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High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance

The king scallop, Pecten maximus is a well-known, commercially important scallop species and is featured with remarkable tolerance to potent phytotoxins such as domoic acid. A high-quality genome can shed light on its biology and innovative evolution of toxin resistance. A reference genome has recen...

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Autores principales: Zeng, Qifan, Liu, Jing, Wang, Chunde, Wang, Hao, Zhang, Lingling, Hu, Jingjie, Bao, Lisui, Wang, Shi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8437780/
https://www.ncbi.nlm.nih.gov/pubmed/34527199
http://dx.doi.org/10.1016/j.csbj.2021.08.038
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author Zeng, Qifan
Liu, Jing
Wang, Chunde
Wang, Hao
Zhang, Lingling
Hu, Jingjie
Bao, Lisui
Wang, Shi
author_facet Zeng, Qifan
Liu, Jing
Wang, Chunde
Wang, Hao
Zhang, Lingling
Hu, Jingjie
Bao, Lisui
Wang, Shi
author_sort Zeng, Qifan
collection PubMed
description The king scallop, Pecten maximus is a well-known, commercially important scallop species and is featured with remarkable tolerance to potent phytotoxins such as domoic acid. A high-quality genome can shed light on its biology and innovative evolution of toxin resistance. A reference genome has recently been published for P. maximus, however, it is suspicious that over 67,700 genes are annotated in this genome, which is unexpectedly larger than its close relatives of pectinids. Herein, we provide an improved high-quality chromosome-level reference genome assembly and annotation for the king scallop P. maximus. A final set of 26,995 genes is annotated after carefully checking and curation of the predicted gene models, which significantly improves the accuracy of gene structure information. The large number of gene duplicates in the previous genome is mainly distorted by the fragmented annotation. Through integrated genomic, evolutionary and transcriptomic analyses, we reveal that the Phi subfamily of ionotropic glutamate receptors (iGluRs) are well preserved in molluscs, and P. maximus experienced the rapid expansion of the Phi class of iGluR (GluF) gene family. The GluF genes exhibit ubiquitously high expression and altered sequence characteristics for ligand selectivity, which may contribute to the remarkable tolerance to neurotoxins in P. maximus. Taken together, our study disapproves the previous claim of the 'gene-rich' genome of this species and provides a high-quality genome assembly for further understanding of its biology and evolution of toxin resistance.
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spelling pubmed-84377802021-09-14 High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance Zeng, Qifan Liu, Jing Wang, Chunde Wang, Hao Zhang, Lingling Hu, Jingjie Bao, Lisui Wang, Shi Comput Struct Biotechnol J Research Article The king scallop, Pecten maximus is a well-known, commercially important scallop species and is featured with remarkable tolerance to potent phytotoxins such as domoic acid. A high-quality genome can shed light on its biology and innovative evolution of toxin resistance. A reference genome has recently been published for P. maximus, however, it is suspicious that over 67,700 genes are annotated in this genome, which is unexpectedly larger than its close relatives of pectinids. Herein, we provide an improved high-quality chromosome-level reference genome assembly and annotation for the king scallop P. maximus. A final set of 26,995 genes is annotated after carefully checking and curation of the predicted gene models, which significantly improves the accuracy of gene structure information. The large number of gene duplicates in the previous genome is mainly distorted by the fragmented annotation. Through integrated genomic, evolutionary and transcriptomic analyses, we reveal that the Phi subfamily of ionotropic glutamate receptors (iGluRs) are well preserved in molluscs, and P. maximus experienced the rapid expansion of the Phi class of iGluR (GluF) gene family. The GluF genes exhibit ubiquitously high expression and altered sequence characteristics for ligand selectivity, which may contribute to the remarkable tolerance to neurotoxins in P. maximus. Taken together, our study disapproves the previous claim of the 'gene-rich' genome of this species and provides a high-quality genome assembly for further understanding of its biology and evolution of toxin resistance. Research Network of Computational and Structural Biotechnology 2021-08-27 /pmc/articles/PMC8437780/ /pubmed/34527199 http://dx.doi.org/10.1016/j.csbj.2021.08.038 Text en © 2021 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Zeng, Qifan
Liu, Jing
Wang, Chunde
Wang, Hao
Zhang, Lingling
Hu, Jingjie
Bao, Lisui
Wang, Shi
High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance
title High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance
title_full High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance
title_fullStr High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance
title_full_unstemmed High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance
title_short High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance
title_sort high-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8437780/
https://www.ncbi.nlm.nih.gov/pubmed/34527199
http://dx.doi.org/10.1016/j.csbj.2021.08.038
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