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Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation

BACKGROUND: Currently available short read genome assemblies of the tetraploid protozoan parasite Giardia intestinalis are highly fragmented, highlighting the need for improved genome assemblies at a reasonable cost. Long nanopore reads are well suited to resolve repetitive genomic regions resulting...

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Autores principales: Pollo, Stephen M. J., Reiling, Sarah J., Wit, Janneke, Workentine, Matthew L., Guy, Rebecca A., Batoff, G. William, Yee, Janet, Dixon, Brent R., Wasmuth, James D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048089/
https://www.ncbi.nlm.nih.gov/pubmed/32111234
http://dx.doi.org/10.1186/s13071-020-3968-8
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author Pollo, Stephen M. J.
Reiling, Sarah J.
Wit, Janneke
Workentine, Matthew L.
Guy, Rebecca A.
Batoff, G. William
Yee, Janet
Dixon, Brent R.
Wasmuth, James D.
author_facet Pollo, Stephen M. J.
Reiling, Sarah J.
Wit, Janneke
Workentine, Matthew L.
Guy, Rebecca A.
Batoff, G. William
Yee, Janet
Dixon, Brent R.
Wasmuth, James D.
author_sort Pollo, Stephen M. J.
collection PubMed
description BACKGROUND: Currently available short read genome assemblies of the tetraploid protozoan parasite Giardia intestinalis are highly fragmented, highlighting the need for improved genome assemblies at a reasonable cost. Long nanopore reads are well suited to resolve repetitive genomic regions resulting in better quality assemblies of eukaryotic genomes. Subsequent addition of highly accurate short reads to long-read assemblies further improves assembly quality. Using this hybrid approach, we assembled genomes for three Giardia isolates, two with published assemblies and one novel, to evaluate the improvement in genome quality gained from long reads. We then used the long reads to predict structural variants to examine this previously unexplored source of genetic variation in Giardia. METHODS: With MinION reads for each isolate, we assembled genomes using several assemblers specializing in long reads. Assembly metrics, gene finding, and whole genome alignments to the reference genomes enabled direct comparison to evaluate the performance of the nanopore reads. Further improvements from adding Illumina reads to the long-read assemblies were evaluated using gene finding. Structural variants were predicted from alignments of the long reads to the best hybrid genome for each isolate and enrichment of key genes was analyzed using random genome sampling and calculation of percentiles to find thresholds of significance. RESULTS: Our hybrid assembly method generated reference quality genomes for each isolate. Consistent with previous findings based on SNPs, examination of heterozygosity using the structural variants found that Giardia BGS was considerably more heterozygous than the other isolates that are from Assemblage A. Further, each isolate was shown to contain structural variant regions enriched for variant-specific surface proteins, a key class of virulence factor in Giardia. CONCLUSIONS: The ability to generate reference quality genomes from a single MinION run and a multiplexed MiSeq run enables future large-scale comparative genomic studies within the genus Giardia. Further, prediction of structural variants from long reads allows for more in-depth analyses of major sources of genetic variation within and between Giardia isolates that could have effects on both pathogenicity and host range. [Image: see text]
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spelling pubmed-70480892020-03-05 Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation Pollo, Stephen M. J. Reiling, Sarah J. Wit, Janneke Workentine, Matthew L. Guy, Rebecca A. Batoff, G. William Yee, Janet Dixon, Brent R. Wasmuth, James D. Parasit Vectors Research BACKGROUND: Currently available short read genome assemblies of the tetraploid protozoan parasite Giardia intestinalis are highly fragmented, highlighting the need for improved genome assemblies at a reasonable cost. Long nanopore reads are well suited to resolve repetitive genomic regions resulting in better quality assemblies of eukaryotic genomes. Subsequent addition of highly accurate short reads to long-read assemblies further improves assembly quality. Using this hybrid approach, we assembled genomes for three Giardia isolates, two with published assemblies and one novel, to evaluate the improvement in genome quality gained from long reads. We then used the long reads to predict structural variants to examine this previously unexplored source of genetic variation in Giardia. METHODS: With MinION reads for each isolate, we assembled genomes using several assemblers specializing in long reads. Assembly metrics, gene finding, and whole genome alignments to the reference genomes enabled direct comparison to evaluate the performance of the nanopore reads. Further improvements from adding Illumina reads to the long-read assemblies were evaluated using gene finding. Structural variants were predicted from alignments of the long reads to the best hybrid genome for each isolate and enrichment of key genes was analyzed using random genome sampling and calculation of percentiles to find thresholds of significance. RESULTS: Our hybrid assembly method generated reference quality genomes for each isolate. Consistent with previous findings based on SNPs, examination of heterozygosity using the structural variants found that Giardia BGS was considerably more heterozygous than the other isolates that are from Assemblage A. Further, each isolate was shown to contain structural variant regions enriched for variant-specific surface proteins, a key class of virulence factor in Giardia. CONCLUSIONS: The ability to generate reference quality genomes from a single MinION run and a multiplexed MiSeq run enables future large-scale comparative genomic studies within the genus Giardia. Further, prediction of structural variants from long reads allows for more in-depth analyses of major sources of genetic variation within and between Giardia isolates that could have effects on both pathogenicity and host range. [Image: see text] BioMed Central 2020-02-28 /pmc/articles/PMC7048089/ /pubmed/32111234 http://dx.doi.org/10.1186/s13071-020-3968-8 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Pollo, Stephen M. J.
Reiling, Sarah J.
Wit, Janneke
Workentine, Matthew L.
Guy, Rebecca A.
Batoff, G. William
Yee, Janet
Dixon, Brent R.
Wasmuth, James D.
Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation
title Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation
title_full Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation
title_fullStr Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation
title_full_unstemmed Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation
title_short Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation
title_sort benchmarking hybrid assemblies of giardia and prediction of widespread intra-isolate structural variation
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048089/
https://www.ncbi.nlm.nih.gov/pubmed/32111234
http://dx.doi.org/10.1186/s13071-020-3968-8
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