Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression
The aim of this work is the full characterization of all the nocturnin ( ) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplicat...
Gespeichert in:
| Veröffentlicht in: | International journal of molecular sciences 2023-12, Vol.25 (1), p.54 |
|---|---|
| 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 | 1 |
| container_start_page | 54 |
| container_title | International journal of molecular sciences |
| container_volume | 25 |
| creator | Madera, Diego Alonso-Gómez, Aitana Delgado, María Jesús Valenciano, Ana Isabel Alonso-Gómez, Ángel Luis |
| description | The aim of this work is the full characterization of all the nocturnin (
) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of
in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplication and the cyprinine 4Rc. After sequencing the full-length mRNA of goldfish, we obtained two isoforms for
(
and
) with two splice variants (I and II), and only one for
(
) with two transcripts (II and III). Using the splicing variant II, the prediction of the secondary and tertiary structures renders a well-conserved 3D distribution of four α-helices and nine β-sheets in the three
isoforms. A synteny analysis based on the localization of
genes in the patrilineal or matrilineal subgenomes and a phylogenetic tree of protein sequences were accomplished to stablish a classification and a long-lasting nomenclature of
in goldfish, and valid to be extrapolated to allotetraploid Cyprininae. Finally, both goldfish and zebrafish showed a broad tissue expression of all the
paralogues. Moreover, the enriched expression of specific paralogues in some tissues argues in favour of neo- or subfunctionalization. |
| doi_str_mv | 10.3390/ijms25010054 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10779419</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A779212571</galeid><sourcerecordid>A779212571</sourcerecordid><originalsourceid>FETCH-LOGICAL-c437t-6b8b121f3dfb82805f30c8f5bc7c6e93d048b609481d69290905333aca77f7d83</originalsourceid><addsrcrecordid>eNptUs1rFDEUH0SxtXrzLAEvHnbbfM1M4qWUpV0LpRZazyGTednNMpOsyYy44h9vhn64FckheXm_D36PVxTvCT5mTOITt-kTLTHBuOQvikPCKZ1jXNUv994HxZuUNhhTRkv5ujhggmJGKT8sfi_BA1qsddRmgOh-6cEFj4JF18EMY_TOo5vc7MJqhIRytQxda11af0YXY9ehRWidX6Fb-D6CN5Bm6HaI40SFGbpZ7zIR_A5p36I7l9II6PznNkJK2eZt8crqLsG7h_uo-HZxfrf4Mr_6urxcnF3NDWf1MK8a0RBKLGttI6jApWXYCFs2pjYVSNZiLpoKSy5IW0kqscQlY0wbXde2bgU7Kk7vdbdj00NrwA85kdpG1-u4U0E79bzj3Vqtwg9FcF1LTmRW-PSgEEMOmgbVu2Sg67SHMCZFJWGci5JMZh__gW5CnmPON6GooJxw-Re10h0o523IxmYSVWfZkxJa1iSjjv-DyqeF3pngwbr8_4wwuyeYGFKKYJ9CEqymdVH765LhH_YH8wR-3A_2B3UluxQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2912824149</pqid></control><display><type>article</type><title>Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression</title><source>MDPI - Multidisciplinary Digital Publishing Institute</source><source>MEDLINE</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Madera, Diego ; Alonso-Gómez, Aitana ; Delgado, María Jesús ; Valenciano, Ana Isabel ; Alonso-Gómez, Ángel Luis</creator><creatorcontrib>Madera, Diego ; Alonso-Gómez, Aitana ; Delgado, María Jesús ; Valenciano, Ana Isabel ; Alonso-Gómez, Ángel Luis</creatorcontrib><description>The aim of this work is the full characterization of all the nocturnin (
) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of
in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplication and the cyprinine 4Rc. After sequencing the full-length mRNA of goldfish, we obtained two isoforms for
(
and
) with two splice variants (I and II), and only one for
(
) with two transcripts (II and III). Using the splicing variant II, the prediction of the secondary and tertiary structures renders a well-conserved 3D distribution of four α-helices and nine β-sheets in the three
isoforms. A synteny analysis based on the localization of
genes in the patrilineal or matrilineal subgenomes and a phylogenetic tree of protein sequences were accomplished to stablish a classification and a long-lasting nomenclature of
in goldfish, and valid to be extrapolated to allotetraploid Cyprininae. Finally, both goldfish and zebrafish showed a broad tissue expression of all the
paralogues. Moreover, the enriched expression of specific paralogues in some tissues argues in favour of neo- or subfunctionalization.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms25010054</identifier><identifier>PMID: 38203224</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Amino acids ; Animals ; Enzymes ; Fishes ; Genes ; Genetic aspects ; Genomes ; Goldfish - genetics ; Metabolism ; Nuclear Proteins ; Photoreceptors ; Phylogeny ; Protein Isoforms - genetics ; Retina ; RNA ; Transcription Factors ; Vertebrates ; Zebrafish ; Zebrafish - genetics</subject><ispartof>International journal of molecular sciences, 2023-12, Vol.25 (1), p.54</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 by the authors. 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c437t-6b8b121f3dfb82805f30c8f5bc7c6e93d048b609481d69290905333aca77f7d83</cites><orcidid>0000-0003-3219-2265 ; 0000-0002-8830-9410 ; 0000-0002-1185-9377</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/PMC10779419/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10779419/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38203224$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Madera, Diego</creatorcontrib><creatorcontrib>Alonso-Gómez, Aitana</creatorcontrib><creatorcontrib>Delgado, María Jesús</creatorcontrib><creatorcontrib>Valenciano, Ana Isabel</creatorcontrib><creatorcontrib>Alonso-Gómez, Ángel Luis</creatorcontrib><title>Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression</title><title>International journal of molecular sciences</title><addtitle>Int J Mol Sci</addtitle><description>The aim of this work is the full characterization of all the nocturnin (
) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of
in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplication and the cyprinine 4Rc. After sequencing the full-length mRNA of goldfish, we obtained two isoforms for
(
and
) with two splice variants (I and II), and only one for
(
) with two transcripts (II and III). Using the splicing variant II, the prediction of the secondary and tertiary structures renders a well-conserved 3D distribution of four α-helices and nine β-sheets in the three
isoforms. A synteny analysis based on the localization of
genes in the patrilineal or matrilineal subgenomes and a phylogenetic tree of protein sequences were accomplished to stablish a classification and a long-lasting nomenclature of
in goldfish, and valid to be extrapolated to allotetraploid Cyprininae. Finally, both goldfish and zebrafish showed a broad tissue expression of all the
paralogues. Moreover, the enriched expression of specific paralogues in some tissues argues in favour of neo- or subfunctionalization.</description><subject>Amino acids</subject><subject>Animals</subject><subject>Enzymes</subject><subject>Fishes</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Goldfish - genetics</subject><subject>Metabolism</subject><subject>Nuclear Proteins</subject><subject>Photoreceptors</subject><subject>Phylogeny</subject><subject>Protein Isoforms - genetics</subject><subject>Retina</subject><subject>RNA</subject><subject>Transcription Factors</subject><subject>Vertebrates</subject><subject>Zebrafish</subject><subject>Zebrafish - genetics</subject><issn>1422-0067</issn><issn>1661-6596</issn><issn>1422-0067</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNptUs1rFDEUH0SxtXrzLAEvHnbbfM1M4qWUpV0LpRZazyGTednNMpOsyYy44h9vhn64FckheXm_D36PVxTvCT5mTOITt-kTLTHBuOQvikPCKZ1jXNUv994HxZuUNhhTRkv5ujhggmJGKT8sfi_BA1qsddRmgOh-6cEFj4JF18EMY_TOo5vc7MJqhIRytQxda11af0YXY9ehRWidX6Fb-D6CN5Bm6HaI40SFGbpZ7zIR_A5p36I7l9II6PznNkJK2eZt8crqLsG7h_uo-HZxfrf4Mr_6urxcnF3NDWf1MK8a0RBKLGttI6jApWXYCFs2pjYVSNZiLpoKSy5IW0kqscQlY0wbXde2bgU7Kk7vdbdj00NrwA85kdpG1-u4U0E79bzj3Vqtwg9FcF1LTmRW-PSgEEMOmgbVu2Sg67SHMCZFJWGci5JMZh__gW5CnmPON6GooJxw-Re10h0o523IxmYSVWfZkxJa1iSjjv-DyqeF3pngwbr8_4wwuyeYGFKKYJ9CEqymdVH765LhH_YH8wR-3A_2B3UluxQ</recordid><startdate>20231219</startdate><enddate>20231219</enddate><creator>Madera, Diego</creator><creator>Alonso-Gómez, Aitana</creator><creator>Delgado, María Jesús</creator><creator>Valenciano, Ana Isabel</creator><creator>Alonso-Gómez, Ángel Luis</creator><general>MDPI AG</general><general>MDPI</general><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>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-3219-2265</orcidid><orcidid>https://orcid.org/0000-0002-8830-9410</orcidid><orcidid>https://orcid.org/0000-0002-1185-9377</orcidid></search><sort><creationdate>20231219</creationdate><title>Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression</title><author>Madera, Diego ; Alonso-Gómez, Aitana ; Delgado, María Jesús ; Valenciano, Ana Isabel ; Alonso-Gómez, Ángel Luis</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c437t-6b8b121f3dfb82805f30c8f5bc7c6e93d048b609481d69290905333aca77f7d83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Amino acids</topic><topic>Animals</topic><topic>Enzymes</topic><topic>Fishes</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Goldfish - genetics</topic><topic>Metabolism</topic><topic>Nuclear Proteins</topic><topic>Photoreceptors</topic><topic>Phylogeny</topic><topic>Protein Isoforms - genetics</topic><topic>Retina</topic><topic>RNA</topic><topic>Transcription Factors</topic><topic>Vertebrates</topic><topic>Zebrafish</topic><topic>Zebrafish - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Madera, Diego</creatorcontrib><creatorcontrib>Alonso-Gómez, Aitana</creatorcontrib><creatorcontrib>Delgado, María Jesús</creatorcontrib><creatorcontrib>Valenciano, Ana Isabel</creatorcontrib><creatorcontrib>Alonso-Gómez, Ángel Luis</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Research Library (Corporate)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>International journal of molecular sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Madera, Diego</au><au>Alonso-Gómez, Aitana</au><au>Delgado, María Jesús</au><au>Valenciano, Ana Isabel</au><au>Alonso-Gómez, Ángel Luis</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression</atitle><jtitle>International journal of molecular sciences</jtitle><addtitle>Int J Mol Sci</addtitle><date>2023-12-19</date><risdate>2023</risdate><volume>25</volume><issue>1</issue><spage>54</spage><pages>54-</pages><issn>1422-0067</issn><issn>1661-6596</issn><eissn>1422-0067</eissn><abstract>The aim of this work is the full characterization of all the nocturnin (
) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of
in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplication and the cyprinine 4Rc. After sequencing the full-length mRNA of goldfish, we obtained two isoforms for
(
and
) with two splice variants (I and II), and only one for
(
) with two transcripts (II and III). Using the splicing variant II, the prediction of the secondary and tertiary structures renders a well-conserved 3D distribution of four α-helices and nine β-sheets in the three
isoforms. A synteny analysis based on the localization of
genes in the patrilineal or matrilineal subgenomes and a phylogenetic tree of protein sequences were accomplished to stablish a classification and a long-lasting nomenclature of
in goldfish, and valid to be extrapolated to allotetraploid Cyprininae. Finally, both goldfish and zebrafish showed a broad tissue expression of all the
paralogues. Moreover, the enriched expression of specific paralogues in some tissues argues in favour of neo- or subfunctionalization.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>38203224</pmid><doi>10.3390/ijms25010054</doi><orcidid>https://orcid.org/0000-0003-3219-2265</orcidid><orcidid>https://orcid.org/0000-0002-8830-9410</orcidid><orcidid>https://orcid.org/0000-0002-1185-9377</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1422-0067 |
| ispartof | International journal of molecular sciences, 2023-12, Vol.25 (1), p.54 |
| issn | 1422-0067 1661-6596 1422-0067 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10779419 |
| source | MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Amino acids Animals Enzymes Fishes Genes Genetic aspects Genomes Goldfish - genetics Metabolism Nuclear Proteins Photoreceptors Phylogeny Protein Isoforms - genetics Retina RNA Transcription Factors Vertebrates Zebrafish Zebrafish - genetics |
| title | Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-28T18%3A47%3A51IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Gene%20Characterization%20of%20Nocturnin%20Paralogues%20in%20Goldfish:%20Full%20Coding%20Sequences,%20Structure,%20Phylogeny%20and%20Tissue%20Expression&rft.jtitle=International%20journal%20of%20molecular%20sciences&rft.au=Madera,%20Diego&rft.date=2023-12-19&rft.volume=25&rft.issue=1&rft.spage=54&rft.pages=54-&rft.issn=1422-0067&rft.eissn=1422-0067&rft_id=info:doi/10.3390/ijms25010054&rft_dat=%3Cgale_pubme%3EA779212571%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2912824149&rft_id=info:pmid/38203224&rft_galeid=A779212571&rfr_iscdi=true |