide recombination rate maps requiring only one or two libraries.

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Dynamic turnover of centromeres drives karyotype evolution in Drosophila

Cited by 15 publications

References 131 publications

Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

Satellite DNA landscapes after allotetraploidisation of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

The Theory and Applications of Measuring Broad-Range and Chromosome-Wide Recombination Rate from Allele Frequency Decay around a Selected Locus

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