Comparative analysis of corrected tiger genome provides clues to its neuronal evolution
The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accura...
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| Veröffentlicht in: | Scientific reports 2019-12, Vol.9 (1), p.18459-11, Article 18459 |
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| description | The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids,
Panthera
, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger. |
| doi_str_mv | 10.1038/s41598-019-54838-z |
| format | Article |
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Panthera
, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-019-54838-z</identifier><identifier>PMID: 31804567</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>45 ; 631/114/2785 ; 631/181/735 ; 631/208/212/2304 ; Adaptation ; Adaptation, Physiological - genetics ; Animals ; Comparative analysis ; Ecological adaptation ; Embryogenesis ; Evolution & development ; Evolution, Molecular ; Evolutionary genetics ; Felidae ; Gene expression ; Genes ; Genetic Variation ; Genome - genetics ; Genomes ; Genomics ; Humanities and Social Sciences ; Male ; Mammals ; Molecular Sequence Annotation ; multidisciplinary ; Non-coding RNA ; Panthera ; Panthera - genetics ; Panthera tigris tigris ; Phylogeny ; Science ; Science (multidisciplinary) ; Sequence Analysis, DNA ; Signal transduction ; Tigers - genetics ; Transcriptome - genetics ; Wildcats</subject><ispartof>Scientific reports, 2019-12, Vol.9 (1), p.18459-11, Article 18459</ispartof><rights>The Author(s) 2019</rights><rights>2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c474t-5392c4f857c60eeb5275d5baa112b6740af9214a67f781b41618cd17b6c723aa3</citedby><cites>FETCH-LOGICAL-c474t-5392c4f857c60eeb5275d5baa112b6740af9214a67f781b41618cd17b6c723aa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895189/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895189/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,725,778,782,862,883,27907,27908,41103,42172,51559,53774,53776</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31804567$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mittal, Parul</creatorcontrib><creatorcontrib>Jaiswal, Shubham K.</creatorcontrib><creatorcontrib>Vijay, Nagarjun</creatorcontrib><creatorcontrib>Saxena, Rituja</creatorcontrib><creatorcontrib>Sharma, Vineet K.</creatorcontrib><title>Comparative analysis of corrected tiger genome provides clues to its neuronal evolution</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids,
Panthera
, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mittal, Parul</au><au>Jaiswal, Shubham K.</au><au>Vijay, Nagarjun</au><au>Saxena, Rituja</au><au>Sharma, Vineet K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative analysis of corrected tiger genome provides clues to its neuronal evolution</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2019-12-05</date><risdate>2019</risdate><volume>9</volume><issue>1</issue><spage>18459</spage><epage>11</epage><pages>18459-11</pages><artnum>18459</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids,
Panthera
, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>31804567</pmid><doi>10.1038/s41598-019-54838-z</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 45 631/114/2785 631/181/735 631/208/212/2304 Adaptation Adaptation, Physiological - genetics Animals Comparative analysis Ecological adaptation Embryogenesis Evolution & development Evolution, Molecular Evolutionary genetics Felidae Gene expression Genes Genetic Variation Genome - genetics Genomes Genomics Humanities and Social Sciences Male Mammals Molecular Sequence Annotation multidisciplinary Non-coding RNA Panthera Panthera - genetics Panthera tigris tigris Phylogeny Science Science (multidisciplinary) Sequence Analysis, DNA Signal transduction Tigers - genetics Transcriptome - genetics Wildcats |
| title | Comparative analysis of corrected tiger genome provides clues to its neuronal evolution |
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