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Molecular phylogenetic and in silico analysis of glyceraldeyde-3-phosphate dehydrogenase (GAPDH) gene from northern bobwhite quail (Colinus virginianus)

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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.

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Data availability

All data generated or analyzed during this study are included in this manuscript. Sequencing data obtained from this study has been submitted in DNA Data Bank of Japan (DDBJ) (Acc No. LC569866).

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Funding

This research received funding and support form Park Cities Quail Coalition (Grant No. 24A125) and the Rolling Plains Quail Research Foundation (Grant No. 23A751).

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Authors and Affiliations

  1. The Wildlife Toxicology Laboratory, Texas Tech University, Lubbock, TX, 79409-3290, USA

    Aravindan Kalyanasundaram, Brett J. Henry, Cassandra Henry & Ronald J. Kendall

Authors
  1. Aravindan Kalyanasundaram
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  2. Brett J. Henry
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  3. Cassandra Henry
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  4. Ronald J. Kendall
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Correspondence to Ronald J. Kendall.

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The authors declare that they have no conflict of interest.

Ethical approval

This experiment was approved by Texas Tech University Animal Care and Use Committee under protocol 18044-05 and 16071-08. All bobwhites were trapped and handled according to Texas Parks and Wildlife permit SRP-0715-095.

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Kalyanasundaram, A., Henry, B.J., Henry, C. et al. Molecular phylogenetic and in silico analysis of glyceraldeyde-3-phosphate dehydrogenase (GAPDH) gene from northern bobwhite quail (Colinus virginianus). Mol Biol Rep 48, 1093–1101 (2021). https://doi.org/10.1007/s11033-021-06186-3

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