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Whole-Genome Sequencing of the Endangered Bovine Species Gayal

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Whole-Genome Sequencing of the Endangered Bovine Species Gayal www.nature.com/scientificreports OPEN Whole-genome sequencing of the endangered bovine species Gayal (Bos frontalis) provides new Received: 06 September 2015 Accepted: 18 December 2015 insights into its genetic features Published: 25 January 2016 Chugang Mei1,*, Hongcheng Wang1,*, Wenjuan Zhu2,*, Hongbao Wang1, Gong Cheng1, Kaixing Qu3, Xuanmin Guang2, Anning Li1, Chunping Zhao1, Wucai Yang1, Chongzhi Wang2, Yaping Xin1 & Linsen Zan1 Gayal (Bos frontalis) is a semi-wild and endangered bovine species that differs from domestic cattle (Bos taurus and Bos indicus), and its genetic background remains unclear. Here, we performed whole- genome sequencing of one Gayal for the first time, with one Red Angus cattle and one Japanese Black cattle as controls. In total, 97.8 Gb of sequencing reads were generated with an average 11.78-fold depth and >98.44% coverage of the reference sequence (UMD3.1). Numerous different variations were identified, 62.24% of the total single nucleotide polymorphisms (SNPs) detected in Gayal were novel, and 16,901 breed-specific nonsynonymous SNPs (BS-nsSNPs) that might be associated with traits of interest in Gayal were further investigated. Moreover, the demographic history of bovine species was first analyzed, and two population expansions and two population bottlenecks were identified. The obvious differences among their population sizes supported that Gayal was notB. taurus. The phylogenic analysis suggested that Gayal was a hybrid descendant from crossing of male wild gaur and female domestic cattle. These discoveries will provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds and may assist relevant departments with future conservation and utilization of Gayal. Gayal (Bos frontalis), also known as mithan or mithun, is a unique semi-wild and endangered bovine species that is distributed in hilly areas of China, India, Bangladesh, Myanmar and Bhutan1. The chromosome number of Gayal (2n = 58) differs from those of domesticated cattle (Bos indicus and Bos taurus, 2n = 60) and gaur (Bos gaurus, 2n = 56)2–4. Thus far, the origin of Gayal remains unclear. Some researchers presumed that Gayal was an independent species5–7, and some thought that it was a hybrid descendant from crossing of wild gaur and domes- tic cattle8,9. Previous reports have shown that Gayal can interbreed with domestic cattle (B. taurus and B. indicus), and that the female offspring may be fertile, whereas the male offspring may not always be fertile10–12. The phe- notypic characteristics of Gayals have been retained under natural selection over time and have not been affected by artificial selection. This animal has a bulging forehead ridge above the nose, a pair of wide and short ears and feet with white stockings that can be used to distinguish them from domesticated cattle2,13. Gayals usually eat any variety of plant, including tree and bamboo leaves, grasses, reeds, etc. and have wide range of adaptations under harsh conditions, and salt is one of the favorite food items of this animal14,15. Moreover, Gayals have better perfor- mance in body size and meat quality than certain indigenous domestic cattle and can be used to breed hybrids to produce better meat and milk traits11,16. Because the population size of Gayal is dwindling rapidly, they have been classified as an endangered species by the International Union for Conservation of Nature and Natural Resources (www.iucnredlist.org/). However, the specific inherited characteristics of Gayals are far from comprehensive, and their potential value has yet to be discovered. Thus, tapping the genetic information of this endangered semi-wild bovine species requires a timely and effective approach, especially considering the value and importance of this genetic resource. 1College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, China. 2BGI-Tech, BGI- Shenzhen, Shenzhen, China. 3Yunnan Academy of Grassland and Animal Science, Xiaoshao Kunming, Yunnan, China. *These authors contributed equally to this work. Correspondence and requests for materials should be addressed to L.S.Z. (email: [email protected]) SCIENTIFIC REPORTS | 6:19787 | DOI: 10.1038/srep19787 1 www.nature.com/scientificreports/ Bos frontalis Bos taurus Summary Gayal RAN JBC Mean depth 13.06 11.94 10.34 Mismatch rate 1.22% 0.48% 0.57% GC content rate 41.82% 41.84% 41.92% Coverage rate 98.44% 98.65% 98.71% Coverage rate (> = 1X) 98.37% 98.62% 98.66% Coverage rate (> = 4X) 96.43% 96.76% 95.15% Coverage rate (> = 8X) 85.92% 81.68% 69.94% Coverage rate (> = 12X) 57.47% 45.20% 28.56% Total reads 362606690 (100%) 333277352 (100%) 282866734 (100%) Mapped reads 357292180 (98.53%) 330198207 (99.08%) 280354187 (99.11%) Reads that are properly paired 340787139 (93.98%) 320590349 (96.19%) 272111559 (96.20%) Only one of the reads are mapped 3690443 (1.02%) 2248862 (0.67%) 1940525 (0.69%) Reads with mate mapped to a 5314158 (1.47%) 3078939 (0.92%) 2512311 (0.89%) different chromosomes unmapped reads 5314510 (1.47%) 3079145 (0.92%) 2512547 (0.89%) Table 1. Summary of sequence read alignments to the reference genome. Since the bovine genome and HapMap projects have been completed17–19, the whole-genome resequencing of multiple cattle breeds has progressed rapidly, including B. taurus (Hereford, Angus, Hanwoo, Yanbian, and Japanese native cattle), B. indicus (Gir, Nellore), dairy cattle (Holstein, Fleckvieh) and yak20–27. With the rapid development of science and technology, whole-genome sequencing has become one of the most important and effective methods for exploring the genetic information of different species. However, the whole-genome sequencing of Gayal has not been performed. In this study, we sequenced the whole genome of one Gayal from Yunnan Province, China using an Illumina HiSeq 2000 and sequenced one Red Angus (RAN) and one Japanese Black cattle (JBC) as controls because both are breeds of the globally popular species B. taurus. A comparative diversity study may lead to a whole-genome analysis of the genetic features of Gayal, increase the understanding of the correlation between their phenotypic characteristics and genetic features and assist relevant departments with their conservation. Results and Discussion Sequencing and mapping. Whole-genome sequencing of one Gayal as well as one RAN and one JBC (Table S1) was performed on a HiSeq 2000 using genomic DNA, and 97.8 Gb of high quality paired-end reads (100 bp) was generated. To the best of our knowledge, this study is the first to perform whole-genome sequencing of Gayal. All of the obtained reads were mapped to the reference genome UMD3.119 using BWA28. The reference sequence was 98.44% covered by the reads for Gayal and presented a 13.06-fold depth. These values are not sig- nificantly lower than are those of RAN (98.65%, 11.94-fold) and JBC (98.66%, 10.34-fold) despite the lower chro- mosome number in Gayal compared with that of B. taurus (Table 1). We argue that this phenomenon is a result of centric fusion involving ROB (2; 28), which has been reported by previous studies2,3, rather than chromosome deletion. Furthermore, the depth and coverage are sufficient to detect high-quality variations compared with previous sequencing studies in cattle20–22. Single nucleotide polymorphisms (SNPs) detection. Through comparisons with the reference genome, 28,493,996 SNPs (Table 2) were detected in these three sequenced cattle genomes. Of these SNPs, 53.23% (15,167,354 SNPs) were novel compared with the latest version of the cattle SNP database (dbSNP Build 140; ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/cow_9913/chr_rpts/). As expected, the total variation number and novel rate in Gayal (23,828,562 SNPs, 62.24% novel) were all much higher than those in RAN (5,785,690 SNPs, 2.53% novel) and JBC (5,956,686 SNPs, 5.10% novel) because of differences between the genome sequences of B. frontalis and B. taurus and because of the semi-wild nature of Gayal compared with the domesticated nature of B. taurus. SNP annotation showed that 78.2% of the SNPs were located in intergenic regions (Gayal: 77.9%; RAN: 79.5%; JBC: 79.4%); 21.1% were located in genic regions, including intronic regions, splicing sites, exonic regions and untranslated regions; and the remaining 0.7% were located in up/downstream regions. The number of Gayal SNPs is as proportional to the length of chromosomes as those of RAN and JBC (Figure S1), which also supports the hypothesis that the two fewer chromosomes in Gayal compared with B. taurus resulted from a centric fusion involving ROB (2; 28). Transition-to-transversion (TS/TV) ratios were calculated as indicators of potential random sequence errors22. Here, the TS/TV ratios (Gayal: 2.32, RAN: 2.17, JBC: 2.18) approximated the empirical human TS/TV ratio > 2.1, indicating the high quality of the identified SNPs in an oblique manner. Furthermore, the homozygous/heterozy- gous ratios of Gayal, RAN and JBC were 1:0.8, 1:1.5 and 1:1.1, respectively. The finding that the ratio of Gayal was higher than were those of the other two breeds was somewhat surprising, because Gayal has been regarded as indigenous with its population size decreasing rapidly over recent thousands of years, which might have been fueled by natural directional selection on genotype. SCIENTIFIC REPORTS | 6:19787 | DOI: 10.1038/srep19787 2 www.nature.com/scientificreports/ SNP Gayal RAN JBC Total Total numbers 23,828,562 5,785,690 5,956,686 28,493,996 Transition/transversion ratio 2.32 2.17 2.18 2.27 Novel rate (%) 62.24% 2.53% 5.10% 53.23% Intergenic 18,565,897 4,601,652 4,731,811 22,276,335 Upstream 80,850 18,804 18,623 96,119 Downstream 91,649 20,039 20,967 108,248 Gene 5,090,166 1,145,195 1,185,285 6,013,294 Intronic 4,947,017 1,111,361 1,150,941 5,842,593 Splicing 166 103 96 79,507 Exonic 142,983 33,731 34,248 91,194 UTR 66,866 15,682 15,629 208 Non-synonymous 20,499 5,652 5,897 25,401 Synonymous 47,996 10,253 10,514 56,278 Stopgain 62 30 26 93 Stoploss 20 8 5 22 Others 7,540 2,106 2,177 9,192 Table 2.
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