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Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies.

ABSTRACT: The application of high-throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran, and Khuzestan provinces, were resequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2× per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain, and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20, and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using resequencing data from other five bovine species as well as the Axiom Buffalo Genotyping Array 90K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.

SUBMITTER: Rafiepour M

PROVIDER: S-EPMC7850101 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Abstract Knowledge of population divergence history is key to understanding organism diversification mechanisms. The geotrupid dung beetle Phelotrupes auratus, which inhabits montane forests and exhibits three color forms (red, green, and indigo), diverged into five local populations (west/red, south/green, south/indigo, south/red, and east/red) in the Kinki District of Honshu, Japan, based on the combined interpretation of genetic cluster and color‐form data. Here, we estimated the demographic histories of these local populations using the newly assembled draft genome sequence of P. auratus and whole‐genome resequencing data obtained from each local population. Using coalescent simulation analysis, we estimated P. auratus population divergences at ca. 3800, 2100, 600, and 200 years ago, with no substantial gene flow between diverged populations, implying the existence of persistent barriers to gene flow. Notably, the last two divergence events led to three local populations with different color forms. The initial divergence may have been affected by climatic cooling around that time, and the last three divergence events may have been associated with the increasing impact of human activities. Both climatic cooling and increasing human activity may have caused habitat fragmentation and a reduction in the numbers of large mammals supplying food (dung) for P. auratus, thereby promoting the decline, segregation, and divergence of local populations. Our research demonstrates that geographic population divergence in an insect with conspicuous differences in traits such as body color may have occurred rapidly under the influence of human activity. Phelotrupes auratus , the geotrupid dung beetle with three color forms diverged into five geographic population groups based on the combined interpretation of genetic cluster and color‐form data. We estimated the demographic histories of these population groups using the newly assembled draft genome sequence of P. auratus and whole‐genome resequencing data obtained from the groups.

Project description:BackgroundElucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution to genetic diversity and association with important pathophysiological states. The present study aimed to elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X and 30X). Post-quality control, the sequence reads were aligned to the latest draft release of the Bubaline genome. The genome-wide CNVs were elucidated using a read-depth approach in CNVnator with different bin sizes. Adjacent CNVs were concatenated into copy number variation regions (CNVRs) in different breeds and their genomic coverage was elucidated.ResultsOverall, the average size of CNVR was lower at 30X coverage, providing finer details. Most of the CNVRs were either deletion or duplication type while the occurrence of mixed events was lesser in number on a comparative basis in all breeds. The average CNVR size was lower at 30X coverage (0.201 Mb) as compared to 10X (0.013 Mb) with the finest variants in Banni buffaloes. The maximum number of CNVs was observed in Murrah (2627) and Pandharpuri (25,688) at 10X and 30X coverages, respectively. Whereas the minimum number of CNVs were scored in Surti at both coverages (2092 and 17,373). On the other hand, the highest and lowest number of CNVRs were scored in Jaffarabadi (833 and 10,179 events) and Surti (783 and 7553 events) at both coverages. Deletion events overnumbered duplications in all breeds at both coverages. Gene profiling of common overlapped genes and longest CNVRs provided important insights into the evolutionary history of these breeds and indicate the genomic regions under selection in respective breeds.ConclusionThe present study is the first of its kind to elucidate the high-resolution CNV map in major buffalo populations using a read-depth approach on whole genome resequencing data. The results revealed important insights into the divergence of major global buffalo breeds along the evolutionary timescale.

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Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies.

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