1
|
Zachariah A, Krishnankutty SP, Manazhi J, Omanakuttan V, Santosh S, Blanchard A, Tarlinton R. Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020-21. Access Microbiol 2024; 6:000686.v3. [PMID: 38361659 PMCID: PMC10866034 DOI: 10.1099/acmi.0.000686.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Spillover of SARS-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white-tailed deer in North America and increasing divergence of the viruses circulating in them from those circulating in the human population has highlighted the ongoing risk this poses for global health. Some parts of the world have seen more intensive monitoring of wildlife species for SARS-CoV-2 and related coronaviruses but there are still very large gaps in geographical and species-specific information. This paper reports negative results for SARS-CoV-2 PCR based testing using a pan coronavirus end point RDRP PCR and a Sarbecovirus specific E gene qPCR on lung and or gut tissue from wildlife from the Indian State of Kerala. These animals included: 121 Rhinolophus rouxii (Rufous Horsehoe Bat), six Rhinolophus bedommei (Lesser Woolly Horseshoe Bat), 15 Rossettus leschenaultii (Fulvous Fruit Bat), 47 Macaca radiata (Bonnet macaques), 35 Paradoxurus hermaphroditus (Common Palm Civet), five Viverricula indica (Small Indian Civet), four Herpestes edwardsii (Common Mongoose), ten Panthera tigris (Bengal Tiger), eight Panthera pardus fusca (Indian Leopard), four Prionailurus bengalensis (Leopard cats), two Felis chaus (Jungle cats), two Cuon alpinus (Wild dogs) and one Melursus ursinus (sloth bear).
Collapse
Affiliation(s)
| | | | | | | | | | - Adam Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| |
Collapse
|
2
|
Shukla H, Suryamohan K, Khan A, Mohan K, Perumal RC, Mathew OK, Menon R, Dixon MD, Muraleedharan M, Kuriakose B, Michael S, Krishnankutty SP, Zachariah A, Seshagiri S, Ramakrishnan U. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. Gigascience 2022; 12:6963323. [PMID: 36576130 PMCID: PMC9795480 DOI: 10.1093/gigascience/giac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/17/2022] [Accepted: 10/20/2022] [Indexed: 12/29/2022] Open
Abstract
The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140 Mb, with 19 scaffolds corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies, which will help improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 transfer RNAs, and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to the tiger's apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of noninvasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.
Collapse
Affiliation(s)
| | | | | | - Krishna Mohan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Rajadurai C Perumal
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Oommen K Mathew
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Ramesh Menon
- MedGenome Labs Ltd., Narayana Health City, Bangalore, Karnataka 560099, India
| | - Mandumpala Davis Dixon
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Megha Muraleedharan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Boney Kuriakose
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Saju Michael
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Sajesh P Krishnankutty
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Arun Zachariah
- SciGenom Research Foundation, Narayana Health City, Bangalore, Karnataka 560099, India,Wayanad Wildlife Sanctuary, Sultan Bathery, Kerala 673592, India
| | - Somasekar Seshagiri
- Correspondence address. Somasekar Seshagiri, Department of Research and Development SciGenom Research Foundation 3rd Floor, Narayana Nethralaya Building, Narayana Health City, #258/A, Bommasandra, Hosur Road, Bangalore 560099, India. E-mail:
| | - Uma Ramakrishnan
- Correspondence address. Uma Ramakrishnan, National Centre for Biological Sciences, TIFR Bellary Road, Bangalore 560065, India. E-mail:
| |
Collapse
|
3
|
Suryamohan K, Krishnankutty SP, Guillory J, Jevit M, Schröder MS, Wu M, Kuriakose B, Mathew OK, Perumal RC, Koludarov I, Goldstein LD, Senger K, Dixon MD, Velayutham D, Vargas D, Chaudhuri S, Muraleedharan M, Goel R, Chen YJJ, Ratan A, Liu P, Faherty B, de la Rosa G, Shibata H, Baca M, Sagolla M, Ziai J, Wright GA, Vucic D, Mohan S, Antony A, Stinson J, Kirkpatrick DS, Hannoush RN, Durinck S, Modrusan Z, Stawiski EW, Wiley K, Raudsepp T, Kini RM, Zachariah A, Seshagiri S. The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. Nat Genet 2020; 52:106-117. [PMID: 31907489 PMCID: PMC8075977 DOI: 10.1038/s41588-019-0559-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/22/2019] [Indexed: 12/30/2022]
Abstract
Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake. Our assembly has a scaffold N50 of 223.35 Mb, with 19 scaffolds containing 95% of the genome. Of the 23,248 predicted protein-coding genes, 12,346 venom-gland-expressed genes constitute the ‘venom-ome’ and this included 139 genes from 33 toxin families. Among the 139 toxin genes were 19 ‘venom-ome-specific toxins’ (VSTs) that showed venom-gland-specific expression, and these probably encode the minimal core venom effector proteins. Synthetic venom reconstituted through recombinant VST expression will aid in the rapid development of safe and effective synthetic antivenom. Additionally, our genome could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery. Analysis of a near-chromosomal genome assembly and transcriptome profiling of the Indian cobra identifies genes expressed in the venom glands. These data should help develop a new antivenom.
Collapse
Affiliation(s)
- Kushal Suryamohan
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,MedGenome Inc., Foster City, CA, USA
| | - Sajesh P Krishnankutty
- AgriGenome Labs Private Ltd, Kochi, India.,SciGenom Research Foundation, Bangalore, India
| | - Joseph Guillory
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Matthew Jevit
- Molecular Cytogenetics laboratory, Texas A&M University, College Station, TX, USA
| | - Markus S Schröder
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Meng Wu
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | | | | | | | - Ivan Koludarov
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
| | - Leonard D Goldstein
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Kate Senger
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | | | | | - Derek Vargas
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,MedGenome Inc., Foster City, CA, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | | | - Ridhi Goel
- AgriGenome Labs Private Ltd, Kochi, India
| | - Ying-Jiun J Chen
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Peter Liu
- Department of Microchemistry Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Brendan Faherty
- Department of Microchemistry Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Guillermo de la Rosa
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuouka, Japan
| | - Miriam Baca
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Meredith Sagolla
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - James Ziai
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Gus A Wright
- College of Veterinary Medicine, Flow Cytometry Shared Resource Laboratory, Texas A&M University, College Station, TX, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Sangeetha Mohan
- Department of Molecular Biology, SciGenom Labs, Kochi, India
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Kochi, India
| | - Jeremy Stinson
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Steffen Durinck
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA.,MedGenome Inc., Foster City, CA, USA
| | | | - Terje Raudsepp
- Molecular Cytogenetics laboratory, Texas A&M University, College Station, TX, USA
| | - R Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Arun Zachariah
- SciGenom Research Foundation, Bangalore, India.,Wayanad Wildlife Sanctuary, Sultan Bathery, India
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA, USA. .,SciGenom Research Foundation, Bangalore, India.
| |
Collapse
|