Genome assembly of indigenous Gaddi dog

C S  MUKHOPADHYAY; KANWALJIT  RANA

doi:10.56093/ijans.v95i2.140822

Authors

C S MUKHOPADHYAY Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab-141002
KANWALJIT RANA Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab-141002

https://doi.org/10.56093/ijans.v95i2.140822

Keywords:

DNA, Gaddi dog, Genome assembly, Indigenous, Sequencing

Abstract

Dog is one of the oldest domesticated animals and the most familiar pet to mankind. The Gaddi dogs are robust and healthy and have been associated with herding and guarding for ancient times in the Himalayan vis-à-vis neighboring states like Himachal Pradesh, Uttarakhand, and Punjab. No information is available about the genetic architecture of these indigenous dogs. The present study was designed to sequence and assemble nuclear genome of Indigenous Gaddi dog for its genetic characterization. The blood samples were collected from five unrelated Gaddi dogs from the state of Punjab and Himachal Pradesh. The Illumina 150bp paired-end sequencing was done and 491.9 G raw data was generated with an error rate of 0.03% for all five samples. The quality of data was checked by using FastQC and Fastp tools. The Q30 of the processed data ranged from 90.5% to 93.3% and %GC from 40.1% to 41.5%. The genome assembly was done using Maryland Super Reads Celera Assembler (MaSuRCA). The number of contigs obtained for individual genome assemblies varied from 437250 to 455342, the N50 value ranged from 10028 to 10839 and the average contig length ranged from 5118 to 5344 bases. The raw sequence reads have been submitted to NCBI Bioproject id PRJNA843534 (SRA Accession: SRR22387066 to SRR22387070). The genetic tapestry of the Gaddi dogs has been revealed through this sequencing shot. Further, the enrichment of the genome assembly and annotation can have a deeper insight into the Gaddi dog’s hidden potential and diverse adaptation behaviour.

Downloads

Download data is not yet available.

References

Armstrong E E, Taylor R W, Prost S, Blinston P, Meer Van Der E, Madzikanda H, Mufute O, Mandisodza- Chikerema R, Stuelpnagel J, Sillero-Zubiri C and Petrov D. 2019. Cost-effective assembly of the African wild dog (Lycaonpictus) genome using linked reads. GigaScience 8(2), giy124. https://doi.org/10.1093/gigascience/giy124

Chen Z, Erickson D L and Meng J. 2020. Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing. BMC genomics 21(1): 631. https://doi.org/10.1186/s12864-020-07041-8

English A C, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny D M, Reid J G, Worley K C and Gibbs R A. 2012. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PloS one 7(11): e47768.

Field M A, Rosen B D, Dudchenko O, Chan E K, Minoche A E, Edwards R J, Barton K, Lyons R J, Tuipulotu D E, Hayes V M, Omer A D, Colaric Z, Keilwagen J, Skvortsova K, Bogdanovic O, Smith M A, Aiden E L, Smith T P L, Zammit R A and Ballard J W O. 2020. Canfam_GSD: De novo chromosome- length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience: 9(4). https://doi. org/10.1093/gigascience/giaa027

Gurevich A, Saveliev V, Vyahhi N and Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8): 1072–5. https://doi.org/10.1093/bioinformatics/btt086

Jung H, Ventura T, Chung J S, Kim W J, Nam B H, Kong H J, Kim Y O, Jeon M S and Eyun S I. 2020. Twelve quick steps for genome assembly and annotation in the classroom. PLoS computational biology 16(11): e1008325. https://doi. org/10.1371/journal.pcbi.1008325.

Kalambhe D, Bhanot R, Malik H, Mukhopadhyay C S and Gill J P S. 2022. The indigenous dogs of india: the forgotten treasure. Project Monitoring Unit- DBT-GADVASU- CRC, Directorate of Research, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana. ISBN: 978-93- 5659-734-1

Kaur B, Kaur J, Kashyap N, Arora J S and Mukhopadhyay C S. 2023a. A comprehensive review of genomic perspectives of canine diseases as a model to study human disorders. Canadian Journal of Veterinary Research 87(1): 3-8.

Kaur B, Rana K and Mukhopadhyay C S. 2022. Ancestry, temperament, facts, and grooming of Indigenous ‘Gaddi’dog breed. Veterinary alumnus 44(2): 86-8.

Kaur B, Yathish H M, Kashyap N and Mukhopadhyay C S. 2023b. Phylogeographic and genetic-diversity analysis through genome-wide snps in indigenous and exotic canine breeds. http://dx.doi.org/10.2139/ssrn.4615672

Leeb T, Roosje P and Welle M. 2022. Genetics of inherited skin disorders in dogs. Veterinary Journal 279: 105782. doi: 10.1016/j.tvjl.2021.105782

Linacre A. 2021. Animal Forensic Genetics. Genes (Basel) 12(4): 515. doi: 10.3390/genes12040515

Lyu G, Feng C, Zhu S, Ren S, Dang W, Irwin D M, Wang Z and Zhang S. 2021. Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog. Breeds. Frontiers in Genetics 12: 671686. doi: 10.3389/fgene.2021.671686.

Marcais G, Yorke J A and Zimin A. 2015. QuorUM: An Error Corrector for Illumina Reads. PLoS ONE 10(6): e0130821. https://doi.org/10.1371/journal.pone.0130821

Marcais G and Kingsford C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6): 764–70. https://doi.org/10.1093/ bioinformatics/btr011

Meadows J R S, Kidd J M, Wang G D, Parker H G, Schall P Z, Bianchi M, Christmas M J, Bougiouri K, Buckley R M, Hitte C, Nguyen A K, Wang C, Jagannathan V, Niskanen J E, Frantz L A F, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina K K, and Ostrander, E A 2023. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome biology, 24(1), 187. https://doi. org/10.1186/s13059-023-03023-7.

Mukhopadhyay C S. 2022. Genomic Characterization of Gaddi breed of Dog to Envisage Molecular Signatures. (Editorial). Acta Scientific Veterinary Sciences 4(10): 1-2. DOI: 10.31080/ ASVS.2022.04.0507

Rana K, Randhawa S S, Mahindroo J, Sethi R S and Mukhopadhyay C S. 2025. Biocomputational identification of microRNAs from indigenous Gaddi dog genome. Gene Reports 39: 102167. https://doi.org/10.1016/j.genrep.2025.102167

Sambrook J and Russell D W. 2001. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, New York 3(1): 2344.

Sankhyan V, Thakur R, Dogra P K and Thakur A. 2022. Phenotypic characterization and documentation of Gaddi dog of western Himalayan region of India. The Indian Journal of Animal Sciences 92(10): 1189-93.

Schatz M C, Delcher A L and Salzberg S L. 2010. Assembly of large genomes using second-generation sequencing. Genome research 20(9): 1165–73. https://doi.org/10.1101/ gr.101360.109

Sandhu Y, Kaur B, Kaur M, Yathish H M and Mukhopadhyay C S. 2025. Microsatellite DNA Analysis of Genetic Diversity and Parentage Testing in Popular Dog Breeds in India. Indian Journal of Animal Research B-5477: 1-8. doi 10.18805/IJAR.B-5477

Srikanth K, von Pfeil D J F, Stanley B J, Griffitts C and Huson H J. 2022. Genome-Wide Association Study with Imputed Whole Genome Sequence Data Identifies a 431 kb Risk Haplotype on CFA18 for Congenital Laryngeal Paralysis in Alaskan Sled Dogs. Genes (Basel) 13(10): 1808. doi: 10.3390/genes13101808

Tewari S and Mukhopadhyay C S. 2023. In silico Mining of Protein-coding and Non-coding RNA (ncRNA) Specific Genes in Exotic versus Indigenous Gaddi Dogs. Current Biotechnology 12(3): 190-202.

Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Pielberg G R, Sigurdsson S, Fall T, H. Seppälä E H, Hansen M S T, Lawley C T, Karlsson E K, The LUPA Consortium, Bannasch D, Vilà C, Lohi H, Galibert F, Fredholm M, Häggström J, Hedhammar A, André C, Lindblad-Toh K, Hitte C and Webster M T. 2011. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS genetics 7(10): e1002316.

Wang W, Yan H J, Chen S Y, Li Z Z, Yi J, Niu L L, Deng J P, Chen W G, Pu Y, Jia X, Qu Y, Chen A, Zhong Y, Yu X M, Pang S, Huang W L, Han Y, Liu G J and Yu J Q. 2019. The sequence and de novo assembly of hog deer genome. Scientific data, 6, 180305. https://doi.org/10.1038/ sdata.2018.305

ZiminAV, Marçais G, Puiu D, Roberts M, Salzberg SLandYorke JA. 2013. The MaSuRCA genome assembler. Bioinformatics 29(21): 2669–77. https://doi.org/10.1093/bioinformatics/ btt476