Origin and fate of supergenes in Atlantic cod

Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four large supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here, we investigate the origin and fate of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate that chromosomal inversions underlie all four supergenes, and show that they originated separately, between 0.40 and 1.66 million years ago. While introgression was not involved in the origin of the four supergenes, we reveal gene flow between inverted and noninverted supergene haplotypes, occurring both through gene conversion and double crossover. Moreover, the presence of genes linked to salinity adaptations in a sequence transferred through double crossover indicates that these sequences exchanged between the haplotypes are subject to selection. Our results suggest that the fate of supergenes is comparable to that of hybridizing species, by depending on the degree to which separation is maintained through purging of introduced genetic variation.

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Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab083 ◽

2021 ◽

Author(s):

Eric S Tvedte ◽

Mark Gasser ◽

Benjamin C Sparklin ◽

Jane Michalski ◽

Carl E Hjelmen ◽

...

Keyword(s):

Bacterial Genome ◽

Hybrid Approach ◽

Cost Effective ◽

Fruit Fly ◽

Drosophila Ananassae ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

E Coli ◽

Hybrid Approaches ◽

Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

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Comprehensive identification of transposable element insertions using multiple sequencing technologies

Nature Communications ◽

10.1038/s41467-021-24041-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Chong Chu ◽

Rebeca Borges-Monroy ◽

Vinayak V. Viswanadham ◽

Soohyun Lee ◽

Heng Li ◽

...

Keyword(s):

Transposable Element ◽

Structure And Function ◽

Endogenous Retroviruses ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Short Read ◽

Sequencing Technologies ◽

Long Read ◽

And Function

AbstractTransposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea.

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Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data

Bioinformatics ◽

10.1093/bioinformatics/btz484 ◽

2019 ◽

Vol 35 (22) ◽

pp. 4809-4811 ◽

Cited By ~ 8

Author(s):

Robert S Harris ◽

Monika Cechova ◽

Kateryna D Makova

Keyword(s):

Tandem Repeats ◽

Error Rates ◽

Superior Performance ◽

Supplementary Information ◽

Whole Genome Sequencing Data ◽

Dna Repeats ◽

Sequencing Data ◽

Heat Shock Stress ◽

Noise Cancelling ◽

Long Read

Abstract Summary Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstrated its superior performance as compared to two alternative tools. Using real human whole-genome sequencing data, NCRF identified long arrays of the (AATGG)n repeat involved in heat shock stress response. Availability and implementation NCRF is implemented in C, supported by several python scripts, and is available in bioconda and at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder. Supplementary information Supplementary data are available at Bioinformatics online.

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Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish

GigaScience ◽

10.1093/gigascience/giaa067 ◽

2020 ◽

Vol 9 (6) ◽

Cited By ~ 3

Author(s):

Lisa K Johnson ◽

Ruta Sahasrabudhe ◽

James Anthony Gill ◽

Jennifer L Roach ◽

Lutz Froenicke ◽

...

Keyword(s):

North American ◽

De Novo ◽

Draft Genome ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Sequence Coverage ◽

Short Read ◽

Oxford Nanopore ◽

Long Read ◽

Genome Assemblies

Abstract Background Whole-genome sequencing data from wild-caught individuals of closely related North American killifish species (Fundulus xenicus, Fundulus catenatus, Fundulus nottii, and Fundulus olivaceus) were obtained using long-read Oxford Nanopore Technology (ONT) PromethION and short-read Illumina platforms. Findings Draft de novo reference genome assemblies were generated using a combination of long and short sequencing reads. For each species, the PromethION platform was used to generate 30–45× sequence coverage, and the Illumina platform was used to generate 50–160× sequence coverage. Illumina-only assemblies were fragmented with high numbers of contigs, while ONT-only assemblies were error prone with low BUSCO scores. The highest N50 values, ranging from 0.4 to 2.7 Mb, were from assemblies generated using a combination of short- and long-read data. BUSCO scores were consistently >90% complete using the Eukaryota database. Conclusions High-quality genomes can be obtained from a combination of using short-read Illumina data to polish assemblies generated with long-read ONT data. Draft assemblies and raw sequencing data are available for public use. We encourage use and reuse of these data for assembly benchmarking and other analyses.

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Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences

Genome Biology ◽

10.1186/s13059-021-02447-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Readman Chiu ◽

Indhu-Shree Rajan-Babu ◽

Jan M. Friedman ◽

Inanc Birol

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Tandem Repeat ◽

Neurological Disorders ◽

Software Tool ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Long Read ◽

Repeat Expansions

AbstractTandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments. We benchmark Straglr using various simulations, targeted genotyping data of cell lines carrying expansions of known diseases, and whole genome sequencing data with chromosome-scale assembly. Our results suggest that Straglr may be useful for investigating disease-associated TR expansions using long-read sequencing.

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Comparison of long read sequencing technologies in resolving bacteria and fly genomes

10.1101/2020.07.21.213975 ◽

2020 ◽

Author(s):

Eric S. Tvedte ◽

Mark Gasser ◽

Benjamin C. Sparklin ◽

Jane Michalski ◽

Xuechu Zhao ◽

...

Keyword(s):

Genome Sequencing ◽

Bacterial Genome ◽

Fruit Fly ◽

Drosophila Ananassae ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

E Coli ◽

Hybrid Approaches ◽

Long Read ◽

Genome Assemblies

ABSTRACTBackgroundThe newest generation of DNA sequencing technology is highlighted by the ability to sequence reads hundreds of kilobases in length, and the increased availability of long read data has democratized the genome sequencing and assembly process. PacBio and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. Released in 2019, the PacBio Sequel II platform advertises substantial enhancements over previous PacBio systems.ResultsWe used whole-genome sequencing data produced by two PacBio platforms (Sequel II and RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. Sequel II assemblies had higher contiguity and consensus accuracy relative to other methods, even after accounting for differences in sequencing throughput. ONT RAPID libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assemblies or combined ONT and Sequel II libraries for eukaryotic genome assemblies. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs.ConclusionsThe ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

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Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data

10.1101/475194 ◽

2018 ◽

Cited By ~ 1

Author(s):

Robert S. Harris ◽

Monika Cechova ◽

Kateryna D. Makova

Keyword(s):

Tandem Repeats ◽

Error Rates ◽

Superior Performance ◽

Whole Genome Sequencing Data ◽

Dna Repeats ◽

Sequencing Data ◽

Heat Shock Stress ◽

Noise Cancelling ◽

Long Reads ◽

Long Read

ABSTRACTSummaryTandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstrated its superior performance as compared to two alternative tools. Using real human whole-genome sequencing data, NCRF identified long arrays of the (AATGG)n repeat involved in heat shock stress response.Availability and implementationNCRF is implemented in C, supported by several python scripts. Source code, under the MIT open source license, and simulation data are available at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder, and also in bioconda.

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Detection of simple and complex de novo mutations without, with, or with multiple reference sequences

10.1101/698910 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kiran V Garimella ◽

Zamin Iqbal ◽

Michael A. Krause ◽

Susana Campino ◽

Mihir Kekre ◽

...

Keyword(s):

De Novo ◽

Structural Diversity ◽

Low Complexity ◽

Graph Connectivity ◽

Data Sources ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

De Novo Mutations ◽

Long Read ◽

Multiple Reference

AbstractThe characterization of de novo mutations in regions of high sequence and structural diversity from whole genome sequencing data remains highly challenging. Complex structural variants tend to arise in regions of high repetitiveness and low complexity, challenging both de novo assembly, where short-reads do not capture the long-range context required for resolution, and mapping approaches, where improper alignment of reads to a reference genome that is highly diverged from that of the sample can lead to false or partial calls. Long-read technologies can potentially solve such problems but are currently unfeasible to use at scale. Here we present Corticall, a graph-based method that combines the advantages of multiple technologies and prior data sources to detect arbitrary classes of genetic variant. We construct multi-sample, coloured de Bruijn graphs from shortread data for all samples, align long-read-derived haplotypes and multiple reference data sources to restore graph connectivity information, and call variants using graph path-finding algorithms and a model for simultaneous alignment and recombination. We validate and evaluate the approach using extensive simulations and use it to characterize the rate and spectrum of de novo mutation events in 119 progeny from four Plasmodium falciparum experimental crosses, using long-read data on the parents to inform reconstructions of the progeny and to detect several known and novel non-allelic homologous recombination events.

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