Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. DNA Extraction and Sequencing of the Genome
2.3. Genome Size Estimation and De Novo Assembly
2.4. Genome Quality Assessment
2.5. Distribution of Repetitive Elements and Genome Annotation
2.6. Genomic Structural Variation Analysis
2.7. Domestication Signal Analysis of Meishan Pigs
3. Results
3.1. Genome Assembly and Evaluation of the Meishan Pig
3.2. Genome Annotation of the Meishan Pig
3.3. Comparison of Genomic Structural Variation
3.4. The Selective Domestication Between Chinese Wild Boar and Meishan Pig
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Assembly | MSjxau | Sscrofa11.1 |
---|---|---|
Total length of assembly (Gb) | 2.45 | 2.5 |
Min length (bp) | 1008 | 15,096 |
Max length (Mb) | 292.79 | 274.33 |
Number of scaffolds | 1144 | 613 |
Number of gaps | 466 | 544 |
Quality values (QV) | 37.06 | NA |
Scaffold N50 (Mb) | 139.17 | 138.97 |
Contig N50 (Mb) | 15.62 | 48.23 |
Assembly | Groups | Levels | Assembly | Groups | Levels |
---|---|---|---|---|---|
PHA_SAMN15809474 | Outgroup | Chromosome | LC_CNA0017742 | Asian | Contig |
PHA_SAMC146517 | Outgroup | Chromosome | TT_CRR307872 | Asian | Contig |
POT_SAMC146518 | Outgroup | Chromosome | MS_CRR307869 | Asian | Contig |
BMX_SAMN09531794 | Asian | Chromosome | RC_CRR307871 | Asian | Contig |
DNXE_SAMC146519 | Asian | Chromosome | LWU_CRR307868 | Asian | Contig |
MS_SAMN14422843 | Asian | Chromosome | AQLB_CRR307865 | Asian | Contig |
MS_jxau | Asian | Chromosome | MIN_CRR307870 | Asian | Contig |
SWT_PRJCA017882 | Asian | Chromosome | OSS_SAMN28857594 | European | Chromosome |
TC_PRJCA017882 | Asian | Chromosome | DU_SAMN15501053 | European | Chromosome |
NX_SAMN12123497 | Asian | Chromosome | DLY_SAMN07325927 | European | Chromosome |
HUAI_SAMN43144123 | Asian | Chromosome | BBH_SAMN37151398 | European | Chromosome |
CH_SAMN36411884 | Asian | Chromosome | LR_SRR24831861 | European | Contig |
KORE_SAMN41069951 | Asian | Chromosome | LW_CRR307874 | European | Contig |
NANC_SAMN34578002 | Asian | Chromosome | LW_CRR307874 | European | Contig |
WZS_CRR307873 | Asian | Contig |
Region | Gene | Top Fst | Description |
---|---|---|---|
chr1:223030001-223100000 | PTAR1 | 0.841 | Protein prenyltransferase activity |
chr3:90190001-90220000 | NRXN1 | 0.827 | Nervous development |
chr4:82660001-82730000 | TBX19 | 0.848 | Developmental processes |
chr4:82660001-82730000 | SFT2D2 | 0.856 | lipid metabolism |
chr6:103930001-103970000 | SMCHD1 | 0.814 | Epigenetic silencing |
chr9:32050001-32070000 | PGR | 0.801 | Progesterone Receptor |
chr14:20450001-20470000 | SH3RF1 | 0.841 | Protein ligase activity |
chr14:39710001-39780000 | TMEM116 | 0.906 | Transmembrane protein |
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Du, H.; Hu, J.; Zhang, Z.; Wu, Z. Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms. Animals 2025, 15, 603. https://doi.org/10.3390/ani15040603
Du H, Hu J, Zhang Z, Wu Z. Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms. Animals. 2025; 15(4):603. https://doi.org/10.3390/ani15040603
Chicago/Turabian StyleDu, Huipeng, Jianchao Hu, Zhiyan Zhang, and Zhongzi Wu. 2025. "Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms" Animals 15, no. 4: 603. https://doi.org/10.3390/ani15040603
APA StyleDu, H., Hu, J., Zhang, Z., & Wu, Z. (2025). Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms. Animals, 15(4), 603. https://doi.org/10.3390/ani15040603