Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake
Abstract Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by a paucity of data for one of the two main extant snake taxa, the highly fossorial Scolecophidia. Here we present and analyze vision genes fro...
Gespeichert in:
Veröffentlicht in: | Genome biology and evolution 2021-12, Vol.13 (12), Article 253 |
---|---|
Hauptverfasser: | , , , , , , , , , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | |
---|---|
container_issue | 12 |
container_start_page | |
container_title | Genome biology and evolution |
container_volume | 13 |
creator | Gower, David J Fleming, James F Pisani, Davide Vonk, Freek J Kerkkamp, Harald M I Peichl, Leo Meimann, Sonja Casewell, Nicholas R Henkel, Christiaan V Richardson, Michael K Sanders, Kate L Simões, Bruno F |
description | Abstract
Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by a paucity of data for one of the two main extant snake taxa, the highly fossorial Scolecophidia. Here we present and analyze vision genes from the first eye-transcriptomic and genome-wide data for Scolecophidia, for Anilios bicolor, and A. bituberculatus, respectively. We also present immunohistochemistry data for retinal anatomy and visual opsin-gene expression in Anilios. Analyzed in the context of 19 lepidosaurian genomes and 12 eye transcriptomes, the new genome-wide and transcriptomic data provide evidence for a much more reduced visual system in Anilios than in non-scolecophidian (=alethinophidian) snakes and in lizards. In Anilios, there is no evidence of the presence of 7 of the 12 genes associated with alethinophidian photopic (cone) phototransduction. This indicates extensive gene loss and many of these candidate gene losses occur also in highly fossorial mammals with reduced vision. Although recent phylogenetic studies have found evidence for scolecophidian paraphyly, the loss in Anilios of visual genes that are present in alethinophidians implies that the ancestral snake had a better-developed visual system than is known for any extant scolecophidian. |
doi_str_mv | 10.1093/gbe/evab253 |
format | Article |
fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmed_primary_34791190</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/gbe/evab253</oup_id><sourcerecordid>2599070097</sourcerecordid><originalsourceid>FETCH-LOGICAL-c478t-6806a61e1e94543732ac0af66a4adb445e81b3e036f071a57d4a4755d6b6e3703</originalsourceid><addsrcrecordid>eNqNkc1v1DAQxSMEoqVw4o5yQkgodLz-SjggVatSVqrEYQscLceZ7BoSO9hJ0Z77j9f7wVIuiJNHM7958-SXZS8JvCNQ0fNVjed4q-sZp4-yUyJ5VQjB6eMH9Un2LMbvAEIwQZ9mJ5TJipAKTrO7yw0WN0G7aIIdRt9jrl2TX6FLZfHNNpgv8eeEzli3ylsf8qXxHRo_rG1j9ft80Q-dNXq03sXdfOFaDGFLj2vMv9o46S5fbuKIfe7bXfPCGYxj2Pad_oHPsyet7iK-OLxn2ZePlzfzT8X156vF_OK6MEyWYyFKEFoQJFgxzqikM21At0JoppuaMY4lqSkCFS1IorlsmGaS80bUAqkEepZ92OsOU91jY9BtPagh2F6HjfLaqr8nzq7Vyt-qUjBKK5EE3hwEgk9_EkfV22iw67RDP0U141UFEqCSCX27R03wMQZsj2cIqG1sKsWmDrEl-tVDZ0f2d05_5H5h7dtobAoEjxgASEZLkOk2AE90-f_03I679OZ-cmNafb1f9dPwT8v3kTvEpQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2599070097</pqid></control><display><type>article</type><title>Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Oxford Journals Open Access Collection</source><source>PubMed Central</source><creator>Gower, David J ; Fleming, James F ; Pisani, Davide ; Vonk, Freek J ; Kerkkamp, Harald M I ; Peichl, Leo ; Meimann, Sonja ; Casewell, Nicholas R ; Henkel, Christiaan V ; Richardson, Michael K ; Sanders, Kate L ; Simões, Bruno F</creator><contributor>Makino, Takashi</contributor><creatorcontrib>Gower, David J ; Fleming, James F ; Pisani, Davide ; Vonk, Freek J ; Kerkkamp, Harald M I ; Peichl, Leo ; Meimann, Sonja ; Casewell, Nicholas R ; Henkel, Christiaan V ; Richardson, Michael K ; Sanders, Kate L ; Simões, Bruno F ; Makino, Takashi</creatorcontrib><description>Abstract
Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by a paucity of data for one of the two main extant snake taxa, the highly fossorial Scolecophidia. Here we present and analyze vision genes from the first eye-transcriptomic and genome-wide data for Scolecophidia, for Anilios bicolor, and A. bituberculatus, respectively. We also present immunohistochemistry data for retinal anatomy and visual opsin-gene expression in Anilios. Analyzed in the context of 19 lepidosaurian genomes and 12 eye transcriptomes, the new genome-wide and transcriptomic data provide evidence for a much more reduced visual system in Anilios than in non-scolecophidian (=alethinophidian) snakes and in lizards. In Anilios, there is no evidence of the presence of 7 of the 12 genes associated with alethinophidian photopic (cone) phototransduction. This indicates extensive gene loss and many of these candidate gene losses occur also in highly fossorial mammals with reduced vision. Although recent phylogenetic studies have found evidence for scolecophidian paraphyly, the loss in Anilios of visual genes that are present in alethinophidians implies that the ancestral snake had a better-developed visual system than is known for any extant scolecophidian.</description><identifier>ISSN: 1759-6653</identifier><identifier>EISSN: 1759-6653</identifier><identifier>DOI: 10.1093/gbe/evab253</identifier><identifier>PMID: 34791190</identifier><language>eng</language><publisher>OXFORD: Oxford University Press</publisher><subject>Animals ; Evolution, Molecular ; Evolutionary Biology ; Genetics & Heredity ; Life Sciences & Biomedicine ; Lizards - genetics ; Mammals - genetics ; Opsins - genetics ; Phylogeny ; Science & Technology ; Snakes - genetics ; Transcriptome</subject><ispartof>Genome biology and evolution, 2021-12, Vol.13 (12), Article 253</ispartof><rights>The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2021</rights><rights>The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</rights><oa>free_for_read</oa><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>0</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000743807700005</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c478t-6806a61e1e94543732ac0af66a4adb445e81b3e036f071a57d4a4755d6b6e3703</citedby><cites>FETCH-LOGICAL-c478t-6806a61e1e94543732ac0af66a4adb445e81b3e036f071a57d4a4755d6b6e3703</cites><orcidid>0000-0001-5390-6541 ; 0000-0003-1222-8101 ; 0000-0001-9838-8215 ; 0000-0002-8035-4719 ; 0000-0003-0949-6682 ; 0000-0002-8141-0911 ; 0000-0002-1725-8863</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8643396/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8643396/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,1599,2108,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34791190$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Makino, Takashi</contributor><creatorcontrib>Gower, David J</creatorcontrib><creatorcontrib>Fleming, James F</creatorcontrib><creatorcontrib>Pisani, Davide</creatorcontrib><creatorcontrib>Vonk, Freek J</creatorcontrib><creatorcontrib>Kerkkamp, Harald M I</creatorcontrib><creatorcontrib>Peichl, Leo</creatorcontrib><creatorcontrib>Meimann, Sonja</creatorcontrib><creatorcontrib>Casewell, Nicholas R</creatorcontrib><creatorcontrib>Henkel, Christiaan V</creatorcontrib><creatorcontrib>Richardson, Michael K</creatorcontrib><creatorcontrib>Sanders, Kate L</creatorcontrib><creatorcontrib>Simões, Bruno F</creatorcontrib><title>Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake</title><title>Genome biology and evolution</title><addtitle>GENOME BIOL EVOL</addtitle><addtitle>Genome Biol Evol</addtitle><description>Abstract
Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by a paucity of data for one of the two main extant snake taxa, the highly fossorial Scolecophidia. Here we present and analyze vision genes from the first eye-transcriptomic and genome-wide data for Scolecophidia, for Anilios bicolor, and A. bituberculatus, respectively. We also present immunohistochemistry data for retinal anatomy and visual opsin-gene expression in Anilios. Analyzed in the context of 19 lepidosaurian genomes and 12 eye transcriptomes, the new genome-wide and transcriptomic data provide evidence for a much more reduced visual system in Anilios than in non-scolecophidian (=alethinophidian) snakes and in lizards. In Anilios, there is no evidence of the presence of 7 of the 12 genes associated with alethinophidian photopic (cone) phototransduction. This indicates extensive gene loss and many of these candidate gene losses occur also in highly fossorial mammals with reduced vision. Although recent phylogenetic studies have found evidence for scolecophidian paraphyly, the loss in Anilios of visual genes that are present in alethinophidians implies that the ancestral snake had a better-developed visual system than is known for any extant scolecophidian.</description><subject>Animals</subject><subject>Evolution, Molecular</subject><subject>Evolutionary Biology</subject><subject>Genetics & Heredity</subject><subject>Life Sciences & Biomedicine</subject><subject>Lizards - genetics</subject><subject>Mammals - genetics</subject><subject>Opsins - genetics</subject><subject>Phylogeny</subject><subject>Science & Technology</subject><subject>Snakes - genetics</subject><subject>Transcriptome</subject><issn>1759-6653</issn><issn>1759-6653</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>HGBXW</sourceid><sourceid>EIF</sourceid><recordid>eNqNkc1v1DAQxSMEoqVw4o5yQkgodLz-SjggVatSVqrEYQscLceZ7BoSO9hJ0Z77j9f7wVIuiJNHM7958-SXZS8JvCNQ0fNVjed4q-sZp4-yUyJ5VQjB6eMH9Un2LMbvAEIwQZ9mJ5TJipAKTrO7yw0WN0G7aIIdRt9jrl2TX6FLZfHNNpgv8eeEzli3ylsf8qXxHRo_rG1j9ft80Q-dNXq03sXdfOFaDGFLj2vMv9o46S5fbuKIfe7bXfPCGYxj2Pad_oHPsyet7iK-OLxn2ZePlzfzT8X156vF_OK6MEyWYyFKEFoQJFgxzqikM21At0JoppuaMY4lqSkCFS1IorlsmGaS80bUAqkEepZ92OsOU91jY9BtPagh2F6HjfLaqr8nzq7Vyt-qUjBKK5EE3hwEgk9_EkfV22iw67RDP0U141UFEqCSCX27R03wMQZsj2cIqG1sKsWmDrEl-tVDZ0f2d05_5H5h7dtobAoEjxgASEZLkOk2AE90-f_03I679OZ-cmNafb1f9dPwT8v3kTvEpQ</recordid><startdate>20211201</startdate><enddate>20211201</enddate><creator>Gower, David J</creator><creator>Fleming, James F</creator><creator>Pisani, Davide</creator><creator>Vonk, Freek J</creator><creator>Kerkkamp, Harald M I</creator><creator>Peichl, Leo</creator><creator>Meimann, Sonja</creator><creator>Casewell, Nicholas R</creator><creator>Henkel, Christiaan V</creator><creator>Richardson, Michael K</creator><creator>Sanders, Kate L</creator><creator>Simões, Bruno F</creator><general>Oxford University Press</general><general>Oxford Univ Press</general><scope>TOX</scope><scope>BLEPL</scope><scope>DTL</scope><scope>HGBXW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-5390-6541</orcidid><orcidid>https://orcid.org/0000-0003-1222-8101</orcidid><orcidid>https://orcid.org/0000-0001-9838-8215</orcidid><orcidid>https://orcid.org/0000-0002-8035-4719</orcidid><orcidid>https://orcid.org/0000-0003-0949-6682</orcidid><orcidid>https://orcid.org/0000-0002-8141-0911</orcidid><orcidid>https://orcid.org/0000-0002-1725-8863</orcidid></search><sort><creationdate>20211201</creationdate><title>Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake</title><author>Gower, David J ; Fleming, James F ; Pisani, Davide ; Vonk, Freek J ; Kerkkamp, Harald M I ; Peichl, Leo ; Meimann, Sonja ; Casewell, Nicholas R ; Henkel, Christiaan V ; Richardson, Michael K ; Sanders, Kate L ; Simões, Bruno F</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c478t-6806a61e1e94543732ac0af66a4adb445e81b3e036f071a57d4a4755d6b6e3703</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animals</topic><topic>Evolution, Molecular</topic><topic>Evolutionary Biology</topic><topic>Genetics & Heredity</topic><topic>Life Sciences & Biomedicine</topic><topic>Lizards - genetics</topic><topic>Mammals - genetics</topic><topic>Opsins - genetics</topic><topic>Phylogeny</topic><topic>Science & Technology</topic><topic>Snakes - genetics</topic><topic>Transcriptome</topic><toplevel>online_resources</toplevel><creatorcontrib>Gower, David J</creatorcontrib><creatorcontrib>Fleming, James F</creatorcontrib><creatorcontrib>Pisani, Davide</creatorcontrib><creatorcontrib>Vonk, Freek J</creatorcontrib><creatorcontrib>Kerkkamp, Harald M I</creatorcontrib><creatorcontrib>Peichl, Leo</creatorcontrib><creatorcontrib>Meimann, Sonja</creatorcontrib><creatorcontrib>Casewell, Nicholas R</creatorcontrib><creatorcontrib>Henkel, Christiaan V</creatorcontrib><creatorcontrib>Richardson, Michael K</creatorcontrib><creatorcontrib>Sanders, Kate L</creatorcontrib><creatorcontrib>Simões, Bruno F</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Web of Science Core Collection</collection><collection>Science Citation Index Expanded</collection><collection>Web of Science - Science Citation Index Expanded - 2021</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome biology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gower, David J</au><au>Fleming, James F</au><au>Pisani, Davide</au><au>Vonk, Freek J</au><au>Kerkkamp, Harald M I</au><au>Peichl, Leo</au><au>Meimann, Sonja</au><au>Casewell, Nicholas R</au><au>Henkel, Christiaan V</au><au>Richardson, Michael K</au><au>Sanders, Kate L</au><au>Simões, Bruno F</au><au>Makino, Takashi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake</atitle><jtitle>Genome biology and evolution</jtitle><stitle>GENOME BIOL EVOL</stitle><addtitle>Genome Biol Evol</addtitle><date>2021-12-01</date><risdate>2021</risdate><volume>13</volume><issue>12</issue><artnum>253</artnum><issn>1759-6653</issn><eissn>1759-6653</eissn><abstract>Abstract
Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by a paucity of data for one of the two main extant snake taxa, the highly fossorial Scolecophidia. Here we present and analyze vision genes from the first eye-transcriptomic and genome-wide data for Scolecophidia, for Anilios bicolor, and A. bituberculatus, respectively. We also present immunohistochemistry data for retinal anatomy and visual opsin-gene expression in Anilios. Analyzed in the context of 19 lepidosaurian genomes and 12 eye transcriptomes, the new genome-wide and transcriptomic data provide evidence for a much more reduced visual system in Anilios than in non-scolecophidian (=alethinophidian) snakes and in lizards. In Anilios, there is no evidence of the presence of 7 of the 12 genes associated with alethinophidian photopic (cone) phototransduction. This indicates extensive gene loss and many of these candidate gene losses occur also in highly fossorial mammals with reduced vision. Although recent phylogenetic studies have found evidence for scolecophidian paraphyly, the loss in Anilios of visual genes that are present in alethinophidians implies that the ancestral snake had a better-developed visual system than is known for any extant scolecophidian.</abstract><cop>OXFORD</cop><pub>Oxford University Press</pub><pmid>34791190</pmid><doi>10.1093/gbe/evab253</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0001-5390-6541</orcidid><orcidid>https://orcid.org/0000-0003-1222-8101</orcidid><orcidid>https://orcid.org/0000-0001-9838-8215</orcidid><orcidid>https://orcid.org/0000-0002-8035-4719</orcidid><orcidid>https://orcid.org/0000-0003-0949-6682</orcidid><orcidid>https://orcid.org/0000-0002-8141-0911</orcidid><orcidid>https://orcid.org/0000-0002-1725-8863</orcidid><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1759-6653 |
ispartof | Genome biology and evolution, 2021-12, Vol.13 (12), Article 253 |
issn | 1759-6653 1759-6653 |
language | eng |
recordid | cdi_pubmed_primary_34791190 |
source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford Journals Open Access Collection; PubMed Central |
subjects | Animals Evolution, Molecular Evolutionary Biology Genetics & Heredity Life Sciences & Biomedicine Lizards - genetics Mammals - genetics Opsins - genetics Phylogeny Science & Technology Snakes - genetics Transcriptome |
title | Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-20T00%3A12%3A24IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Eye-Transcriptome%20and%20Genome-Wide%20Sequencing%20for%20Scolecophidia:%20Implications%20for%20Inferring%20the%20Visual%20System%20of%20the%20Ancestral%20Snake&rft.jtitle=Genome%20biology%20and%20evolution&rft.au=Gower,%20David%20J&rft.date=2021-12-01&rft.volume=13&rft.issue=12&rft.artnum=253&rft.issn=1759-6653&rft.eissn=1759-6653&rft_id=info:doi/10.1093/gbe/evab253&rft_dat=%3Cproquest_pubme%3E2599070097%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2599070097&rft_id=info:pmid/34791190&rft_oup_id=10.1093/gbe/evab253&rfr_iscdi=true |