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Chromosome-length genome assembly of Teladorsagia circumcincta – a globally important helminth parasite in livestock

BACKGROUND: Gastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta, infects the abomasum and causes production losses, reductions in weight gain, diarrhoe...

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Autores principales: Hassan, Shamshad Ul, Chua, Eng Guan, Paz, Erwin A., Tay, Chin Yen, Greeff, Johan C., Palmer, Dieter G., Dudchenko, Olga, Aiden, Erez Lieberman, Martin, Graeme B., Kaur, Parwinder
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9933375/
https://www.ncbi.nlm.nih.gov/pubmed/36792983
http://dx.doi.org/10.1186/s12864-023-09172-0
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author Hassan, Shamshad Ul
Chua, Eng Guan
Paz, Erwin A.
Tay, Chin Yen
Greeff, Johan C.
Palmer, Dieter G.
Dudchenko, Olga
Aiden, Erez Lieberman
Martin, Graeme B.
Kaur, Parwinder
author_facet Hassan, Shamshad Ul
Chua, Eng Guan
Paz, Erwin A.
Tay, Chin Yen
Greeff, Johan C.
Palmer, Dieter G.
Dudchenko, Olga
Aiden, Erez Lieberman
Martin, Graeme B.
Kaur, Parwinder
author_sort Hassan, Shamshad Ul
collection PubMed
description BACKGROUND: Gastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta, infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta, such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics. RESULTS: We have constructed a high-quality reference genome, with chromosome-length scaffolds, by purging alternative haplotypes from the existing draft genome assembly and scaffolding the result using chromosome conformation, capture-based, in situ Hi-C technique. The improved (Hi-C) assembly resulted in six chromosome-length scaffolds with length ranging from 66.6 Mbp to 49.6 Mbp, 35% fewer sequences and reduction in size. Substantial improvements were also achieved in both the values for N50 (57.1 Mbp) and L50 (5 Mbp). A higher and comparable level of genome and proteome completeness was achieved for Hi-C assembly on BUSCO parameters. The Hi-C assembly had a greater synteny and number of orthologs with a closely related nematode, Haemonchus contortus. CONCLUSION: This improved genomic resource is suitable as a foundation for the identification of potential targets for vaccine and drug development. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09172-0.
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spelling pubmed-99333752023-02-17 Chromosome-length genome assembly of Teladorsagia circumcincta – a globally important helminth parasite in livestock Hassan, Shamshad Ul Chua, Eng Guan Paz, Erwin A. Tay, Chin Yen Greeff, Johan C. Palmer, Dieter G. Dudchenko, Olga Aiden, Erez Lieberman Martin, Graeme B. Kaur, Parwinder BMC Genomics Research BACKGROUND: Gastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta, infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta, such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics. RESULTS: We have constructed a high-quality reference genome, with chromosome-length scaffolds, by purging alternative haplotypes from the existing draft genome assembly and scaffolding the result using chromosome conformation, capture-based, in situ Hi-C technique. The improved (Hi-C) assembly resulted in six chromosome-length scaffolds with length ranging from 66.6 Mbp to 49.6 Mbp, 35% fewer sequences and reduction in size. Substantial improvements were also achieved in both the values for N50 (57.1 Mbp) and L50 (5 Mbp). A higher and comparable level of genome and proteome completeness was achieved for Hi-C assembly on BUSCO parameters. The Hi-C assembly had a greater synteny and number of orthologs with a closely related nematode, Haemonchus contortus. CONCLUSION: This improved genomic resource is suitable as a foundation for the identification of potential targets for vaccine and drug development. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09172-0. BioMed Central 2023-02-15 /pmc/articles/PMC9933375/ /pubmed/36792983 http://dx.doi.org/10.1186/s12864-023-09172-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This 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/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://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
Hassan, Shamshad Ul
Chua, Eng Guan
Paz, Erwin A.
Tay, Chin Yen
Greeff, Johan C.
Palmer, Dieter G.
Dudchenko, Olga
Aiden, Erez Lieberman
Martin, Graeme B.
Kaur, Parwinder
Chromosome-length genome assembly of Teladorsagia circumcincta – a globally important helminth parasite in livestock
title Chromosome-length genome assembly of Teladorsagia circumcincta – a globally important helminth parasite in livestock
title_full Chromosome-length genome assembly of Teladorsagia circumcincta – a globally important helminth parasite in livestock
title_fullStr Chromosome-length genome assembly of Teladorsagia circumcincta – a globally important helminth parasite in livestock
title_full_unstemmed Chromosome-length genome assembly of Teladorsagia circumcincta – a globally important helminth parasite in livestock
title_short Chromosome-length genome assembly of Teladorsagia circumcincta – a globally important helminth parasite in livestock
title_sort chromosome-length genome assembly of teladorsagia circumcincta – a globally important helminth parasite in livestock
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9933375/
https://www.ncbi.nlm.nih.gov/pubmed/36792983
http://dx.doi.org/10.1186/s12864-023-09172-0
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