Genome sequencing of captive white tigers from Bangladesh

Genome sequencing of captive white tigers from Bangladesh | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Data Note Genome sequencing of captive white tigers from Bangladesh Ashutosh Das, Md Shahadat Hossain Suvo, Mishuk Shaha, Mukta Das Gupta This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3945697/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 8 You are reading this latest preprint version Abstract Objectives : The Bengal tiger Panthera tigris tigris , is an emblematic animal for Bangladesh. Despite being the apex predator in the wild, their number is decreasing due to anthropogenic activities such as hunting, urbanization, expansion of agriculture and deforestation. By contrast, captive tigers are flourishing due to practical conservation efforts. Breeding within the small captive population can produce inbreeding depression and genetic bottlenecks, which may limit the success of conservation efforts. Despite past decades of research, a comprehensive database on genetic variation in the captive and wild Bengal tigers in Bangladesh still needs to be included. Therefore, this research aimed to investigate the White Bengal tiger genome to create a resource for future studies to understand variation underlying important functional traits. Data description: Blood samples from Chattogram Zoo were collected for three white Bengal tigers. Genomic DNA for all collected samples were extracted using a commercial DNA extraction kit. Whole genome sequencing was performed using a DNBseq platform. We generated 77 Gb of whole-genome sequencing (WGS) data for three white Bengal tigers (Average 11X coverage/sample). The data we generated will establish a paradigm for tiger research in Bangladesh by providing a genomic resource for future functional studies on the Bengal white tiger. White Bengal tigers whole genome sequencing Figures Figure 1 Objective The critically endangered Bengal tiger, Panthera tigris tigris , is a native subspecies of the Indian subcontinent. The Bengal tiger population in India started to drop over a century ago. By 1970, less than 2,000 tigers remained in the wild, similar to the global tiger population reduction. Approximately 2,900 wild tigers remain in Indian reserves, making up over 60% of the total number of wild tigers worldwide [ 1 ]. According to estimates from the Bengal Tiger Conservation Activity (BAGH) project, there were 114 tigers in the Bangladesh Sundarbans [ 2 ]. Despite several conservation efforts, numerous factors, including habitat loss, deforestation, altered land cover, human disturbance of the forests, poaching, hunting, illegal wildlife trade, climate change, natural disasters and inadequate legal frameworks [ 3 ], are contributing to the extinction of the tiger population in the Sundarbans. By contrast, captive tigers are flourishing. Appropriately maintained captive populations of wild animals have been shown to represent a "genetic reservoir" of their natural counterparts, providing insurance against extinction in the wild and aiding in public education, research, and fundraising. Small, isolated populations that experience inbreeding have minimal genetic variety among their individuals and are very vulnerable to extinction. According to estimates, the Bengal tiger population possesses the most genetic diversity, making it the ideal gene pool reservoir for conservation efforts [ 4 , 5 ]. Using available genomic resources, a high-quality reference genome for Bengal tigers [ 6 ] and other tiger genomic data (5, 7–10), we can conduct a comparative genomic analysis and determine the genetic diversity of Bengal tigers. Therefore, we generated this data to compile more comprehensive genomic information, which will be helpful for future research into the variants causing significant colour phenotypes. Data description Following the ethical rules and procedures of Chattogram Zoo Bangladesh, blood samples were taken from three white tiger cubs. Total genomic DNA was extracted from blood samples using Monarch Genomic DNA Purification Kit (New England Biolabs, UK) according to the manufacturer's guidelines. Thermo Scientific, USA's NanoDropTM One Microvolume UV-Vis Spectrophotometer was used to evaluate the extracted DNA's quality and purity. For sequencing and library construction (Short Insert library), purified genomic DNA was transferred to Beijing Genomics Institute (BGI, Hong Kong). The DNBSEQ Short-read library preparation instructions provided by the manufacturer were followed for the development of the sequencing libraries. We used a DNBseq platform to do whole genome sequencing(WGS). High-performance computing resources were used for WGS bioinformatics. Low-quality raw paired readings were removed using SOAPnuke [ 11 ] after the raw reads were assessed for quality. In a nutshell, low-quality or adapter sequences in the raw data were filtered first. Many data processing steps were taken to get rid of contaminants and provide reliable data. The filter parameters for the SOAPnuke program were "-n 0.001 -l 10 --adaMR 0.25". The filtering steps were 1) Filter adapter: delete the whole read if the sequencing read matches 25.0% or more of the adapter sequence (a maximum of two base mismatches is permitted); 2) Filter low-quality data: remove the whole sequencing read if bases with a quality value of less than 10 make up at least 50.0% of the read; 3) Eliminate N: Delete the whole read and discard any N information that makes up 0.1% or more of the sequencing read; 4) To obtain clean readings, Phred + 33 was set as the output read quality value for the system. The quality of data was examined after filtering. Base percentage compositions showed all sequenced samples had high-quality data after filtering (Additional file 1). Burrows-Wheeler Aligner (BWA) software [ 12 ] was used to align high-quality reads to the reference Panthera tigris tigris genomes, the PanTigT.SI.v4 (Shukla et al., 2023), using the default BWA mem settings. For three white Bengal tigers that were sequenced, we produced 77 Gb of data (Data file 1, 2 and 3). The average genome coverage was 11X. A description of the clean data is shown in Additional file 2 (Table 1 ). Mapping reads encompass 98.46% of the reference tiger genome in the current investigation. Table 1 Overview of data files/data sets. Label Name of data file/data set File types (file extension) Data repository and identifier (DOI or accession number) Additional file 1 Figure 1 The distribution of base percentage and qualities along reads Document file (.pdf) Figshare, https://doi.org/10.6084/m9.figshare.24996869 [ 13 ] Data file 1 WGS data of white Bengal tiger sample 1 SRA file (.fastq.gz) NCBI Sequence Read Archive https://trace.ncbi.nlm.nih.gov/Traces?run=SRR24305815 [ 14 ] Data file 2 WGS data of white Bengal tiger sample 2 SRA file (.fastq.gz) NCBI Sequence Read Archive https://trace.ncbi.nlm.nih.gov/Traces?run=SRR24459545 [ 15 ] Data file 3 WGS data of white Bengal tiger sample 3 SRA file (.fastq.gz) NCBI Sequence Read Archive https://trace.ncbi.nlm.nih.gov/Traces/?run=SRR24632529 [ 16 ] Additional file 2 Table 1 Basic statistics of whole genome sequence data for captive white tiger from Bangladesh Document file (.docx) Figshare, https://doi.org/10.6084/m9.figshare.24913884.v1 [ 17 ] Limitations Since all the samples come from individuals from the same parent, performing a genome-wide association study to identify genomic regions associated with a particular phenotype were not possible. Abbreviations BWA Burrows-Wheeler Aligner DNA Deoxyribonucleic acid Gb Giga base WGS Whole Genome Sequencing Declarations Ethics approval All animal procedures including collecting blood samples from tigers were approved by the research ethics committee of Chattogram Veterinary and Animal Sciences University Consent for publication Not applicable Availability of data and materials The Additional files 1 and 2 described in this Data Note can be freely and openly accessed on FigShare (https://figshare.com/) [13, 15]. The data described in this Data note can be freely and openly accessed from the NCBI Bioproject PRJNA961947. Raw data have been deposited separately in the Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra) with open accession ID SRP434520 [14-16]. Competing interests The authors declare no competing interests. Funding This work was financially supported by a grant from the University Grants Commission, Bangladesh through research allocation of Chattogram Veterinary and Animal Sciences University, Bangladesh. Authors’ contributions AD conceived the experiments and performed bioinformatics analyses; MSHS provided the samples; MS performed the sample collection and PCR in the lab; AD and MDG wrote and edited the manuscript. All authors approved the final manuscript. Acknowledgments Not applicable References Jhala YV, Qureshi Q, Nayak AK. Status of Tigers, Copredators and Prey in India, 2018, New Delhi: National Tiger Conservation Authority, Government of India; 2020. Aziz MA, Kabir MJ, Shamsuddoha M, Ahsan MM, Sharma S, Chakma S et al. Second phase status of tigers in Bangladesh Sundarban 2018. Department of Zoology, Janhangirnagar University; WildTeam Bangladesh; Forest Department, Bangladesh. Islam MZ. A Reality Check of the Global TX2 Goals of Doubling the Bengal Tiger (Panthera tigris tigris) Population by 2022 in the Sundarbans Mangrove Forest. Contemp Probl Ecol. 2023;16(6):868–85. Armstrong EE, Khan A, Taylor RW, Gouy A, Greenbaum G, Thiéry A, et al. Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection. Mol Biol Evol. 2021;38(6):2366–79. Luo SJ, Liu YC, Xu X. Tigers of the world: Genomics and conservation. Annu Rev Anim Biosci. 2019;15:7:521–48. Shukla H, Suryamohan K, Khan A, Mohan K, Perumal RC, Mathew OK, Menon R, Dixon MD, Muraleedharan M, Kuriakose B, Michael S. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. GigaScience. 2023;12:giac112. Zhang L, Lan T, Lin C, Fu W, Yuan Y, Lin K, et al. Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger. Mol Ecol Resour. 2022;23:330–47. https://doi.org/10.1111/1755-0998.13669 . Khan A, Patel K, Shukla H, et al. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proc Natl Acad Sci. 2021;118(49):e2023018118. Liu YC, Sun X, Driscoll C, et al. Genome-wide evolutionary analysis of natural history and adaptation in the world’s tigers. Curr Biol. 2018;28(23):3840–9. Cho YS, Hu L, Hou H, et al. The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun. 2013;4(1):2433. Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience. 2018;7(1):gix120. Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754–60. Das A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. Figshare. 2024. https://doi.org/10.6084/m9.figshare.24996869 . Das A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. NCBI Seq Read Archive. 2024. https://trace.ncbi.nlm.nih.gov/Traces?run=SRR24305815 . Das A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. NCBI Seq Read Archive. 2024. https://trace.ncbi.nlm.nih.gov/Traces?run=SRR24459545 . Das A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. NCBI Seq Read Archive. 2024. https://trace.ncbi.nlm.nih.gov/Traces?run= SRR24632529. Das A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. Figshare. 2024. https://doi.org/10.6084/m9.figshare.24913884.v1 . Additional Declarations No competing interests reported. Supplementary Files Table1.docx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 20 Mar, 2024 Reviews received at journal 23 Feb, 2024 Reviewers agreed at journal 19 Feb, 2024 Reviewers agreed at journal 19 Feb, 2024 Reviewers invited by journal 19 Feb, 2024 Editor assigned by journal 13 Feb, 2024 Submission checks completed at journal 13 Feb, 2024 First submitted to journal 10 Feb, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-3945697","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Data Note","associatedPublications":[],"authors":[{"id":272761607,"identity":"e9140ac2-08c6-44c6-93df-a87d782b6e02","order_by":0,"name":"Ashutosh Das","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA/UlEQVRIiWNgGAWjYFACHjCZAEYfEMIHGBvwaTkA1cI4g2QtzDzEaOHvP3tM+kNFXR4De/LjzzY1h+XlZyQwfvjBcEcWlxaJG3lpEgfOHC5m4HlmJp1z7LDhhhsJzJI9DM+McTrsBo+ZxMG2A4kNEglmzLkNaYwbJBIYpBkYDifi0iJ//gxISx1QS/rnz5YNafbzZyQw/8anxeBADkgLM1BLjoE0Y4NNYsONBDa8thjeyDG2OHPmcGIbz5syyZ5jNskbzjxss+wxwO0XufNnDG9UVNQl9rOnb/7wo0bCdn578uEbPypwhxgcsCGYoBgxIKR+FIyCUTAKRgE+AABQe18bz70iDwAAAABJRU5ErkJggg==","orcid":"","institution":"Chattogram Veterinary and Animal Sciences University","correspondingAuthor":true,"prefix":"","firstName":"Ashutosh","middleName":"","lastName":"Das","suffix":""},{"id":272761608,"identity":"3ba86d47-8dcf-451f-9be6-40378cdbec06","order_by":1,"name":"Md Shahadat Hossain Suvo","email":"","orcid":"","institution":"Chattogram zoo","correspondingAuthor":false,"prefix":"","firstName":"Md","middleName":"Shahadat Hossain","lastName":"Suvo","suffix":""},{"id":272761609,"identity":"1c506585-70ad-416a-8dd2-3d55de2454c9","order_by":2,"name":"Mishuk Shaha","email":"","orcid":"","institution":"Chattogram Veterinary and Animal Sciences University","correspondingAuthor":false,"prefix":"","firstName":"Mishuk","middleName":"","lastName":"Shaha","suffix":""},{"id":272761610,"identity":"866f4580-88c9-49d0-8567-07a497d10132","order_by":3,"name":"Mukta Das Gupta","email":"","orcid":"","institution":"Chattogram Veterinary and Animal Sciences University","correspondingAuthor":false,"prefix":"","firstName":"Mukta","middleName":"Das","lastName":"Gupta","suffix":""}],"badges":[],"createdAt":"2024-02-10 11:14:14","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3945697/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3945697/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":51183170,"identity":"8ab61c27-de4e-4254-b79f-4061b8a4a630","added_by":"auto","created_at":"2024-02-15 15:35:05","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":255149,"visible":true,"origin":"","legend":"\u003cp\u003eThe distribution of base percentage and qualities along reads. In the left figures, x-axis represents base position along reads, y-axis represents base percentage at the position; each color represents a type of nucleotide. Under normal conditions, the sample does not have AT/GC separation. It is normal to see fluctuations in the first several bp positions, which is caused by random primer and the instability of enzyme-substrate binding at the beginning of the sequencing reaction In the right figures, x-axis represents base position along reads, y-axis represents base quality; each dot represents the base quality of the corresponding position along reads, color intensity reflects the number of nucleotides, a more intense color along a quality value indicates a higher proportion of this quality in the sequencing data. A, B and C represent for sample no. 1, 2 and 3 respectively.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-3945697/v1/d95202d29f8175e896336520.png"},{"id":51184044,"identity":"94256fdc-c614-41af-91dc-354bf1889322","added_by":"auto","created_at":"2024-02-15 15:43:05","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":459422,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3945697/v1/ed4f358e-b71a-4092-9a4f-331f7ee01fc0.pdf"},{"id":51183169,"identity":"8100719a-9382-4cfd-9716-630ed5fe2582","added_by":"auto","created_at":"2024-02-15 15:35:05","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":12507,"visible":true,"origin":"","legend":"","description":"","filename":"Table1.docx","url":"https://assets-eu.researchsquare.com/files/rs-3945697/v1/19867205b8ceb74a327e2159.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Genome sequencing of captive white tigers from Bangladesh","fulltext":[{"header":"Objective","content":"\u003cp\u003eThe critically endangered Bengal tiger, \u003cem\u003ePanthera tigris tigris\u003c/em\u003e, is a native subspecies of the Indian subcontinent. The Bengal tiger population in India started to drop over a century ago. By 1970, less than 2,000 tigers remained in the wild, similar to the global tiger population reduction. Approximately 2,900 wild tigers remain in Indian reserves, making up over 60% of the total number of wild tigers worldwide [\u003cspan class=\"CitationRef\"\u003e1\u003c/span\u003e]. According to estimates from the Bengal Tiger Conservation Activity (BAGH) project, there were 114 tigers in the Bangladesh Sundarbans [\u003cspan class=\"CitationRef\"\u003e2\u003c/span\u003e]. Despite several conservation efforts, numerous factors, including habitat loss, deforestation, altered land cover, human disturbance of the forests, poaching, hunting, illegal wildlife trade, climate change, natural disasters and inadequate legal frameworks [\u003cspan class=\"CitationRef\"\u003e3\u003c/span\u003e], are contributing to the extinction of the tiger population in the Sundarbans.\u003c/p\u003e\n\u003cp\u003eBy contrast, captive tigers are flourishing. Appropriately maintained captive populations of wild animals have been shown to represent a \u0026quot;genetic reservoir\u0026quot; of their natural counterparts, providing insurance against extinction in the wild and aiding in public education, research, and fundraising. Small, isolated populations that experience inbreeding have minimal genetic variety among their individuals and are very vulnerable to extinction. According to estimates, the Bengal tiger population possesses the most genetic diversity, making it the ideal gene pool reservoir for conservation efforts [\u003cspan class=\"CitationRef\"\u003e4\u003c/span\u003e, \u003cspan class=\"CitationRef\"\u003e5\u003c/span\u003e]. Using available genomic resources, a high-quality reference genome for Bengal tigers [\u003cspan class=\"CitationRef\"\u003e6\u003c/span\u003e] and other tiger genomic data (5, 7\u0026ndash;10), we can conduct a comparative genomic analysis and determine the genetic diversity of Bengal tigers. Therefore, we generated this data to compile more comprehensive genomic information, which will be helpful for future research into the variants causing significant colour phenotypes.\u003c/p\u003e"},{"header":"Data description","content":"\u003cp\u003eFollowing the ethical rules and procedures of Chattogram Zoo Bangladesh, blood samples were taken from three white tiger cubs. Total genomic DNA was extracted from blood samples using Monarch Genomic DNA Purification Kit (New England Biolabs, UK) according to the manufacturer\u0026apos;s guidelines. Thermo Scientific, USA\u0026apos;s NanoDropTM One Microvolume UV-Vis Spectrophotometer was used to evaluate the extracted DNA\u0026apos;s quality and purity. For sequencing and library construction (Short Insert library), purified genomic DNA was transferred to Beijing Genomics Institute (BGI, Hong Kong). The DNBSEQ Short-read library preparation instructions provided by the manufacturer were followed for the development of the sequencing libraries. We used a DNBseq platform to do whole genome sequencing(WGS).\u003c/p\u003e\n\u003cp\u003eHigh-performance computing resources were used for WGS bioinformatics. Low-quality raw paired readings were removed using SOAPnuke [\u003cspan class=\"CitationRef\"\u003e11\u003c/span\u003e] after the raw reads were assessed for quality. In a nutshell, low-quality or adapter sequences in the raw data were filtered first. Many data processing steps were taken to get rid of contaminants and provide reliable data. The filter parameters for the SOAPnuke program were \u0026quot;-n 0.001 -l 10 --adaMR 0.25\u0026quot;. The filtering steps were 1) Filter adapter: delete the whole read if the sequencing read matches 25.0% or more of the adapter sequence (a maximum of two base mismatches is permitted); 2) Filter low-quality data: remove the whole sequencing read if bases with a quality value of less than 10 make up at least 50.0% of the read; 3) Eliminate N: Delete the whole read and discard any N information that makes up 0.1% or more of the sequencing read; 4) To obtain clean readings, Phred\u0026thinsp;+\u0026thinsp;33 was set as the output read quality value for the system. The quality of data was examined after filtering. Base percentage compositions showed all sequenced samples had high-quality data after filtering (Additional file 1). Burrows-Wheeler Aligner (BWA) software [\u003cspan class=\"CitationRef\"\u003e12\u003c/span\u003e] was used to align high-quality reads to the reference \u003cem\u003ePanthera tigris tigris\u003c/em\u003e genomes, the PanTigT.SI.v4 (Shukla et al., 2023), using the default BWA mem settings.\u003c/p\u003e\n\u003cp\u003eFor three white Bengal tigers that were sequenced, we produced 77 Gb of data (Data file 1, 2 and 3). The average genome coverage was 11X. A description of the clean data is shown in Additional file 2 (Table \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e). Mapping reads encompass 98.46% of the reference tiger genome in the current investigation.\u0026nbsp;\u003c/p\u003e\n\u003ctable id=\"Tab1\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eOverview of data files/data sets.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eLabel\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eName of data file/data set\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eFile types\u003c/p\u003e\n \u003cp\u003e(file extension)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eData repository and identifier (DOI or accession number)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAdditional file 1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eFigure 1 The distribution of base percentage and qualities along reads\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDocument file (.pdf)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eFigshare,\u003c/p\u003e\n \u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.24996869\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp\u003e[\u003cspan class=\"CitationRef\"\u003e13\u003c/span\u003e]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eData file 1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWGS data of white Bengal tiger sample 1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSRA file (.fastq.gz)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNCBI Sequence Read Archive \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://trace.ncbi.nlm.nih.gov/Traces?run=SRR24305815\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp\u003e[\u003cspan class=\"CitationRef\"\u003e14\u003c/span\u003e]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eData file 2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWGS data of white Bengal tiger sample 2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSRA file (.fastq.gz)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNCBI Sequence Read Archive \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://trace.ncbi.nlm.nih.gov/Traces?run=SRR24459545\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp\u003e[\u003cspan class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eData file 3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWGS data of white Bengal tiger sample 3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSRA file (.fastq.gz)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNCBI Sequence Read Archive\u003c/p\u003e\n \u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://trace.ncbi.nlm.nih.gov/Traces/?run=SRR24632529\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp\u003e[\u003cspan class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAdditional file 2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eTable \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e Basic statistics of whole genome sequence data for captive white tiger from\u003c/p\u003e\n \u003cp\u003eBangladesh\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDocument file (.docx)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eFigshare, \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.24913884.v1\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003cp\u003e[\u003cspan class=\"CitationRef\"\u003e17\u003c/span\u003e]\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e"},{"header":"Limitations","content":"\u003cp\u003eSince all the samples come from individuals from the same parent, performing a genome-wide association study to identify genomic regions associated with a particular phenotype were not possible.\u003c/p\u003e"},{"header":"Abbreviations","content":" \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"No\" id=\"Taba\" border=\"1\"\u003e \u003ccolgroup cols=\"2\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003eBWA\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003eBurrows-Wheeler Aligner\u003c/div\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003eDNA\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003eDeoxyribonucleic acid\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003eGb\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003eGiga base\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003eWGS\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003eWhole Genome Sequencing\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003cbr/\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll\u0026nbsp;animal\u0026nbsp;procedures\u0026nbsp;including collecting\u0026nbsp;blood\u0026nbsp;samples\u0026nbsp;from\u0026nbsp;tigers were approved by the research ethics committee of Chattogram Veterinary and Animal Sciences University\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThe Additional files 1 and 2 described in this Data Note can be freely and openly accessed on FigShare (https://figshare.com/) [13, 15]. The data described in this Data note can be freely and openly accessed from the NCBI Bioproject PRJNA961947. Raw data have been deposited separately in the Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra) with open accession ID SRP434520 [14-16].\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was financially supported by a grant from the University Grants Commission, Bangladesh through research allocation of Chattogram Veterinary and Animal Sciences University, Bangladesh.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026rsquo; contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAD conceived the experiments and performed bioinformatics analyses; MSHS provided the samples; MS performed the sample collection and PCR in the lab; AD and MDG wrote and edited the manuscript. All authors approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eJhala YV, Qureshi Q, Nayak AK. Status of Tigers, Copredators and Prey in India, 2018, New Delhi: National Tiger Conservation Authority, Government of India; 2020.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAziz MA, Kabir MJ, Shamsuddoha M, Ahsan MM, Sharma S, Chakma S et al. Second phase status of tigers in Bangladesh Sundarban 2018. Department of Zoology, Janhangirnagar University; WildTeam Bangladesh; Forest Department, Bangladesh.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eIslam MZ. A Reality Check of the Global TX2 Goals of Doubling the Bengal Tiger (Panthera tigris tigris) Population by 2022 in the Sundarbans Mangrove Forest. Contemp Probl Ecol. 2023;16(6):868\u0026ndash;85.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eArmstrong EE, Khan A, Taylor RW, Gouy A, Greenbaum G, Thi\u0026eacute;ry A, et al. Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection. Mol Biol Evol. 2021;38(6):2366\u0026ndash;79.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLuo SJ, Liu YC, Xu X. Tigers of the world: Genomics and conservation. Annu Rev Anim Biosci. 2019;15:7:521\u0026ndash;48.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eShukla H, Suryamohan K, Khan A, Mohan K, Perumal RC, Mathew OK, Menon R, Dixon MD, Muraleedharan M, Kuriakose B, Michael S. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. GigaScience. 2023;12:giac112.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang L, Lan T, Lin C, Fu W, Yuan Y, Lin K, et al. Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger. Mol Ecol Resour. 2022;23:330\u0026ndash;47. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1111/1755-0998.13669\u003c/span\u003e\u003cspan address=\"10.1111/1755-0998.13669\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKhan A, Patel K, Shukla H, et al. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proc Natl Acad Sci. 2021;118(49):e2023018118.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLiu YC, Sun X, Driscoll C, et al. Genome-wide evolutionary analysis of natural history and adaptation in the world\u0026rsquo;s tigers. Curr Biol. 2018;28(23):3840\u0026ndash;9.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eCho YS, Hu L, Hou H, et al. The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun. 2013;4(1):2433.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience. 2018;7(1):gix120.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi H, Durbin R. Fast and accurate short read alignment with Burrows\u0026ndash;Wheeler transform. Bioinformatics. 2009;25(14):1754\u0026ndash;60.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDas A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. Figshare. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.24996869\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.24996869\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDas A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. NCBI Seq Read Archive. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://trace.ncbi.nlm.nih.gov/Traces?run=SRR24305815\u003c/span\u003e\u003cspan address=\"https://trace.ncbi.nlm.nih.gov/Traces?run=SRR24305815\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDas A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. NCBI Seq Read Archive. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://trace.ncbi.nlm.nih.gov/Traces?run=SRR24459545\u003c/span\u003e\u003cspan address=\"https://trace.ncbi.nlm.nih.gov/Traces?run=SRR24459545\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDas A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. NCBI Seq Read Archive. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://trace.ncbi.nlm.nih.gov/Traces?run=\u003c/span\u003e\u003cspan address=\"https://trace.ncbi.nlm.nih.gov/Traces?run=\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e SRR24632529.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDas A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tiger from Bangladesh. Figshare. 2024. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.6084/m9.figshare.24913884.v1\u003c/span\u003e\u003cspan address=\"10.6084/m9.figshare.24913884.v1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomic-data","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gtic","sideBox":"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gtic/default.aspx","title":"BMC Genomic Data","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"White Bengal tigers, whole genome sequencing","lastPublishedDoi":"10.21203/rs.3.rs-3945697/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3945697/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eObjectives\u003c/strong\u003e:\u003c/p\u003e\n\u003cp\u003eThe Bengal tiger \u003cem\u003ePanthera tigris tigris\u003c/em\u003e, is an emblematic animal for Bangladesh. Despite being the apex predator in the wild, their number is decreasing due to anthropogenic activities such as hunting, urbanization, expansion of agriculture and deforestation. By contrast, captive tigers are flourishing due to practical conservation efforts. Breeding within the small captive population can produce inbreeding depression and genetic bottlenecks, which may limit the success of conservation efforts. Despite past decades of research, a comprehensive database on genetic variation in the captive and wild Bengal tigers in Bangladesh still needs to be included. Therefore, this research aimed to investigate the White Bengal tiger genome to create a resource for future studies to understand variation underlying important functional traits.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData description:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eBlood samples from Chattogram Zoo were collected for three white Bengal tigers. Genomic DNA for all collected samples were extracted using a commercial DNA extraction kit. Whole genome sequencing was performed using a DNBseq platform. We generated 77 Gb of whole-genome sequencing (WGS) data for three white Bengal tigers (Average 11X coverage/sample). The data we generated will establish a paradigm for tiger research in Bangladesh by providing a genomic resource for future functional studies on the Bengal white tiger.\u003c/p\u003e","manuscriptTitle":"Genome sequencing of captive white tigers from Bangladesh","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-02-15 15:35:01","doi":"10.21203/rs.3.rs-3945697/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2024-03-20T10:42:34+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-02-23T14:36:38+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"55655630-4c29-4af7-99db-572bf6f8ca03","date":"2024-02-19T14:02:11+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"4d7f0d1b-98d7-4057-bb35-3a8f99aad89d","date":"2024-02-19T10:45:31+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-02-19T10:12:13+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-02-14T04:22:16+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2024-02-14T04:22:16+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomic Data","date":"2024-02-10T11:11:18+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomic-data","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gtic","sideBox":"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gtic/default.aspx","title":"BMC Genomic Data","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"92dec447-343d-4708-a36e-307fc325fc1b","owner":[],"postedDate":"February 15th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2024-05-30T08:22:54+00:00","versionOfRecord":[],"versionCreatedAt":"2024-02-15 15:35:01","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-3945697","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3945697","identity":"rs-3945697","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}