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Bai Y, Xi Y, He X, Twumasi G, Ma S, Tao Q, Xu M, Jiang S, Zhang T, Lu Y, Han X, Qi J, Li L, Bai L, Liu H. Genome-wide characterization and comparison of endogenous retroviruses among 3 duck reference genomes. Poult Sci 2024; 103:103543. [PMID: 38447307 PMCID: PMC11067759 DOI: 10.1016/j.psj.2024.103543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
Endogenous retroviruses (ERV) are viral genomes integrated into the host genome and can be stably inherited. Although ERV sequences have been reported in some avian species' genome, the duck endogenous retroviruses (DERV) genome has yet to be quantified. This study aimed to identify ERV sequences and characterize genes near ERVs in the duck genome by utilizing LTRhavest and LTRdigest tools to forecast the duck genome and analyze the distribution of ERV copies. The results revealed 1,607, 2,031, and 1,908 full-length ERV copies in the Pekin duck (ZJU1.0), Mallard (CAU_wild_1.0), and Shaoxing duck (CAU_laying_1.0) genomes, respectively, with average lengths of 7,046, 7,027, and 6,945 bp. ERVs are mainly distributed on the 1, 2, and sex chromosomes. Phylogenetic analysis demonstrated the presence of Betaretrovirus in 3 duck genomes, whereas Alpharetrovirus was exclusively identified in the Shaoxing duck genome. Through screening, 596, 315, and 343 genes adjacent to ERV were identified in 3 duck genomes, respectively, and their functions of ERV neighboring genes were predicted. Functional enrichment analysis of ERV-adjacent genes revealed enrichment for Focal adhesion, Calcium signaling pathway, and Adherens junction in 3 duck genomes. The overlapped genes were highly expressed in 8 tissues (brain, fat, heart, kidney, liver, lung, skin, and spleen) of 8-wk-old Mallard, revealing their important expression in different tissues. Our study provides a new perspective for understanding the quantity and function of DERVs, and may also provide important clues for regulating nearby genes and affecting the traits of organisms.
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Affiliation(s)
- Yuan Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Yang Xi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Xinxin He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Grace Twumasi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Shengchao Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Qiuyu Tao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Mengru Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Shuaixue Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Tao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Yinjuan Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Xu Han
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Jingjing Qi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Liang Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Lili Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Hehe Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China.
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Gangopadhayya A, Lole K, Ghuge O, Ramdasi A, Kamble A, Roy D, Thakar S, Nath A, Sudeep AB, Cherian S. Metagenomic Analysis of Viromes of Aedes Mosquitoes across India. Viruses 2024; 16:109. [PMID: 38257809 PMCID: PMC10818685 DOI: 10.3390/v16010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
Metagenomic analysis of Aedes aegypti and Ae. albopictus mosquitoes from diverse geographical regions of India revealed the presence of several insect viruses of human interest. Most abundant reads found in Ae. aegypti mosquitoes were of Phasi Charoen-like virus (PCLV), Choristoneura fumiferana granulovirus (CfGV), Cell fusing agent virus (CFAV), and Wenzhou sobemo-like virus 4 (WSLV4), whereas WSLV4 and CfGV constituted the highest percentage of reads in Ae. albopictus viromes. Other reads that were of low percentage included Hubei mosquito virus 2 (HMV2), Porcine astrovirus 4 (PAstV4), and Wild Boar astrovirus (WBAstV). PCLV and CFAV, which were found to be abundant in Ae. aegypti viromes were absent in Ae. albopictus viromes. Among the viromes analyzed, Ae. aegypti sampled from Pune showed the highest percentage (79.82%) of viral reads, while Ae. aegypti mosquitoes sampled from Dibrugarh showed the lowest percentage (3.47%). Shamonda orthobunyavirus (SHAV), African swine fever virus (ASFV), Aroa virus (AROAV), and Ilheus virus (ILHV), having the potential to infect vertebrates, including humans, were also detected in both mosquito species, albeit with low read numbers. Reads of gemykibivirus, avian retrovirus, bacteriophages, herpesviruses, and viruses infecting protozoans, algae, etc., were also detected in the mosquitoes. A high percentage of reads in the Ae. albopictus mosquito samples belonged to unclassified viruses and warrant further investigation. The data generated in the present work may not only lead to studies to explain the influence of these viruses on the replication and transmission of viruses of clinical importance but also to find applications as biocontrol agents against pathogenic viruses.
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Affiliation(s)
- Abhranil Gangopadhayya
- Hepatitis Group, Indian Council of Medical Research-National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India; (A.G.); (K.L.); (O.G.); (A.R.); (S.T.); (A.N.)
| | - Kavita Lole
- Hepatitis Group, Indian Council of Medical Research-National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India; (A.G.); (K.L.); (O.G.); (A.R.); (S.T.); (A.N.)
| | - Onkar Ghuge
- Hepatitis Group, Indian Council of Medical Research-National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India; (A.G.); (K.L.); (O.G.); (A.R.); (S.T.); (A.N.)
| | - Ashwini Ramdasi
- Hepatitis Group, Indian Council of Medical Research-National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India; (A.G.); (K.L.); (O.G.); (A.R.); (S.T.); (A.N.)
| | - Asmita Kamble
- Bioinformatics and Data Management Group, Indian Council of Medical Research-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (A.K.); (D.R.)
| | - Diya Roy
- Bioinformatics and Data Management Group, Indian Council of Medical Research-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (A.K.); (D.R.)
| | - Shivani Thakar
- Hepatitis Group, Indian Council of Medical Research-National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India; (A.G.); (K.L.); (O.G.); (A.R.); (S.T.); (A.N.)
| | - Amol Nath
- Hepatitis Group, Indian Council of Medical Research-National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India; (A.G.); (K.L.); (O.G.); (A.R.); (S.T.); (A.N.)
| | - AB Sudeep
- Hepatitis Group, Indian Council of Medical Research-National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India; (A.G.); (K.L.); (O.G.); (A.R.); (S.T.); (A.N.)
| | - Sarah Cherian
- Bioinformatics and Data Management Group, Indian Council of Medical Research-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (A.K.); (D.R.)
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Wang L, Sun J, Liu Z, Zheng Q, Wang G. Comparison of Multiple Strategies for Precision Transgene Knock-In in Gallus gallus Genome via Microhomology-Mediated End Joining. Int J Mol Sci 2023; 24:15731. [PMID: 37958714 PMCID: PMC10649300 DOI: 10.3390/ijms242115731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 11/15/2023] Open
Abstract
Precision exogenous gene knock-in is an attractive field for transgenic Gallus gallus (chicken) generation. In this article, we constructed multiple Precise Integration into Target Chromosome (PITCh) plasmid systems mediated by microhomology-mediated end-joining (MMEJ) for large-fragment integration in DF-1 cells and further assess the possibility of GAPDH (glyceraldehyde-3-phosphate dehydrogenase) as a genomic safe harbor for chickens. We designed three targeted sgRNAs for the all-in-one plasmid at the 3'UTR of GAPDH near the stop codon. The donor-plasmid-carrying microhomology arms correspond to sgRNA and EGFP fragments in the forward and reverse directions. MMEJ-mediated EGFP insertion can be efficiently expressed in DF-1 cells. Moreover, the differences between the forward and reverse fragments indicated that promoter interference does affect the transfection efficiency of plasmids and cell proliferation. The comparison of the 20 bp and 40 bp microhomology arms declared that the short one has higher knock-in efficiency. Even though all three different transgene insertion sites in GAPDH could be used to integrate the foreign gene, we noticed that the G2-20R-EGFP cell reduced the expression of GAPDH, and the G3-20R-EGFP cell exhibited significant growth retardation. Taken together, G1, located at the 3'UTR of GAPDH on the outer side of the last base of the terminator, can be a candidate genomic safe harbor (GSH) loci for the chicken genome. In addition, deleted-in-azoospermia-like (DAZL) and actin beta (ACTB) site-specific gene knock-in indicated that MMEJ has broad applicability and high-precision knock-in efficiency for genetically engineered chickens.
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Affiliation(s)
| | | | | | | | - Guojun Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (L.W.); (J.S.); (Z.L.); (Q.Z.)
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Ishihara S. Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing. Sci Rep 2023; 13:7380. [PMID: 37149699 PMCID: PMC10164170 DOI: 10.1038/s41598-023-34520-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
Endogenous retroviruses (ERVs) are genetic elements present in the genome that retain traces of past viral infections. Characterization of ERVs can provide crucial insights into avian evolution. This study aimed to identify novel long terminal repeat (LTR) loci derived from ERVs (ERV-LTRs) absent in the reference genome using whole-genome sequencing data of red junglefowl, gray junglefowl, Ceylon junglefowl, and green junglefowl. In total, 835 ERV-LTR loci were identified across the four Gallus species. The numbers of ERV-LTRs loci detected in red junglefowl and its subspecies gray junglefowl, Ceylon junglefowl, and green junglefowl were 362, 216, 193, and 128, respectively. The phylogenetic tree was congruent with previously reported trees, suggesting the potential for inferring relationships among past junglefowl populations from the identified ERV-LTR loci. Of the detected loci, 306 ERV-LTRs were identified near or within the genes, and some were associated with cell adhesion. The detected ERV-LTR sequences were classified as endogenous avian retrovirus family, avian leukosis virus subgroup E, Ovex-1, and murine leukemia virus-related ERVs. In addition, the sequence of the EAV family was divided into four patterns by combining the U3, R, and U5 regions. These findings contribute to a more comprehensive understanding of the characteristics of junglefowl ERVs.
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Affiliation(s)
- Shinya Ishihara
- Department of Animal Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonancho, Musashino, Tokyo, 180-8602, Japan.
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The association between microbial community and ileal gene expression on intestinal wall thickness alterations in chickens. Poult Sci 2020; 99:1847-1861. [PMID: 32241465 PMCID: PMC7587722 DOI: 10.1016/j.psj.2019.10.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/05/2019] [Accepted: 10/11/2019] [Indexed: 12/17/2022] Open
Abstract
The dynamic development of the animal intestine with a concurrent succession of microbiota and changes in microbial community and metabolite spectrum can exert far-reaching effects on host physiology. However, the precise mechanism of mutual response between microbiota and the gut is yet to be fully elucidated. Broilers with varying developmental degrees of intestinal wall thickness were selected, and they were divided into the thick group (H type) and the thin group (B type), using multiomics data integration analysis to reveal the fundamental regulatory mechanisms of gut–microbiota interplay. Our data showed, in broilers with similar body weight, the intestinal morphological parameters were improved in H type and the diversity of microbial communities is distinguishable from each other. The beneficial bacteria such as Bifidobacterium breve was increased whereas avian endogenous retrovirus EAV-HP was decreased in the H type compared with the B type. Furthermore, microbial metabolic potentials were more active, especially the biosynthesis of folate was improved in the H type. Similarly, the consolidation of absorption, immunity, metabolism, and development was noticed in the thick group. Correlation analysis indicated that the expression levels of material transport and immunomodulatory-related genes were positively correlated with the relative abundance of several probiotics such as B. breve, Lactobacillus saerimneri, and Butyricicoccus pullicaecorum. Our findings suggest that the chickens with well-developed ileal thickness own exclusive microbial composition and metabolic potential, which is closely related to small intestinal morphogenesis and homeostasis.
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Lawal RA, Al-Atiyat RM, Aljumaah RS, Silva P, Mwacharo JM, Hanotte O. Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species. Front Genet 2018; 9:264. [PMID: 30079080 PMCID: PMC6062655 DOI: 10.3389/fgene.2018.00264] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
Abstract
The red junglefowl Gallus gallus is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic control for production traits have been well studied in commercial chicken, but the selection pressures underlying unique adaptation and production to local environments remain largely unknown in indigenous village chicken. Likewise, the genome regions under positive selection in the wild red junglefowl remain untapped. Here, using the pool heterozygosity approach, we analyzed indigenous village chicken populations from Ethiopia, Saudi Arabia, and Sri Lanka, alongside six red junglefowl, for signatures of positive selection across the autosomes. Two red junglefowl candidate selected regions were shared with all domestic chicken populations. Four candidates sweep regions, unique to and shared among all indigenous domestic chicken, were detected. Only one region includes annotated genes (TSHR and GTF2A1). Candidate regions that were unique to each domestic chicken population with functions relating to adaptation to temperature gradient, production, reproduction and immunity were identified. Our results provide new insights on the consequence of the selection pressures that followed domestication on the genome landscape of the domestic village chicken.
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Affiliation(s)
- Raman A. Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Raed M. Al-Atiyat
- Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan
- Animal Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Riyadh S. Aljumaah
- Animal Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Pradeepa Silva
- Department of Animal Sciences, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene – CTLGH, International Livestock Research Institute, Addis Ababa, Ethiopia
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Wang L, Yang L, Guo Y, Du W, Yin Y, Zhang T, Lu H. Enhancing Targeted Genomic DNA Editing in Chicken Cells Using the CRISPR/Cas9 System. PLoS One 2017; 12:e0169768. [PMID: 28068387 PMCID: PMC5222187 DOI: 10.1371/journal.pone.0169768] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/21/2016] [Indexed: 12/02/2022] Open
Abstract
The CRISPR/Cas9 system has enabled highly efficient genome targeted editing for various organisms. However, few studies have focused on CRISPR/Cas9 nuclease-mediated chicken genome editing compared with mammalian genomes. The current study combined CRISPR with yeast Rad52 (yRad52) to enhance targeted genomic DNA editing in chicken DF-1 cells. The efficiency of CRISPR/Cas9 nuclease-induced targeted mutations in the chicken genome was increased to 41.9% via the enrichment of the dual-reporter surrogate system. In addition, the combined effect of CRISPR nuclease and yRad52 dramatically increased the efficiency of the targeted substitution in the myostatin gene using 50-mer oligodeoxynucleotides (ssODN) as the donor DNA, resulting in a 36.7% editing efficiency after puromycin selection. Furthermore, based on the effect of yRad52, the frequency of exogenous gene integration in the chicken genome was more than 3-fold higher than that without yRad52. Collectively, these results suggest that ssODN is an ideal donor DNA for targeted substitution and that CRISPR/Cas9 combined with yRad52 significantly enhances chicken genome editing. These findings could be extensively applied in other organisms.
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Affiliation(s)
- Ling Wang
- School of Biological Science and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, China
| | - Likai Yang
- School of Biological Science and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, China
| | - Yijie Guo
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jitong University, Xi'an, Shaanxi, China
| | - Weili Du
- School of Biological Science and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, China
| | - Yajun Yin
- School of Biological Science and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi SCI-TECH University, Hanzhong, Shaanxi, China
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Cui P, Löber U, Alquezar-Planas DE, Ishida Y, Courtiol A, Timms P, Johnson RN, Lenz D, Helgen KM, Roca AL, Hartman S, Greenwood AD. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome. PeerJ 2016; 4:e1847. [PMID: 27069793 PMCID: PMC4824918 DOI: 10.7717/peerj.1847] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/04/2016] [Indexed: 11/20/2022] Open
Abstract
Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.
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Affiliation(s)
- Pin Cui
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute of Biochemistry & Biology, University of Potsdam, Potsdam, Germany
| | - David E Alquezar-Planas
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Alexandre Courtiol
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Peter Timms
- University of the Sunshine Coast, Sippy Downs Queensland, Australia
| | - Rebecca N Johnson
- Australian Centre for Wildlife Genomics, Australian Museum, Sydney, Australia
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Kristofer M Helgen
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Stefanie Hartman
- Institute of Biochemistry & Biology, University of Potsdam, Potsdam, Germany
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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