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High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing

BACKGROUND: Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting >100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecu...

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Autores principales: Stroehlein, Andreas J, Korhonen, Pasi K, Chong, Teik Min, Lim, Yan Lue, Chan, Kok Gan, Webster, Bonnie, Rollinson, David, Brindley, Paul J, Gasser, Robin B, Young, Neil D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736295/
https://www.ncbi.nlm.nih.gov/pubmed/31494670
http://dx.doi.org/10.1093/gigascience/giz108
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author Stroehlein, Andreas J
Korhonen, Pasi K
Chong, Teik Min
Lim, Yan Lue
Chan, Kok Gan
Webster, Bonnie
Rollinson, David
Brindley, Paul J
Gasser, Robin B
Young, Neil D
author_facet Stroehlein, Andreas J
Korhonen, Pasi K
Chong, Teik Min
Lim, Yan Lue
Chan, Kok Gan
Webster, Bonnie
Rollinson, David
Brindley, Paul J
Gasser, Robin B
Young, Neil D
author_sort Stroehlein, Andreas J
collection PubMed
description BACKGROUND: Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting >100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecular level, little is known about this blood fluke and the pathogenesis of the disease that it causes. To support molecular studies of this carcinogenic worm, we reported a draft genome for S. haematobium in 2012. Although a useful resource, its utility has been somewhat limited by its fragmentation. FINDINGS: Here, we systematically enhanced the draft genome of S. haematobium using a single-molecule and long-range DNA-sequencing approach. We achieved a major improvement in the accuracy and contiguity of the genome assembly, making it superior or comparable to assemblies for other schistosome species. We transferred curated gene models to this assembly and, using enhanced gene annotation pipelines, inferred a gene set with as many or more complete gene models as those of other well-studied schistosomes. Using conserved, single-copy orthologs, we assessed the phylogenetic position of S. haematobium in relation to other parasitic flatworms for which draft genomes were available. CONCLUSIONS: We report a substantially enhanced genomic resource that represents a solid foundation for molecular research on S. haematobium and is poised to better underpin population and functional genomic investigations and to accelerate the search for new disease interventions.
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spelling pubmed-67362952019-09-16 High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing Stroehlein, Andreas J Korhonen, Pasi K Chong, Teik Min Lim, Yan Lue Chan, Kok Gan Webster, Bonnie Rollinson, David Brindley, Paul J Gasser, Robin B Young, Neil D Gigascience Data Note BACKGROUND: Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting >100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecular level, little is known about this blood fluke and the pathogenesis of the disease that it causes. To support molecular studies of this carcinogenic worm, we reported a draft genome for S. haematobium in 2012. Although a useful resource, its utility has been somewhat limited by its fragmentation. FINDINGS: Here, we systematically enhanced the draft genome of S. haematobium using a single-molecule and long-range DNA-sequencing approach. We achieved a major improvement in the accuracy and contiguity of the genome assembly, making it superior or comparable to assemblies for other schistosome species. We transferred curated gene models to this assembly and, using enhanced gene annotation pipelines, inferred a gene set with as many or more complete gene models as those of other well-studied schistosomes. Using conserved, single-copy orthologs, we assessed the phylogenetic position of S. haematobium in relation to other parasitic flatworms for which draft genomes were available. CONCLUSIONS: We report a substantially enhanced genomic resource that represents a solid foundation for molecular research on S. haematobium and is poised to better underpin population and functional genomic investigations and to accelerate the search for new disease interventions. Oxford University Press 2019-09-05 /pmc/articles/PMC6736295/ /pubmed/31494670 http://dx.doi.org/10.1093/gigascience/giz108 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Stroehlein, Andreas J
Korhonen, Pasi K
Chong, Teik Min
Lim, Yan Lue
Chan, Kok Gan
Webster, Bonnie
Rollinson, David
Brindley, Paul J
Gasser, Robin B
Young, Neil D
High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing
title High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing
title_full High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing
title_fullStr High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing
title_full_unstemmed High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing
title_short High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing
title_sort high-quality schistosoma haematobium genome achieved by single-molecule and long-range sequencing
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736295/
https://www.ncbi.nlm.nih.gov/pubmed/31494670
http://dx.doi.org/10.1093/gigascience/giz108
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