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Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes

Lepidopteran species are mostly pests, causing serious annual economic losses. High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. Long-read sequencing technology and assembly algorithm advances have improved t...

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Autores principales: Zhang, Tong, Xing, Weiqing, Wang, Aoming, Zhang, Na, Jia, Ling, Ma, Sanyuan, Xia, Qingyou
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9820851/
https://www.ncbi.nlm.nih.gov/pubmed/36614092
http://dx.doi.org/10.3390/ijms24010649
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author Zhang, Tong
Xing, Weiqing
Wang, Aoming
Zhang, Na
Jia, Ling
Ma, Sanyuan
Xia, Qingyou
author_facet Zhang, Tong
Xing, Weiqing
Wang, Aoming
Zhang, Na
Jia, Ling
Ma, Sanyuan
Xia, Qingyou
author_sort Zhang, Tong
collection PubMed
description Lepidopteran species are mostly pests, causing serious annual economic losses. High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. Long-read sequencing technology and assembly algorithm advances have improved the ability to timeously produce high-quality genomes. Lepidoptera includes a wide variety of insects with high genetic diversity and heterozygosity. Therefore, the selection of an appropriate sequencing and assembly strategy to obtain high-quality genomic information is urgently needed. This research used silkworm as a model to test genome sequencing and assembly through high-coverage datasets by de novo assemblies. We report the first nearly complete telomere-to-telomere reference genome of silkworm Bombyx mori (P50T strain) produced by Pacific Biosciences (PacBio) HiFi sequencing, and highly contiguous and complete genome assemblies of two other silkworm strains by Oxford Nanopore Technologies (ONT) or PacBio continuous long-reads (CLR) that were unrepresented in the public database. Assembly quality was evaluated by use of BUSCO, Inspector, and EagleC. It is necessary to choose an appropriate assembler for draft genome construction, especially for low-depth datasets. For PacBio CLR and ONT sequencing, NextDenovo is superior. For PacBio HiFi sequencing, hifiasm is better. Quality assessment is essential for genome assembly and can provide better and more accurate results. For chromosome-level high-quality genome construction, we recommend using 3D-DNA with EagleC evaluation. Our study references how to obtain and evaluate high-quality genome assemblies, and is a resource for biological control, comparative genomics, and evolutionary studies of Lepidopteran pests and related species.
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spelling pubmed-98208512023-01-07 Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes Zhang, Tong Xing, Weiqing Wang, Aoming Zhang, Na Jia, Ling Ma, Sanyuan Xia, Qingyou Int J Mol Sci Article Lepidopteran species are mostly pests, causing serious annual economic losses. High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. Long-read sequencing technology and assembly algorithm advances have improved the ability to timeously produce high-quality genomes. Lepidoptera includes a wide variety of insects with high genetic diversity and heterozygosity. Therefore, the selection of an appropriate sequencing and assembly strategy to obtain high-quality genomic information is urgently needed. This research used silkworm as a model to test genome sequencing and assembly through high-coverage datasets by de novo assemblies. We report the first nearly complete telomere-to-telomere reference genome of silkworm Bombyx mori (P50T strain) produced by Pacific Biosciences (PacBio) HiFi sequencing, and highly contiguous and complete genome assemblies of two other silkworm strains by Oxford Nanopore Technologies (ONT) or PacBio continuous long-reads (CLR) that were unrepresented in the public database. Assembly quality was evaluated by use of BUSCO, Inspector, and EagleC. It is necessary to choose an appropriate assembler for draft genome construction, especially for low-depth datasets. For PacBio CLR and ONT sequencing, NextDenovo is superior. For PacBio HiFi sequencing, hifiasm is better. Quality assessment is essential for genome assembly and can provide better and more accurate results. For chromosome-level high-quality genome construction, we recommend using 3D-DNA with EagleC evaluation. Our study references how to obtain and evaluate high-quality genome assemblies, and is a resource for biological control, comparative genomics, and evolutionary studies of Lepidopteran pests and related species. MDPI 2022-12-30 /pmc/articles/PMC9820851/ /pubmed/36614092 http://dx.doi.org/10.3390/ijms24010649 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhang, Tong
Xing, Weiqing
Wang, Aoming
Zhang, Na
Jia, Ling
Ma, Sanyuan
Xia, Qingyou
Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes
title Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes
title_full Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes
title_fullStr Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes
title_full_unstemmed Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes
title_short Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes
title_sort comparison of long-read methods for sequencing and assembly of lepidopteran pest genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9820851/
https://www.ncbi.nlm.nih.gov/pubmed/36614092
http://dx.doi.org/10.3390/ijms24010649
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