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Sun K, Gu L, Ma L, Duan Y. Atlas of ACE2 gene expression reveals novel insights into transmission of SARS-CoV-2. Heliyon 2021; 7:e05850. [PMID: 33392409 PMCID: PMC7762714 DOI: 10.1016/j.heliyon.2020.e05850] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/03/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
The recent pandemic, COVID-19, is caused by a novel coronavirus, SARS-CoV-2, with elusive origin. SARS-CoV-2 infects mammalian cells via ACE2, a transmembrane protein. Therefore, the conservation and expression patterns of ACE2 may provide valuable insights into tracing the carriers of SARS-CoV-2. In this work, we analyzed the conservation of ACE2 and its expression pattern among various mammalian species that are close to human beings. We show that mammalian ACE2 gene is deeply conserved at both DNA and peptide levels, suggesting that a broad range of mammals can potentially host SARS-CoV-2. We further report that ACE2 expression in certain human tissues are consistent with clinical symptoms of COVID-19 patients. Furthermore, we have built the first atlas of ACE2 expression in various common mammals, which shows that ACE2 expresses in mammalian tissues in a species-specific manner. Most notably, we observe exceptionally high expression of ACE2 in external body parts of cats and dogs, suggesting that these household pet animals could be vulnerable to viral infections and/or may serve as intermediate hosts, thus yielding novel insights into the transmission of SARS-CoV-2.
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Affiliation(s)
- Kun Sun
- Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Liuqi Gu
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS, 66045, USA
- Beijing Huayuan Academy of Biotechnology, Beijing, 100192, China
| | - Li Ma
- Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Yunfeng Duan
- Beijing Huayuan Academy of Biotechnology, Beijing, 100192, China
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Jia B, Wang G, Zheng J, Yang W, Chang S, Zhang J, Liu Y, Li Q, Ge C, Chen G, Liu D, Yang F. Development of novel EST microsatellite markers for genetic diversity analysis and correlation analysis of velvet antler growth characteristics in Sika deer. Hereditas 2020; 157:24. [PMID: 32591015 PMCID: PMC7320565 DOI: 10.1186/s41065-020-00137-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sika deer is one of the most popular and valued animals in China. However, few studies have been conducted on the microsatellite of Sika deer, which has hampered the progress of genetic selection breeding. To develop and characterize a set of microsatellites for Sika deer which provide helpful information for protection of Sika deer natural resources and effectively increase the yield and quantity of velvet antler. RESULTS We conducted a transcriptome survey of Sika deer using next-generation sequencing technology. One hundred eighty-two thousand two hundred ninety-five microsatellite markers were identified in the transcriptome, 170 of 200 loci were successfully amplified across panels of 140 individuals from Shuangyang Sika deer population. And 29 loci were found to be obvious polymorphic. Number of alleles is from 3 to 14. The expected heterozygosity ranged from 0.3087 to 0.7644. The observed heterozygosity ranged from 0 to 0.7698. The polymorphism information content values of those microsatellites varied ranged from 0.2602 to 0.7507. The marker-trait association was tested for 6 important and kernel characteristics of two-branched velvet antler in Shuangyang Sika deer through one-way analysis of variance. The results showed that marker-trait associations were identified with 8 different markers, especially M009 and M027. CONCLUSIONS This study not only provided a large scale of microsatellites which were valuable for future genetic mapping and trait association in Sika deer, but also offers available information for molecular breeding in Sika deer.
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Affiliation(s)
- Boyin Jia
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Guiwu Wang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Junjun Zheng
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Wanyun Yang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Shuzhuo Chang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Jiali Zhang
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Yuan Liu
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Qining Li
- College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Chenxia Ge
- College of Vocational and Technical Education, Changchun Sci-Tech University, 1699 Donghua Street, Changchun, 130606, China
| | - Guang Chen
- Key laboratory of Straw Biology and Utilization, The Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Dongdong Liu
- Key laboratory of Straw Biology and Utilization, The Ministry of Education, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China. .,College of Engineering and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China.
| | - Fuhe Yang
- Institute of Wild Economic Animals and Plants and State Key Laboratory for Molecular Biology of Special Economical Animals, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China.
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Guo Q, Wang JX, Su LZ, Lv W, Sun YH, Li Y. Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.). Genes (Basel) 2017; 8:genes8070177. [PMID: 28686183 PMCID: PMC5541310 DOI: 10.3390/genes8070177] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/20/2022] Open
Abstract
Black locust (Robinia pseudoacacia L. of the family Fabaceae) is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification. Forty-five primers were verified as polymorphic, with clear bands. The polymorphism information content values were 0.033–0.765, the number of alleles per locus ranged from 2 to 10, and the observed and expected heterozygosities were 0.000–0.931 and 0.035–0.810, respectively, indicating a high level of informativeness. Subsequently, 45 polymorphic EST-SSR loci were tested for amplification efficiency, using the verified primers, in an additional nine species of Leguminosae, 23 loci were amplified in more than three species, of which two loci were amplified successfully in all species. These EST-SSR markers provide a valuable tool for investigating the genetic diversity and population structure of R. pseudoacacia, constructing a DNA fingerprint database, performing quantitative trait locus mapping, and preserving genetic information.
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Affiliation(s)
- Qi Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Jin-Xing Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Li-Zhuo Su
- State-owned Linghai Hongqi Forest, Jinzhou 121228, China.
| | - Wei Lv
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yu-Han Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yun Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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De Novo RNA Sequencing and Transcriptome Analysis of Monascus purpureus and Analysis of Key Genes Involved in Monacolin K Biosynthesis. PLoS One 2017; 12:e0170149. [PMID: 28114365 PMCID: PMC5256959 DOI: 10.1371/journal.pone.0170149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/29/2016] [Indexed: 12/25/2022] Open
Abstract
Monascus purpureus is an important medicinal and edible microbial resource. To facilitate biological, biochemical, and molecular research on medicinal components of M. purpureus, we investigated the M. purpureus transcriptome by RNA sequencing (RNA-seq). An RNA-seq library was created using RNA extracted from a mixed sample of M. purpureus expressing different levels of monacolin K output. In total 29,713 unigenes were assembled from more than 60 million high-quality short reads. A BLAST search revealed hits for 21,331 unigenes in at least one of the protein or nucleotide databases used in this study. The 22,365 unigenes were categorized into 48 functional groups based on Gene Ontology classification. Owing to the economic and medicinal importance of M. purpureus, most studies on this organism have focused on the pharmacological activity of chemical components and the molecular function of genes involved in their biogenesis. In this study, we performed quantitative real-time PCR to detect the expression of genes related to monacolin K (mokA-mokI) at different phases (2, 5, 8, and 12 days) of M. purpureus M1 and M1-36. Our study found that mokF modulates monacolin K biogenesis in M. purpureus. Nine genes were suggested to be associated with the monacolin K biosynthesis. Studies on these genes could provide useful information on secondary metabolic processes in M. purpureus. These results indicate a detailed resource through genetic engineering of monacolin K biosynthesis in M. purpureus and related species.
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