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A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae)
Cipangopaludina cathayensis (Gastropoda: Prosobranchia; Mesogastropoda; Viviparidae) is widely distributed in the freshwater habitats of China. It is an economically important snail with high edible and medicinal value. However, the genomic resources and the reference genome of this snail are lackin...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10379862/ https://www.ncbi.nlm.nih.gov/pubmed/37510270 http://dx.doi.org/10.3390/genes14071365 |
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author | Ma, Benhe Jin, Wu Fu, Huiyun Sun, Bing Yang, Su Ma, Xueyan Wen, Haibo Wu, Xiaoping Wang, Haihua Cao, Xiaojuan |
author_facet | Ma, Benhe Jin, Wu Fu, Huiyun Sun, Bing Yang, Su Ma, Xueyan Wen, Haibo Wu, Xiaoping Wang, Haihua Cao, Xiaojuan |
author_sort | Ma, Benhe |
collection | PubMed |
description | Cipangopaludina cathayensis (Gastropoda: Prosobranchia; Mesogastropoda; Viviparidae) is widely distributed in the freshwater habitats of China. It is an economically important snail with high edible and medicinal value. However, the genomic resources and the reference genome of this snail are lacking. In this study, we assembled the first chromosome-level genome of C. cathayensis. The preliminary assembly genome was 1.48 Gb in size, with a contig N50 size of 93.49 Mb. The assembled sequences were anchored to nine pseudochromosomes using Hi-C data. The final genome after Hi-C correction was 1.48 Gb, with a contig N50 of 98.49 Mb and scaffold N50 of 195.21 Mb. The anchored rate of the chromosome was 99.99%. A total of 22,702 protein-coding genes were predicted. Phylogenetic analyses indicated that C. cathayensis diverged with Bellamya purificata approximately 158.10 million years ago. There were 268 expanded and 505 contracted gene families in C. cathayensis when compared with its most recent common ancestor. Five putative genes under positive selection in C. cathayensis were identified (false discovery rate <0.05). These genome data provide a valuable resource for evolutionary studies of the family Viviparidae, and for the genetic improvement of C. cathayensis. |
format | Online Article Text |
id | pubmed-10379862 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-103798622023-07-29 A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae) Ma, Benhe Jin, Wu Fu, Huiyun Sun, Bing Yang, Su Ma, Xueyan Wen, Haibo Wu, Xiaoping Wang, Haihua Cao, Xiaojuan Genes (Basel) Article Cipangopaludina cathayensis (Gastropoda: Prosobranchia; Mesogastropoda; Viviparidae) is widely distributed in the freshwater habitats of China. It is an economically important snail with high edible and medicinal value. However, the genomic resources and the reference genome of this snail are lacking. In this study, we assembled the first chromosome-level genome of C. cathayensis. The preliminary assembly genome was 1.48 Gb in size, with a contig N50 size of 93.49 Mb. The assembled sequences were anchored to nine pseudochromosomes using Hi-C data. The final genome after Hi-C correction was 1.48 Gb, with a contig N50 of 98.49 Mb and scaffold N50 of 195.21 Mb. The anchored rate of the chromosome was 99.99%. A total of 22,702 protein-coding genes were predicted. Phylogenetic analyses indicated that C. cathayensis diverged with Bellamya purificata approximately 158.10 million years ago. There were 268 expanded and 505 contracted gene families in C. cathayensis when compared with its most recent common ancestor. Five putative genes under positive selection in C. cathayensis were identified (false discovery rate <0.05). These genome data provide a valuable resource for evolutionary studies of the family Viviparidae, and for the genetic improvement of C. cathayensis. MDPI 2023-06-28 /pmc/articles/PMC10379862/ /pubmed/37510270 http://dx.doi.org/10.3390/genes14071365 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 Ma, Benhe Jin, Wu Fu, Huiyun Sun, Bing Yang, Su Ma, Xueyan Wen, Haibo Wu, Xiaoping Wang, Haihua Cao, Xiaojuan A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae) |
title | A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae) |
title_full | A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae) |
title_fullStr | A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae) |
title_full_unstemmed | A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae) |
title_short | A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae) |
title_sort | high-quality chromosome-level genome assembly of a snail cipangopaludina cathayensis (gastropoda: viviparidae) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10379862/ https://www.ncbi.nlm.nih.gov/pubmed/37510270 http://dx.doi.org/10.3390/genes14071365 |
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