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The Chromosome-Level Genome Assembly of Bean Blossom Thrips (Megalurothrips usitatus) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants

Megalurothrips usitatus (Bagnall) is a destructive pest of legumes, such as cowpea. The biology, population dynamics and control strategies of this pest have been well studied. However, the lack of a high-quality reference genome for M. usitatus has hindered the understanding of key biological quest...

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Autores principales: Zhang, Zhijun, Bao, Jiandong, Chen, Qizhang, He, Jianyun, Li, Xiaowei, Zhang, Jiahui, Liu, Zhixing, Wu, Yixuan, Wang, Yunsheng, Lu, Yaobin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10379191/
https://www.ncbi.nlm.nih.gov/pubmed/37511029
http://dx.doi.org/10.3390/ijms241411268
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author Zhang, Zhijun
Bao, Jiandong
Chen, Qizhang
He, Jianyun
Li, Xiaowei
Zhang, Jiahui
Liu, Zhixing
Wu, Yixuan
Wang, Yunsheng
Lu, Yaobin
author_facet Zhang, Zhijun
Bao, Jiandong
Chen, Qizhang
He, Jianyun
Li, Xiaowei
Zhang, Jiahui
Liu, Zhixing
Wu, Yixuan
Wang, Yunsheng
Lu, Yaobin
author_sort Zhang, Zhijun
collection PubMed
description Megalurothrips usitatus (Bagnall) is a destructive pest of legumes, such as cowpea. The biology, population dynamics and control strategies of this pest have been well studied. However, the lack of a high-quality reference genome for M. usitatus has hindered the understanding of key biological questions, such as the mechanism of adaptation to feed preferentially on high-protein host plants and the resistance to proteinase inhibitors (PIs). In this study, we generated a high-resolution chromosome-level reference genome assembly (247.82 Mb, 16 chromosomes) of M. usitatus by combining Oxford Nanopore Technologies (ONT) and Hi-C sequencing. The genome assembly showed higher proportions of GC and repeat content compared to other Thripinae species. Genome annotation revealed 18,624 protein-coding genes, including 4613 paralogs that were preferentially located in TE-rich regions. GO and KEGG enrichment analyses of the paralogs revealed significant enrichment in digestion-related genes. Genome-wide identification uncovered 506 putative digestion-related enzymes; of those, proteases, especially their subgroup serine proteases (SPs), are significantly enriched in paralogs. We hypothesized that the diversity and expansion of the digestion-related genes, especially SPs, could be driven by mobile elements (TEs), which promote the adaptive evolution of M. usitatus to high-protein host plants with high serine protease inhibitors (SPIs). The current study provides a valuable genomic resource for understanding the genetic variation among different pest species adapting to different plant hosts.
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spelling pubmed-103791912023-07-29 The Chromosome-Level Genome Assembly of Bean Blossom Thrips (Megalurothrips usitatus) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants Zhang, Zhijun Bao, Jiandong Chen, Qizhang He, Jianyun Li, Xiaowei Zhang, Jiahui Liu, Zhixing Wu, Yixuan Wang, Yunsheng Lu, Yaobin Int J Mol Sci Article Megalurothrips usitatus (Bagnall) is a destructive pest of legumes, such as cowpea. The biology, population dynamics and control strategies of this pest have been well studied. However, the lack of a high-quality reference genome for M. usitatus has hindered the understanding of key biological questions, such as the mechanism of adaptation to feed preferentially on high-protein host plants and the resistance to proteinase inhibitors (PIs). In this study, we generated a high-resolution chromosome-level reference genome assembly (247.82 Mb, 16 chromosomes) of M. usitatus by combining Oxford Nanopore Technologies (ONT) and Hi-C sequencing. The genome assembly showed higher proportions of GC and repeat content compared to other Thripinae species. Genome annotation revealed 18,624 protein-coding genes, including 4613 paralogs that were preferentially located in TE-rich regions. GO and KEGG enrichment analyses of the paralogs revealed significant enrichment in digestion-related genes. Genome-wide identification uncovered 506 putative digestion-related enzymes; of those, proteases, especially their subgroup serine proteases (SPs), are significantly enriched in paralogs. We hypothesized that the diversity and expansion of the digestion-related genes, especially SPs, could be driven by mobile elements (TEs), which promote the adaptive evolution of M. usitatus to high-protein host plants with high serine protease inhibitors (SPIs). The current study provides a valuable genomic resource for understanding the genetic variation among different pest species adapting to different plant hosts. MDPI 2023-07-10 /pmc/articles/PMC10379191/ /pubmed/37511029 http://dx.doi.org/10.3390/ijms241411268 Text en © 2023 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, Zhijun
Bao, Jiandong
Chen, Qizhang
He, Jianyun
Li, Xiaowei
Zhang, Jiahui
Liu, Zhixing
Wu, Yixuan
Wang, Yunsheng
Lu, Yaobin
The Chromosome-Level Genome Assembly of Bean Blossom Thrips (Megalurothrips usitatus) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants
title The Chromosome-Level Genome Assembly of Bean Blossom Thrips (Megalurothrips usitatus) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants
title_full The Chromosome-Level Genome Assembly of Bean Blossom Thrips (Megalurothrips usitatus) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants
title_fullStr The Chromosome-Level Genome Assembly of Bean Blossom Thrips (Megalurothrips usitatus) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants
title_full_unstemmed The Chromosome-Level Genome Assembly of Bean Blossom Thrips (Megalurothrips usitatus) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants
title_short The Chromosome-Level Genome Assembly of Bean Blossom Thrips (Megalurothrips usitatus) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants
title_sort chromosome-level genome assembly of bean blossom thrips (megalurothrips usitatus) reveals an expansion of protein digestion-related genes in adaption to high-protein host plants
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10379191/
https://www.ncbi.nlm.nih.gov/pubmed/37511029
http://dx.doi.org/10.3390/ijms241411268
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