First Whole Genome Sequencing Data of Six Greek Sheep Breeds
Abstract
1. Summary
2. Data Description
2.1. Sequencing Data
2.2. Variants’ Quality
2.3. Variants’ Annotation
3. Methods
3.1. Sample Collection and DNA Extraction
3.2. Library Construction and Sequencing
3.3. Data Preprocessing and Variant Discovery
3.4. Variant Filtering
3.5. Data Availability
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- EUROSTAT. Available online: https://ec.europa.eu/eurostat/ (accessed on 31 March 2025).
- Ligda, C.; Altarayrah, J.; Georgoudis, A. Genetic Analysis of Greek Sheep Breeds Using Microsatellite Markers for Setting Conservation Priorities. Small Rumin. Res. 2009, 83, 42–48. [Google Scholar] [CrossRef]
- Sossidou, E.; Ligda, C.; Mastranestasis, I.; Tsiokos, D.; Samartzi, F. Sheep and Goat Farming in Greece: Implications and Challenges for the Sustainable Development of Less Favoured Areas. Sci. Pap. Anim. Sci. Biotechnol. 2013, 46, 446–449. [Google Scholar]
- Loukovitis, D.; Siasiou, A.; Mitsopoulos, I.; Lymberopoulos, A.G.; Laga, V.; Chatziplis, D. Genetic Diversity of Greek Sheep Breeds and Transhumant Populations Utilizing Microsatellite Markers. Small Rumin. Res. 2016, 136, 238–242. [Google Scholar] [CrossRef]
- Billinis, C.; Psychas, V.; Leontides, L.; Spyrou, V.; Argyroudis, S.; Vlemmas, I.; Leontides, S.; Sklaviadis, T.; Papadopoulos, O. Prion Protein Gene Polymorphisms in Healthy and Scrapie-Affected Sheep in Greece. J. Gen. Virol. 2004, 85, 547–554. [Google Scholar] [CrossRef]
- Triantaphyllopoulos, K.A.; Koutsouli, P.; Kandris, A.; Papachristou, D.; Markopoulou, K.E.; Mataragka, A.; Massouras, T.; Bizelis, I. Effect of β-Lactoglobulin Gene Polymorphism, Lactation Stage and Breed on Milk Traits in Chios and Karagouniko Sheep Breeds. Ann. Anim. Sci. 2017, 17, 371–384. [Google Scholar] [CrossRef]
- Michailidou, S.; Tsangaris, G.; Fthenakis, G.C.; Tzora, A.; Skoufos, I.; Karkabounas, S.C.; Banos, G.; Argiriou, A.; Arsenos, G. Genomic Diversity and Population Structure of Three Autochthonous Greek Sheep Breeds Assessed with Genome-Wide DNA Arrays. Mol. Genet. Genom. 2018, 293, 753–768. [Google Scholar] [CrossRef]
- Georgatou, S.; Papachristou, D.; Medugorac, I.; Laliotis, G.; Kassinis, N.; Bizelis, I.; Koutsouli, P. Phenotypic traits, diversity levels and genetic relationships of Cretan sheep breeds. Agrofor Int. J. 2024, 9, 68–76. [Google Scholar] [CrossRef]
- Uffelmann, E.; Huang, Q.Q.; Munung, N.S.; de Vries, J.; Okada, Y.; Martin, A.R.; Martin, H.C.; Lappalainen, T.; Posthuma, D. Genome-Wide Association Studies. Nat. Rev. Methods Primers 2021, 1, 59. [Google Scholar] [CrossRef]
- Jiang, Y.; Xie, M.; Chen, W.; Talbot, R.; Maddox, J.F.; Faraut, T.; Wu, C.; Muzny, D.M.; Li, Y.; Zhang, W.; et al. The Sheep Genome Illuminates Biology of the Rumen and Lipid Metabolism. Science 2014, 344, 1168–1173. [Google Scholar] [CrossRef]
- Guo, Y.; Ye, F.; Sheng, Q.; Clark, T.; Samuels, D.C. Three-Stage Quality Control Strategies for DNA Re-Sequencing Data. Brief. Bioinform. 2013, 15, 879–889. [Google Scholar] [CrossRef]
- Lv, F.H.; Cao, Y.H.; Liu, G.J.; Luo, L.Y.; Lu, R.; Liu, M.J.; Li, W.R.; Zhou, P.; Wang, X.H.; Shen, M.; et al. Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci. Mol. Biol. Evol. 2022, 39, msab353. [Google Scholar] [CrossRef] [PubMed]
- Sun, X.; Guo, J.; Li, R.; Zhang, H.; Zhang, Y.; Liu, G.E.; Emu, Q.; Zhang, H. Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep. Animals 2024, 14, 444. [Google Scholar] [CrossRef] [PubMed]
- Li, X.; Yang, J.; Shen, M.; Xie, X.L.; Liu, G.J.; Xu, Y.X.; Lv, F.H.; Yang, H.; Yang, Y.L.; Liu, C.B.; et al. Whole-Genome Resequencing of Wild and Domestic Sheep Identifies Genes Associated with Morphological and Agronomic Traits. Nat. Commun. 2020, 11, 2815. [Google Scholar] [CrossRef] [PubMed]
- Poplin, R.; Ruano-Rubio, V.; DePristo, M.A.; Fennell, T.J.; Carneiro, M.O.; Van der Auwera, G.A.; Kling, D.E.; Gauthier, L.D.; Levy-Moonshine, A.; Roazen, D.; et al. Scaling Accurate Genetic Variant Discovery to Tens of Thousands of Samples. bioRxiv 2018, preprint. [Google Scholar] [CrossRef]
- Baer, C.F.; Miyamoto, M.M.; Denver, D.R. Mutation Rate Variation in Multicellular Eukaryotes: Causes and Consequences. Nat. Rev. Genet. 2007, 8, 619–631. [Google Scholar] [CrossRef]
- Nishant, K.T.; Singh, N.D.; Alani, E. Genomic Mutation Rates: What High-Throughput Methods Can Tell Us. BioEssays 2009, 31, 912–920. [Google Scholar] [CrossRef]
- Tian, D.; Han, B.; Li, X.; Liu, D.; Zhou, B.; Zhao, C.; Zhang, N.; Wang, L.; Pei, Q.; Zhao, K. Genetic Diversity and Selection of Tibetan Sheep Breeds Revealed by Whole-Genome Resequencing. Anim. Biosci. 2023, 36, 991–1002. [Google Scholar] [CrossRef]
- Amane, A.; Belay, G.; Tijjani, A.; Dessie, T.; Musa, H.H.; Hanotte, O. Genome-Wide Genetic Diversity and Population Structure of Local Sudanese Sheep Populations Revealed by Whole-Genome Sequencing. Diversity 2022, 14, 895. [Google Scholar] [CrossRef]
- Yi, W.; Hu, M.; Shi, L.; Li, T.; Bai, C.; Sun, F.; Ma, H.; Zhao, Z.; Yan, S. Whole Genome Sequencing Identified Genomic Diversity and Candidated Genes Associated with Economic Traits in Northeasern Merino in China. Front. Genet. 2024, 15, 1302222. [Google Scholar] [CrossRef]
- Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed on 6 February 2025).
- Ewels, P.; Magnusson, M.; Lundin, S.; Käller, M. MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report. Bioinformatics 2016, 32, 3047–3048. [Google Scholar] [CrossRef]
- Krueger, F.; James, F.; Ewels, P.; Afyounian, E.; Schuster-Boeckler, B. TrimGalore. Available online: https://github.com/FelixKrueger/TrimGalore (accessed on 7 February 2025).
- NVIDIA ClaraTM Parabricks 2025. Available online: https://www.nvidia.com/en-us/clara/genomics/ (accessed on 11 February 2025).
- Broad Institute, Picard Toolkit. 2019. Available online: https://github.com/broadinstitute/picard (accessed on 17 February 2025).
- Dyer, S.C.; Austine-Orimoloye, O.; Azov, A.G.; Barba, M.; Barnes, I.; Barrera-Enriquez, V.P.; Becker, A.; Bennett, R.; Beracochea, M.; Berry, A.; et al. Ensembl 2025. Nucleic Acids Res. 2025, 53, 948–957. [Google Scholar] [CrossRef] [PubMed]
- European Variation Archive EVA Database. Available online: https://www.ebi.ac.uk/eva/ (accessed on 20 March 2025).
- Van der Auwera, G.A.; O’Connor, B.D. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra, 1st ed.; O’Reilly Media, Inc.: Sebastopol, CA, USA, 2020. [Google Scholar]
- Danecek, P.; Auton, A.; Abecasis, G.; Albers, C.A.; Banks, E.; DePristo, M.A.; Handsaker, R.E.; Lunter, G.; Marth, G.T.; Sherry, S.T.; et al. The Variant Call Format and VCFtools. Bioinformatics 2011, 27, 2156–2158. [Google Scholar] [CrossRef] [PubMed]
- Cingolani, P.; Platts, A.; Wang, L.L.; Coon, M.; Nguyen, T.; Wang, L.; Land, S.J.; Lu, X.; Ruden, D.M. A Program for Annotating and Predicting the Effects of Single Nucleotide Polymorphisms, SnpEff: SNPs in the Genome of Drosophila Melanogaster Strain W1118. Fly 2012, 6, 80–92. [Google Scholar] [CrossRef] [PubMed]
- R Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2021. [Google Scholar]
- Wickham, H. ggplot2: Elegant Graphics for Data Analysis; Springer: New York, NY, USA, 2016; ISBN 978-3-319-24277-4. Available online: https://ggplot2.tidyverse.org (accessed on 7 March 2025).
Sample | Sequencing Depth (X) | No. of Raw Reads | Raw Reads with Q-Score > 30 (%) | No. of Filtered Reads | Filtered Reads with Q-Score > 30 (%) | Alignment Rate (%) |
---|---|---|---|---|---|---|
Chios | 41.4 | 372,243,261 | 93.49 | 361,941,831 | 94.80 | 99.86 |
Kalarritiko | 35.3 | 317,860,409 | 93.18 | 308,121,356 | 94.57 | 99.80 |
Karagouniko | 33.3 | 299,574,996 | 93.26 | 290,336,550 | 94.72 | 99.86 |
Lesvos | 35.4 | 318,636,312 | 93.44 | 309,470,068 | 94.78 | 99.87 |
Serres | 37.2 | 334,823,282 | 93.92 | 326,127,757 | 95.17 | 99.85 |
Thraki | 38.6 | 347,585,658 | 93.37 | 337,203,717 | 94.75 | 99.85 |
Sample | Ti/Tv Ratio | Het/Hom Ratio |
---|---|---|
Chios | 2.450 | 1.40 |
Kalarritiko | 2.448 | 1.65 |
Karagouniko | 2.450 | 1.15 |
Lesvos | 2.448 | 1.74 |
Serres | 2.448 | 1.48 |
Thraki | 2.452 | 1.51 |
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Tsoureki, A.; Tsiolas, G.; Kyritsi, M.; Pavlou, E.; Argiriou, A.; Michailidou, S. First Whole Genome Sequencing Data of Six Greek Sheep Breeds. Data 2025, 10, 75. https://doi.org/10.3390/data10050075
Tsoureki A, Tsiolas G, Kyritsi M, Pavlou E, Argiriou A, Michailidou S. First Whole Genome Sequencing Data of Six Greek Sheep Breeds. Data. 2025; 10(5):75. https://doi.org/10.3390/data10050075
Chicago/Turabian StyleTsoureki, Antiopi, George Tsiolas, Maria Kyritsi, Eleftherios Pavlou, Anagnostis Argiriou, and Sofia Michailidou. 2025. "First Whole Genome Sequencing Data of Six Greek Sheep Breeds" Data 10, no. 5: 75. https://doi.org/10.3390/data10050075
APA StyleTsoureki, A., Tsiolas, G., Kyritsi, M., Pavlou, E., Argiriou, A., & Michailidou, S. (2025). First Whole Genome Sequencing Data of Six Greek Sheep Breeds. Data, 10(5), 75. https://doi.org/10.3390/data10050075