Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle (<i>Bos indicus</i>) breeds

<p>Indigenous cattle of India belong to the species, <i>Bos indicus</i> and they possess various adaptability and production traits. However, little is known about the genetic diversity and origin of these breeds. To investigate the status, we sequenced and analyzed the whole mitochondrial DNA (mtDNA) of seven Indian cattle breeds. In total, 49 single-nucleotide variants (SNVs) were identified among the seven breeds analyzed. We observed a common synonymous SNV in the COII gene (m.7583G > A) of all the breeds studied. The phylogenetic analysis and genetic distance estimation showed the close genetic relationship among the Indian cattle breeds, whereas distinct genetic differences were observed between <i>Bos indicus</i> and <i>Bos taurus</i> cattle. Our results indicate a common ancestor for European Zwergzebu breed and South Indian cattle. The estimated divergence time demonstrated that the <i>Bos indicus</i> and <i>Bos taurus</i> cattle lineages diverged 0.92 million years ago. Our study also demonstrates that ancestors of present zebu breeds originated in South and North India separately ∼30,000 to 20,000 years ago. In conclusion, the identified genetic variants and results of the phylogenetic analysis may provide baseline information to develop appropriate strategies for management and conservation of Indian cattle breeds.</p

Additional file 1: Table S1a. of Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India

Sample information and clinical characteristics. Table S1b. Summary of clinical characteristics of MODY patient samples. Table S2a. Sequencing statistics of combined exome and WGS. Table S2b. Sequencing statistics of targeted exome samples. Table S3. Targeted gene panel. Table S4. Candidate variants identified in MODY samples. Table S5. Differentially expressed genes - NKX6–1 (XLS 292 kb

Additional file 2: Figure S1. of Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India

Box plot showing (a) fasting plasma glucose, (b) fasting insulin, (c) C-peptide fasting, (d) C-peptide stimulated and (e) creatinine in MODY and control samples. The median value is shown as a line with the whiskers extending from the highest value within 1.5 * IQR of the third quartile to the lowest value within 1.5 * IQR of the first quartile where IQR is the inter-quartile range. Figure S2. Heatmap depicting the genotype based identity of the discovery and validation MODY cohort and control samples. Genomic regions for which we obtained data for the validation cohort samples and corresponding regions from the discovery set samples using GATK joint-variant caller. The sample identity was computed based on the high-confidence set of single nucleotide variants (SNVs) that passed GATK Hard-Filtering criteria. Figure S3. Expression level of mouse Nkx6–1 (top) or human NKX6–1 (bottom) following induction in cells stably expressing the indicated variant or wildtype. Figure S4. Western blot showing the expression of NKX6–1 48 h post dox induction. Hsp90 was used as a loading control. (ZIP 5136 kb