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

Abstract 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 contro...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Guilherme B. Dias, Musaad A. Altammami, Hamadttu A. F. El-Shafie, Fahad M. Alhoshani, Mohamed B. Al-Fageeh, Casey M. Bergman, Manee M. Manee
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/41f6308fa46242ac8647c605a7ed142d
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:41f6308fa46242ac8647c605a7ed142d
record_format	dspace
spelling	oai:doaj.org-article:41f6308fa46242ac8647c605a7ed142d2021-12-02T17:01:49ZHaplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus10.1038/s41598-021-89091-w2045-2322https://doaj.org/article/41f6308fa46242ac8647c605a7ed142d2021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-89091-whttps://doaj.org/toc/2045-2322Abstract 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 ( $$\sim$$ ∼ 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.Guilherme B. DiasMusaad A. AltammamiHamadttu A. F. El-ShafieFahad M. AlhoshaniMohamed B. Al-FageehCasey M. BergmanManee M. ManeeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Guilherme B. Dias Musaad A. Altammami Hamadttu A. F. El-Shafie Fahad M. Alhoshani Mohamed B. Al-Fageeh Casey M. Bergman Manee M. Manee Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus
description	Abstract 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 ( $$\sim$$ ∼ 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.
format	article
author	Guilherme B. Dias Musaad A. Altammami Hamadttu A. F. El-Shafie Fahad M. Alhoshani Mohamed B. Al-Fageeh Casey M. Bergman Manee M. Manee
author_facet	Guilherme B. Dias Musaad A. Altammami Hamadttu A. F. El-Shafie Fahad M. Alhoshani Mohamed B. Al-Fageeh Casey M. Bergman Manee M. Manee
author_sort	Guilherme B. Dias
title	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_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_sort	haplotype-resolved genome assembly enables gene discovery in the red palm weevil rhynchophorus ferrugineus
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/41f6308fa46242ac8647c605a7ed142d
work_keys_str_mv	AT guilhermebdias haplotyperesolvedgenomeassemblyenablesgenediscoveryintheredpalmweevilrhynchophorusferrugineus AT musaadaaltammami haplotyperesolvedgenomeassemblyenablesgenediscoveryintheredpalmweevilrhynchophorusferrugineus AT hamadttuafelshafie haplotyperesolvedgenomeassemblyenablesgenediscoveryintheredpalmweevilrhynchophorusferrugineus AT fahadmalhoshani haplotyperesolvedgenomeassemblyenablesgenediscoveryintheredpalmweevilrhynchophorusferrugineus AT mohamedbalfageeh haplotyperesolvedgenomeassemblyenablesgenediscoveryintheredpalmweevilrhynchophorusferrugineus AT caseymbergman haplotyperesolvedgenomeassemblyenablesgenediscoveryintheredpalmweevilrhynchophorusferrugineus AT maneemmanee haplotyperesolvedgenomeassemblyenablesgenediscoveryintheredpalmweevilrhynchophorusferrugineus
_version_	1718382023612039168

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

Ejemplares similares