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Current Biotechnology

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ISSN (Print): 2211-5501
ISSN (Online): 2211-551X

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Research Article

In silico Mining of Protein-coding and Non-coding RNA (ncRNA) Specific Genes in Exotic versus Indigenous Gaddi Dogs

Author(s): Shilpa Tewari and Chandra Shekhar Mukhopadhyay*

Volume 12, Issue 3, 2023

Published on: 24 October, 2023

Page: [190 - 202] Pages: 13

DOI: 10.2174/0122115501261640231017061158

Price: $65

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Abstract

Background: Comparative functional genomics will aid in the molecular identification of diverse dog breeds.

Methods: The current proposal aimed at conducting a differential study between the genomes of exotic canines (Labrador, Basenji, Tasha-Boxer breed, Mischka breed German Shepherd, Zoey breed Great Dane) and indigenous (Gaddi) breeds through whole genome annotation.

Results: The prediction analysis by GeneMark tool yielded an average of 46484 transcripts, in Gaddi dogs and exotic breeds ranging from 29669 to 30956. A total of 57 miRNAs were discovered in exotic breeds and 22 miRNAs in Gaddi dogs, 18 are common in both, while 4 were unique to Gaddi dogs. lncRNA was predicted using the PLEK, CPAT, and LGC tools, resulting in 3201, 396, and 4188 noncoding sequences in exotic breeds, respectively. Approximately, 31 thousand lncRNA transcripts were identified in the Gaddi dog genome. Microsatellites were found to be distributed through approximately 0.3% of both genomes. The average island length of CpG ranged between 24246.48 to 28080.66 in exotic breeds at chromosome level assembly and 697.15 in indigenous Gaddi dogs at contig level assembly. The predicted protein-coding genes were subjected to pathway analysis by DAVID and PANTHER. Five genes that are expressed in the blood (INSL3, CLDN3, MYH1, CLN5, and GALC) were selected for validation through qPCR. The results indicated that the genes were expressed in both groups.

Conclusion: The study is the maiden report on the comparative genome analysis between indigenous Gaddi dogs and exotic dog breeds. The findings set the stage for further research into the known and novel genes, which might be employed as biomarkers for disease diagnosis and to investigate their regulatory role.

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[1]
Kuntz K, Ballantyne KC, Cousins E, Spitznagel MB. Assessment of caregiver burden in owners of dogs with behavioral problems and factors related to its presence. J Vet Behav 2023; 64-65: 41-6.
[http://dx.doi.org/10.1016/j.jveb.2023.05.006]
[2]
Ensminger J. Police and military dogs: Criminal detection, forensic evidence, and judicial admissibility. CRC Press 2011.
[3]
Sankhyan V, Thakur R, Dogra PK, Thakur A. Phenotypic characterization and documentation of Gaddi dog of western Himalayan region of India. Indian J Anim Sci 2022; 92(10): 1189-93.
[http://dx.doi.org/10.56093/ijans.v92i10.123423]
[4]
Morey DF. Burying key evidence: The social bond between dogs and people. J Archaeol Sci 2006; 33(2): 158-75.
[http://dx.doi.org/10.1016/j.jas.2005.07.009]
[5]
Albuquerque N, Mills DS, Guo K, Wilkinson A, Resende B. Dogs can infer implicit information from human emotional expressions. Anim Cogn 2022; 25(2): 231-40.
[http://dx.doi.org/10.1007/s10071-021-01544-x] [PMID: 34390430]
[6]
de Freitas KEJ, Busanello C, Viana VE, et al. An empirical analysis of mtSSRs: Could microsatellite distribution patterns explain the evolution of mitogenomes in plants? Funct Integr Genomics 2022; 22(1): 35-53.
[http://dx.doi.org/10.1007/s10142-021-00815-7] [PMID: 34751851]
[7]
Stein L. Genome annotation: From sequence to biology. Nat Rev Genet 2001; 2(7): 493-503.
[http://dx.doi.org/10.1038/35080529] [PMID: 11433356]
[8]
Stefani G, Slack FJ. Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol 2008; 9(3): 219-30.
[http://dx.doi.org/10.1038/nrm2347] [PMID: 18270516]
[9]
Diener C, Keller A, Meese E. Emerging concepts of miRNA therapeutics: From cells to clinic. Trends Genet 2022; 38(6): 613-26.
[http://dx.doi.org/10.1016/j.tig.2022.02.006] [PMID: 35303998]
[10]
Zhan S, Dong Y, Zhao W, et al. Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. BMC Genomics 2016; 17(1): 666.
[http://dx.doi.org/10.1186/s12864-016-3009-3] [PMID: 27550073]
[11]
Shah IM, Dar MA, Bhat KA, Dar TA, Ahmad F, Ahmad SM. Long Non-Coding RNAs: Biogenesis, Mechanism of Action and Role in Different Biological and Pathological Processes. In: Recent Advances in Noncoding RNAs. IntechOpen 2022.
[12]
Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2022; 33(2): 248-70.
[PMID: 34773482]
[13]
Beier S, Thiel T, Münch T, Scholz U, Mascher M. MISA-web: A web server for microsatellite prediction. Bioinformatics 2017; 33(16): 2583-5.
[http://dx.doi.org/10.1093/bioinformatics/btx198] [PMID: 28398459]
[14]
Zhao Z, Han L. CpG islands: Algorithms and applications in methylation studies. Biochem Biophys Res Commun 2009; 382(4): 643-5.
[http://dx.doi.org/10.1016/j.bbrc.2009.03.076] [PMID: 19302978]
[15]
Xia J, Han L, Zhao Z. Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. BMC Genomics 2012; 13(S8): S7.
[http://dx.doi.org/10.1186/1471-2164-13-S8-S7] [PMID: 23281708]
[16]
Brůna T, Lomsadze A, Borodovsky M. GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genom Bioinform 2020; 2(2): lqaa026.
[http://dx.doi.org/10.1093/nargab/lqaa026] [PMID: 32440658]
[17]
Manku HK, Dhanoa JK, Kaur S, Arora JS, Mukhopadhyay CS. Biocomputational identification and validation of novel microRNAs predicted from bubaline whole genome shotgun sequences. Comput Biol Chem 2017; 70: 96-106.
[http://dx.doi.org/10.1016/j.compbiolchem.2017.08.005] [PMID: 28844020]
[18]
Sambrook J, Russell DW. The condensed protocols from molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press 2006.
[19]
Hannan MA, Kawate N, Kubo Y, et al. Expression analyses of insulin-like peptide 3, RXFP2, LH receptor, and 3β-hydroxysteroid dehydrogenase in testes of normal and cryptorchid dogs. Theriogenology 2015; 84(7): 1176-84.
[http://dx.doi.org/10.1016/j.theriogenology.2015.06.021] [PMID: 26220663]
[20]
Matschurat C, Rode K, Hollenbach J, et al. Impaired spermatogenesis, tubular wall disruption, altered blood-testis barrier composition and intratubular lymphocytes in an infertile Beagle dog - a putative case of autoimmune orchitis. Histol Histopathol 2019; 34(5): 525-35.
[21]
de Rojas-P I, Albiñana V, Recio-Poveda L, Rodriguez-Rufián A, Cuesta ÁM, Botella LM. CLN5 in heterozygosis may protect against the development of tumors in a VHL patient. Orphanet J Rare Dis 2020; 15(1): 132.
[http://dx.doi.org/10.1186/s13023-020-01410-y] [PMID: 32487141]
[22]
Finno CJ, Gianino G, Perumbakkam S, et al. A missense mutation in MYH1 is associated with susceptibility to immune-mediated myositis in Quarter Horses. Skelet Muscle 2018; 8(1): 7.
[http://dx.doi.org/10.1186/s13395-018-0155-0] [PMID: 29510741]
[23]
Peng J, Chen B, Shen Z, et al. DNA promoter hypermethylation contributes to down-regulation of galactocerebrosidase gene in lung and head and neck cancers. Int J Clin Exp Pathol 2015; 8(9): 11042-50.
[PMID: 26617822]
[24]
Bidone J, Schuh RS, Farinon M, et al. Intra-articular nonviral gene therapy in mucopolysaccharidosis I mice. Int J Pharm 2018; 548(1): 151-8.
[http://dx.doi.org/10.1016/j.ijpharm.2018.06.049] [PMID: 29940298]
[25]
Bonefeld BE, Elfving B, Wegener G. Reference genes for normalization: A study of rat brain tissue. Synapse 2008; 62(4): 302-9.
[http://dx.doi.org/10.1002/syn.20496] [PMID: 18241047]
[26]
Rana K. Molecular characterization of indigenous dogs through whole genome analysis. PhD dissertation Guru Angad Dev Veterinary and Animal Sciences University 2022.
[27]
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 2001; 25(4): 402-208.
[28]
Svec D, Tichopad A, Novosadova V, Pfaffl MW, Kubista M. How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments. Biomol Detect Quantif 2015; 3: 9-16.
[http://dx.doi.org/10.1016/j.bdq.2015.01.005] [PMID: 27077029]
[29]
Sahabi K, Selvarajah GT, Abdullah R, Cheah YK, Tan GC. Comparative aspects of microRNA expression in canine and human cancers. J Vet Sci 2018; 19(2): 162-71.
[http://dx.doi.org/10.4142/jvs.2018.19.2.162] [PMID: 28927253]
[30]
Gourbault O, Llobat L. MicroRNAs as biomarkers in canine osteosarcoma: A new future? Vet Sci 2020; 7(4): 146.
[http://dx.doi.org/10.3390/vetsci7040146] [PMID: 33008041]
[31]
Lu B, Wu J, Chen H, Li S, Jia K. LncRNA expression profiles in canine mammary tumors identify lnc34977 as a promoter of proliferation, migration and invasion of canine mammary tumor cells. Vet Sci 2022; 9(2): 82.
[http://dx.doi.org/10.3390/vetsci9020082] [PMID: 35202335]
[32]
Irion DN, Schaffer AL, Famula TR, Eggleston ML, Hughes SS, Pedersen NC. Analysis of genetic variation in 28 dog breed populations with 100 microsatellite markers. J Hered 2003; 94(1): 81-7.
[http://dx.doi.org/10.1093/jhered/esg004] [PMID: 12692167]
[33]
Yamazaki J, Matsumoto Y, Jelinek J, et al. DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing. Sci Rep 2021; 11(1): 10005.
[http://dx.doi.org/10.1038/s41598-021-89279-0] [PMID: 33976289]

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