Molecular phylogenetic and in silico analysis of glyceraldeyde-3-phosphate dehydrogenase (GAPDH) gene from northern bobwhite quail (Colinus virginianus)
Many recent studies have been focused on prevalence and impact of two helminth parasites, eyeworm Oxyspirura petrowi and caecal worm Aulonocephalus pennula, in the northern bobwhite quail ( Colinus virginianus ). However, few studies have attempted to examine the effect of these parasites on the bob...
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| creator | Kalyanasundaram, Aravindan Henry, Brett J. Henry, Cassandra Kendall, Ronald J. |
| description | Many recent studies have been focused on prevalence and impact of two helminth parasites, eyeworm
Oxyspirura petrowi
and caecal worm
Aulonocephalus pennula,
in the northern bobwhite quail (
Colinus virginianus
). However, few studies have attempted to examine the effect of these parasites on the bobwhite immune system. This is likely due to the lack of proper reference genes for relative gene expression studies. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that is often utilized as a reference gene, and in this preliminary study, we evaluated the similarity of bobwhite GAPDH to GAPDH in other avian species to evaluate its potential as a reference gene in bobwhite. GAPDH was identified in the bobwhite full genome sequence and multiple sets of PCR primers were designed to generate overlapping PCR products. These products were then sequenced and then aligned to generate the sequence for the full-length open reading frame (ORF) of bobwhite GAPDH. Utilizing this sequence, phylogenetic analyses and comparative analysis of the exon–intron pattern were conducted that revealed high similarity of GAPDH encoding sequences among bobwhite and other Galliformes. Additionally, This ORF sequence was also used to predict the encoded protein and its three-dimensional structure which like the phylogenetic analyses reveal that bobwhite GAPDH is similar to GAPDH in other Galliformes. Finally, GAPDH qPCR primers were designed, standardized, and tested with bobwhite both uninfected and infected with
O. petrowi
, and this preliminary test showed no statistical difference in expression of GAPDH between the two groups. These analyses are the first to investigate GAPDH in bobwhite. These efforts in phylogeny, sequence analysis, and protein structure suggest that there is > 97% conservation of GADPH among Galliformes. Furthermore, the results of these in silico tests and the preliminary qPCR indicate that GAPDH is a prospective candidate for use in gene expression analyses in bobwhite. |
| doi_str_mv | 10.1007/s11033-021-06186-3 |
| format | Article |
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Oxyspirura petrowi
and caecal worm
Aulonocephalus pennula,
in the northern bobwhite quail (
Colinus virginianus
). However, few studies have attempted to examine the effect of these parasites on the bobwhite immune system. This is likely due to the lack of proper reference genes for relative gene expression studies. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that is often utilized as a reference gene, and in this preliminary study, we evaluated the similarity of bobwhite GAPDH to GAPDH in other avian species to evaluate its potential as a reference gene in bobwhite. GAPDH was identified in the bobwhite full genome sequence and multiple sets of PCR primers were designed to generate overlapping PCR products. These products were then sequenced and then aligned to generate the sequence for the full-length open reading frame (ORF) of bobwhite GAPDH. Utilizing this sequence, phylogenetic analyses and comparative analysis of the exon–intron pattern were conducted that revealed high similarity of GAPDH encoding sequences among bobwhite and other Galliformes. Additionally, This ORF sequence was also used to predict the encoded protein and its three-dimensional structure which like the phylogenetic analyses reveal that bobwhite GAPDH is similar to GAPDH in other Galliformes. Finally, GAPDH qPCR primers were designed, standardized, and tested with bobwhite both uninfected and infected with
O. petrowi
, and this preliminary test showed no statistical difference in expression of GAPDH between the two groups. These analyses are the first to investigate GAPDH in bobwhite. These efforts in phylogeny, sequence analysis, and protein structure suggest that there is > 97% conservation of GADPH among Galliformes. Furthermore, the results of these in silico tests and the preliminary qPCR indicate that GAPDH is a prospective candidate for use in gene expression analyses in bobwhite.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-021-06186-3</identifier><identifier>PMID: 33580461</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Amino acid sequence ; Animal Anatomy ; Animal Biochemistry ; Animals ; Biomedical and Life Sciences ; Colinus - genetics ; Colinus virginianus ; Comparative analysis ; Computer Simulation ; Conserved sequence ; Dehydrogenases ; Galliformes ; Gene expression ; Genomes ; Glyceraldehyde ; Glyceraldehyde 3-phosphate ; Glyceraldehyde-3-phosphate dehydrogenase ; Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - classification ; Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - genetics ; Glycolysis ; Histology ; Immune system ; Life Sciences ; Morphology ; Nucleotide sequence ; Open reading frames ; Original Article ; Parasites ; Phylogenetics ; Phylogeny ; Protein structure ; Quail - genetics ; Sequence analysis</subject><ispartof>Molecular biology reports, 2021-02, Vol.48 (2), p.1093-1101</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature 2021</rights><rights>The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-693483dc922aefb5b641b2bbd2c966f98852efad4d2c1df7c9c5d7cd70db263c3</citedby><cites>FETCH-LOGICAL-c375t-693483dc922aefb5b641b2bbd2c966f98852efad4d2c1df7c9c5d7cd70db263c3</cites><orcidid>0000-0003-0527-5399</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11033-021-06186-3$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-021-06186-3$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33580461$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kalyanasundaram, Aravindan</creatorcontrib><creatorcontrib>Henry, Brett J.</creatorcontrib><creatorcontrib>Henry, Cassandra</creatorcontrib><creatorcontrib>Kendall, Ronald J.</creatorcontrib><title>Molecular phylogenetic and in silico analysis of glyceraldeyde-3-phosphate dehydrogenase (GAPDH) gene from northern bobwhite quail (Colinus virginianus)</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>Many recent studies have been focused on prevalence and impact of two helminth parasites, eyeworm
Oxyspirura petrowi
and caecal worm
Aulonocephalus pennula,
in the northern bobwhite quail (
Colinus virginianus
). However, few studies have attempted to examine the effect of these parasites on the bobwhite immune system. This is likely due to the lack of proper reference genes for relative gene expression studies. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that is often utilized as a reference gene, and in this preliminary study, we evaluated the similarity of bobwhite GAPDH to GAPDH in other avian species to evaluate its potential as a reference gene in bobwhite. GAPDH was identified in the bobwhite full genome sequence and multiple sets of PCR primers were designed to generate overlapping PCR products. These products were then sequenced and then aligned to generate the sequence for the full-length open reading frame (ORF) of bobwhite GAPDH. Utilizing this sequence, phylogenetic analyses and comparative analysis of the exon–intron pattern were conducted that revealed high similarity of GAPDH encoding sequences among bobwhite and other Galliformes. Additionally, This ORF sequence was also used to predict the encoded protein and its three-dimensional structure which like the phylogenetic analyses reveal that bobwhite GAPDH is similar to GAPDH in other Galliformes. Finally, GAPDH qPCR primers were designed, standardized, and tested with bobwhite both uninfected and infected with
O. petrowi
, and this preliminary test showed no statistical difference in expression of GAPDH between the two groups. These analyses are the first to investigate GAPDH in bobwhite. These efforts in phylogeny, sequence analysis, and protein structure suggest that there is > 97% conservation of GADPH among Galliformes. Furthermore, the results of these in silico tests and the preliminary qPCR indicate that GAPDH is a prospective candidate for use in gene expression analyses in bobwhite.</description><subject>Amino acid sequence</subject><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Animals</subject><subject>Biomedical and Life Sciences</subject><subject>Colinus - genetics</subject><subject>Colinus virginianus</subject><subject>Comparative analysis</subject><subject>Computer Simulation</subject><subject>Conserved sequence</subject><subject>Dehydrogenases</subject><subject>Galliformes</subject><subject>Gene expression</subject><subject>Genomes</subject><subject>Glyceraldehyde</subject><subject>Glyceraldehyde 3-phosphate</subject><subject>Glyceraldehyde-3-phosphate dehydrogenase</subject><subject>Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - classification</subject><subject>Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - genetics</subject><subject>Glycolysis</subject><subject>Histology</subject><subject>Immune system</subject><subject>Life Sciences</subject><subject>Morphology</subject><subject>Nucleotide sequence</subject><subject>Open reading frames</subject><subject>Original Article</subject><subject>Parasites</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Protein structure</subject><subject>Quail - genetics</subject><subject>Sequence analysis</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kc1u1DAUhS1ERYfCC7BAlti0Cxf_xsmympYWqQgWsLb8l4krT5zaCShvwuPiYQrsWF3f63O-K_sA8IbgS4KxfF8IwYwhTAnCDWkbxJ6BDRGSId7J9jnYYIYJ4q0gp-BlKQ8YY06keAFOGRMt5g3ZgJ-fUvR2iTrDaVhj2vnRz8FCPToYRlhCDDbVTse1hAJTD3dxtT7r6PzqPGJoGlKZBj176PywunxA6OLh-e3Vl-u7C3ggwj6nPRxTngefR2iS-TGE6nhcdIjwfJtiGJcCv4e8C2PQ9XzxCpz0Ohb_-qmegW8fbr5u79D959uP26t7ZJkUM2o6xlvmbEep9r0RpuHEUGMctV3T9F3bCup77XgdENdL21nhpHUSO0MbZtkZeHfkTjk9Lr7M6iEtub63KCqklJxTTqqKHlU2p1Ky79WUw17nVRGsDmGoYxiqhqF-h6FYNb19Qi9m791fy5_frwJ2FJR6Ne58_rf7P9hff_qX6Q</recordid><startdate>20210201</startdate><enddate>20210201</enddate><creator>Kalyanasundaram, Aravindan</creator><creator>Henry, Brett J.</creator><creator>Henry, Cassandra</creator><creator>Kendall, Ronald J.</creator><general>Springer Netherlands</general><general>Springer Nature B.V</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>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope><orcidid>https://orcid.org/0000-0003-0527-5399</orcidid></search><sort><creationdate>20210201</creationdate><title>Molecular phylogenetic and in silico analysis of glyceraldeyde-3-phosphate dehydrogenase (GAPDH) gene from northern bobwhite quail (Colinus virginianus)</title><author>Kalyanasundaram, Aravindan ; Henry, Brett J. ; Henry, Cassandra ; Kendall, Ronald J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-693483dc922aefb5b641b2bbd2c966f98852efad4d2c1df7c9c5d7cd70db263c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Amino acid sequence</topic><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Animals</topic><topic>Biomedical and Life Sciences</topic><topic>Colinus - genetics</topic><topic>Colinus virginianus</topic><topic>Comparative analysis</topic><topic>Computer Simulation</topic><topic>Conserved sequence</topic><topic>Dehydrogenases</topic><topic>Galliformes</topic><topic>Gene expression</topic><topic>Genomes</topic><topic>Glyceraldehyde</topic><topic>Glyceraldehyde 3-phosphate</topic><topic>Glyceraldehyde-3-phosphate dehydrogenase</topic><topic>Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - classification</topic><topic>Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - genetics</topic><topic>Glycolysis</topic><topic>Histology</topic><topic>Immune system</topic><topic>Life Sciences</topic><topic>Morphology</topic><topic>Nucleotide sequence</topic><topic>Open reading frames</topic><topic>Original Article</topic><topic>Parasites</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Protein structure</topic><topic>Quail - genetics</topic><topic>Sequence analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kalyanasundaram, Aravindan</creatorcontrib><creatorcontrib>Henry, Brett J.</creatorcontrib><creatorcontrib>Henry, Cassandra</creatorcontrib><creatorcontrib>Kendall, Ronald J.</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>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</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>Genetics Abstracts</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kalyanasundaram, Aravindan</au><au>Henry, Brett J.</au><au>Henry, Cassandra</au><au>Kendall, Ronald J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Molecular phylogenetic and in silico analysis of glyceraldeyde-3-phosphate dehydrogenase (GAPDH) gene from northern bobwhite quail (Colinus virginianus)</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2021-02-01</date><risdate>2021</risdate><volume>48</volume><issue>2</issue><spage>1093</spage><epage>1101</epage><pages>1093-1101</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>Many recent studies have been focused on prevalence and impact of two helminth parasites, eyeworm
Oxyspirura petrowi
and caecal worm
Aulonocephalus pennula,
in the northern bobwhite quail (
Colinus virginianus
). However, few studies have attempted to examine the effect of these parasites on the bobwhite immune system. This is likely due to the lack of proper reference genes for relative gene expression studies. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that is often utilized as a reference gene, and in this preliminary study, we evaluated the similarity of bobwhite GAPDH to GAPDH in other avian species to evaluate its potential as a reference gene in bobwhite. GAPDH was identified in the bobwhite full genome sequence and multiple sets of PCR primers were designed to generate overlapping PCR products. These products were then sequenced and then aligned to generate the sequence for the full-length open reading frame (ORF) of bobwhite GAPDH. Utilizing this sequence, phylogenetic analyses and comparative analysis of the exon–intron pattern were conducted that revealed high similarity of GAPDH encoding sequences among bobwhite and other Galliformes. Additionally, This ORF sequence was also used to predict the encoded protein and its three-dimensional structure which like the phylogenetic analyses reveal that bobwhite GAPDH is similar to GAPDH in other Galliformes. Finally, GAPDH qPCR primers were designed, standardized, and tested with bobwhite both uninfected and infected with
O. petrowi
, and this preliminary test showed no statistical difference in expression of GAPDH between the two groups. These analyses are the first to investigate GAPDH in bobwhite. These efforts in phylogeny, sequence analysis, and protein structure suggest that there is > 97% conservation of GADPH among Galliformes. Furthermore, the results of these in silico tests and the preliminary qPCR indicate that GAPDH is a prospective candidate for use in gene expression analyses in bobwhite.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>33580461</pmid><doi>10.1007/s11033-021-06186-3</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0003-0527-5399</orcidid></addata></record> |
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| subjects | Amino acid sequence Animal Anatomy Animal Biochemistry Animals Biomedical and Life Sciences Colinus - genetics Colinus virginianus Comparative analysis Computer Simulation Conserved sequence Dehydrogenases Galliformes Gene expression Genomes Glyceraldehyde Glyceraldehyde 3-phosphate Glyceraldehyde-3-phosphate dehydrogenase Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - classification Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - genetics Glycolysis Histology Immune system Life Sciences Morphology Nucleotide sequence Open reading frames Original Article Parasites Phylogenetics Phylogeny Protein structure Quail - genetics Sequence analysis |
| title | Molecular phylogenetic and in silico analysis of glyceraldeyde-3-phosphate dehydrogenase (GAPDH) gene from northern bobwhite quail (Colinus virginianus) |
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