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Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution
The masked palm civet (Paguma larvata) is a small carnivore with distinct biological characteristics, that likes an omnivorous diet and also serves as a vector of pathogens. Although this species is not an endangered animal, its population is reportedly declining. Since the severe acute respiratory...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8815822/ https://www.ncbi.nlm.nih.gov/pubmed/35126472 http://dx.doi.org/10.3389/fgene.2021.819493 |
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author | Lan, Tianming Fang, Dongming Li, Haimeng Sahu, Sunil Kumar Wang, Qing Yuan, Hao Zhu, Yixin Yang, Zipeng Zhang, Le Yang, Shangchen Lu, Haorong Han, Lei Zhang, Shaofang Yu, Jieyao Mahmmod, Yasser S. Xu, Yanchun Hua, Yan He, Fengping Yuan, Ziguo Liu, Huan |
author_facet | Lan, Tianming Fang, Dongming Li, Haimeng Sahu, Sunil Kumar Wang, Qing Yuan, Hao Zhu, Yixin Yang, Zipeng Zhang, Le Yang, Shangchen Lu, Haorong Han, Lei Zhang, Shaofang Yu, Jieyao Mahmmod, Yasser S. Xu, Yanchun Hua, Yan He, Fengping Yuan, Ziguo Liu, Huan |
author_sort | Lan, Tianming |
collection | PubMed |
description | The masked palm civet (Paguma larvata) is a small carnivore with distinct biological characteristics, that likes an omnivorous diet and also serves as a vector of pathogens. Although this species is not an endangered animal, its population is reportedly declining. Since the severe acute respiratory syndrome (SARS) epidemic in 2003, the public has been particularly concerned about this species. Here, we present the first genome of the P. larvata, comprising 22 chromosomes assembled using single-tube long fragment read (stLFR) and Hi-C technologies. The genome length is 2.41 Gb with a scaffold N50 of 105.6 Mb. We identified the 107.13 Mb X chromosome and one 1.34 Mb Y-linked scaffold and validated them by resequencing 45 P. larvata individuals. We predicted 18,340 protein-coding genes, among which 18,333 genes were functionally annotated. Interestingly, several biological pathways related to immune defenses were found to be significantly expanded. Also, more than 40% of the enriched pathways on the positively selected genes (PSGs) were identified to be closely related to immunity and survival. These enriched gene families were inferred to be essential for the P. larvata for defense against the pathogens. However, we did not find a direct genomic basis for its adaptation to omnivorous diet despite multiple attempts of comparative genomic analysis. In addition, we evaluated the susceptibility of the P. larvata to the SARS-CoV-2 by screening the RNA expression of the ACE2 and TMPRSS2/TMPRSS4 genes in 16 organs. Finally, we explored the genome-wide heterozygosity and compared it with other animals to evaluate the population status of this species. Taken together, this chromosome-scale genome of the P. larvata provides a necessary resource and insights for understanding the genetic basis of its biological characteristics, evolution, and disease transmission control. |
format | Online Article Text |
id | pubmed-8815822 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-88158222022-02-05 Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution Lan, Tianming Fang, Dongming Li, Haimeng Sahu, Sunil Kumar Wang, Qing Yuan, Hao Zhu, Yixin Yang, Zipeng Zhang, Le Yang, Shangchen Lu, Haorong Han, Lei Zhang, Shaofang Yu, Jieyao Mahmmod, Yasser S. Xu, Yanchun Hua, Yan He, Fengping Yuan, Ziguo Liu, Huan Front Genet Genetics The masked palm civet (Paguma larvata) is a small carnivore with distinct biological characteristics, that likes an omnivorous diet and also serves as a vector of pathogens. Although this species is not an endangered animal, its population is reportedly declining. Since the severe acute respiratory syndrome (SARS) epidemic in 2003, the public has been particularly concerned about this species. Here, we present the first genome of the P. larvata, comprising 22 chromosomes assembled using single-tube long fragment read (stLFR) and Hi-C technologies. The genome length is 2.41 Gb with a scaffold N50 of 105.6 Mb. We identified the 107.13 Mb X chromosome and one 1.34 Mb Y-linked scaffold and validated them by resequencing 45 P. larvata individuals. We predicted 18,340 protein-coding genes, among which 18,333 genes were functionally annotated. Interestingly, several biological pathways related to immune defenses were found to be significantly expanded. Also, more than 40% of the enriched pathways on the positively selected genes (PSGs) were identified to be closely related to immunity and survival. These enriched gene families were inferred to be essential for the P. larvata for defense against the pathogens. However, we did not find a direct genomic basis for its adaptation to omnivorous diet despite multiple attempts of comparative genomic analysis. In addition, we evaluated the susceptibility of the P. larvata to the SARS-CoV-2 by screening the RNA expression of the ACE2 and TMPRSS2/TMPRSS4 genes in 16 organs. Finally, we explored the genome-wide heterozygosity and compared it with other animals to evaluate the population status of this species. Taken together, this chromosome-scale genome of the P. larvata provides a necessary resource and insights for understanding the genetic basis of its biological characteristics, evolution, and disease transmission control. Frontiers Media S.A. 2022-01-21 /pmc/articles/PMC8815822/ /pubmed/35126472 http://dx.doi.org/10.3389/fgene.2021.819493 Text en Copyright © 2022 Lan, Fang, Li, Sahu, Wang, Yuan, Zhu, Yang, Zhang, Yang, Lu, Han, Zhang, Yu, Mahmmod, Xu, Hua, He, Yuan and Liu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Lan, Tianming Fang, Dongming Li, Haimeng Sahu, Sunil Kumar Wang, Qing Yuan, Hao Zhu, Yixin Yang, Zipeng Zhang, Le Yang, Shangchen Lu, Haorong Han, Lei Zhang, Shaofang Yu, Jieyao Mahmmod, Yasser S. Xu, Yanchun Hua, Yan He, Fengping Yuan, Ziguo Liu, Huan Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution |
title | Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution |
title_full | Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution |
title_fullStr | Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution |
title_full_unstemmed | Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution |
title_short | Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution |
title_sort | chromosome-scale genome of masked palm civet (paguma larvata) shows genomic signatures of its biological characteristics and evolution |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8815822/ https://www.ncbi.nlm.nih.gov/pubmed/35126472 http://dx.doi.org/10.3389/fgene.2021.819493 |
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