Whole genome sequence and analysis of the Marwari horse breed and its genetic origin

Jun, JeHoon; Cho, Yun Sung; Hu, Hae‐Jin; Kim, Hak-Min; Jho, Sungwoong; Gadhvi, Priyvrat; Park, Kyung Mi; Lim, Jeongheui; Paek, Woon Kee; Han, Kyudong; Manica, Andrea; Edwards, Jeremy S.; Bhak, Jong

doi:10.1186/1471-2164-15-s9-s4

Cited by 28 publications

(15 citation statements)

References 64 publications

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“…Similar to most previous studies [ 34 , 35 ], we consistently observed a higher SNV frequency in intergenic rather than genic regions for all species. As shown in Figure 2 , 34.23~36.31% of total SNVs were genic variants, including 0.60~0.69% that were in exons.…”

Section: Resultssupporting

confidence: 91%

Comparative Genome-Wide Survey of Single Nucleotide Variation Uncovers the Genetic Diversity and Potential Biomedical Applications among Six Macaca Species

Fan

Sun

et al. 2018

IJMS

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Macaca is of great importance in evolutionary and biomedical research. Aiming at elucidating genetic diversity patterns and potential biomedical applications of macaques, we characterized single nucleotide variations (SNVs) of six Macaca species based on the reference genome of Macaca mulatta. Using eight whole-genome sequences, representing the most comprehensive genomic SNV study in Macaca to date, we focused on discovery and comparison of nonsynonymous SNVs (nsSNVs) with bioinformatic tools. We observed that SNV distribution patterns were generally congruent among the eight individuals. Outlier tests of nsSNV distribution patterns detected 319 bins with significantly distinct genetic divergence among macaques, including differences in genes associated with taste transduction, homologous recombination, and fat and protein digestion. Genes with specific nsSNVs in various macaques were differentially enriched for metabolism pathways, such as glycolysis, protein digestion and absorption. On average, 24.95% and 11.67% specific nsSNVs were putatively deleterious according to PolyPhen2 and SIFT4G, respectively, among which the shared deleterious SNVs were located in 564–1981 genes. These genes displayed enrichment signals in the ‘obesity-related traits’ disease category for all surveyed macaques, confirming that they were suitable models for obesity related studies. Additional enriched disease categories were observed in some macaques, exhibiting promising potential for biomedical application. Positively selected genes identified by PAML in most tested Macaca species played roles in immune and nervous system, growth and development, and fat metabolism. We propose that metabolism and body size play important roles in the evolutionary adaptation of macaques.

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Section: Resultssupporting

confidence: 91%

Comparative Genome-Wide Survey of Single Nucleotide Variation Uncovers the Genetic Diversity and Potential Biomedical Applications among Six Macaca Species

Fan

Sun

et al. 2018

IJMS

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“…In our study, the average number of CNVs per individual was 96, ranging from 88 to 108, significantly fewer than the number identified by Jun et al . (; 353/1; NGS) and Doan et al . (2012b; 282/1; NGS) and slightly fewer than identified by Doan et al .…”

Section: Resultsmentioning

confidence: 99%

Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array

et al. 2016

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Copy number variation (CNV), an essential form of genetic variation, has been increasingly recognized as one promising genetic marker in the analysis of animal genomes. Here, we used the Equine 70K single nucleotide polymorphism genotyping array for the genome-wide detection of CNVs in 96 horses from three diverse Chinese breeds: Debao pony (DB), Mongolian horse (MG) and Yili horse (YL). A total of 287 CNVs were determined and merged into 122 CNV regions (CNVRs) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVRs were integrated with seven existing reports to generate a composite genome-wide dataset of 1558 equine CNVRs, revealing 69 (56.6%) novel CNVRs. The majority (69.7%) of the 122 CNVRs overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVRs, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed-specific ss were identified in DB, MG and YL respectively. Among these genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1 and GALR may have potential relevance to breed-specific traits. These findings provide valuable information for understanding the equine genome and facilitating association studies of economically important traits with equine CNVRs in the future.

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“…The clean reads were aligned to the reference genome of E. caballus, which is the most accurate and commonly used reference genome for horses [23,24], using TopHat v2.0.12 ( Table 2). In total, 84.85% (BSM1), 85.05% (BSM2), 84.25% (BSM3), 84.38% (ASM1), 84.14% (ASM2), and 84.23% (ASM3) clean reads were uniquely mapped to the reference genome.…”

Section: Mrna Expression Profiles In Mongolian Horse Testis Developmentmentioning

confidence: 99%

Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

Zhao

et al. 2020

Preprint

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Background: Horse testis development and spermatogenesis are complex physiological processes. Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to “spermatogenesis,” male gamete generation,” “spermatid development” and “oocyte meiosis” were significantly involved in different stages of testis development and spermatogenesis. Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

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Whole genome sequence and analysis of the Marwari horse breed and its genetic origin

Cited by 28 publications

References 64 publications

Comparative Genome-Wide Survey of Single Nucleotide Variation Uncovers the Genetic Diversity and Potential Biomedical Applications among Six Macaca Species

Comparative Genome-Wide Survey of Single Nucleotide Variation Uncovers the Genetic Diversity and Potential Biomedical Applications among Six Macaca Species

Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array

Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

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