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Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus

The red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strateg...

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Autores principales: Dias, Guilherme B., Altammami, Musaad A., El-Shafie, Hamadttu A. F., Alhoshani, Fahad M., Al-Fageeh, Mohamed B., Bergman, Casey M., Manee, Manee M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8113489/
https://www.ncbi.nlm.nih.gov/pubmed/33976235
http://dx.doi.org/10.1038/s41598-021-89091-w
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author Dias, Guilherme B.
Altammami, Musaad A.
El-Shafie, Hamadttu A. F.
Alhoshani, Fahad M.
Al-Fageeh, Mohamed B.
Bergman, Casey M.
Manee, Manee M.
author_facet Dias, Guilherme B.
Altammami, Musaad A.
El-Shafie, Hamadttu A. F.
Alhoshani, Fahad M.
Al-Fageeh, Mohamed B.
Bergman, Casey M.
Manee, Manee M.
author_sort Dias, Guilherme B.
collection PubMed
description The red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly for R. ferrugineus from a single heterozygous individual with modest sequencing coverage ([Formula: see text] 62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in our R. ferrugineus genome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci in R. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% of R. ferrugineus chemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest.
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spelling pubmed-81134892021-05-12 Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus Dias, Guilherme B. Altammami, Musaad A. El-Shafie, Hamadttu A. F. Alhoshani, Fahad M. Al-Fageeh, Mohamed B. Bergman, Casey M. Manee, Manee M. Sci Rep Article The red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly for R. ferrugineus from a single heterozygous individual with modest sequencing coverage ([Formula: see text] 62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in our R. ferrugineus genome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci in R. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% of R. ferrugineus chemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest. Nature Publishing Group UK 2021-05-11 /pmc/articles/PMC8113489/ /pubmed/33976235 http://dx.doi.org/10.1038/s41598-021-89091-w Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Dias, Guilherme B.
Altammami, Musaad A.
El-Shafie, Hamadttu A. F.
Alhoshani, Fahad M.
Al-Fageeh, Mohamed B.
Bergman, Casey M.
Manee, Manee M.
Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus
title Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus
title_full Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus
title_fullStr Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus
title_full_unstemmed Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus
title_short Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus
title_sort haplotype-resolved genome assembly enables gene discovery in the red palm weevil rhynchophorus ferrugineus
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8113489/
https://www.ncbi.nlm.nih.gov/pubmed/33976235
http://dx.doi.org/10.1038/s41598-021-89091-w
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