- Investigation of ancestral alleles in the Bovinae subfamily. - In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study.. - Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. - High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - 6 Agricultural Research Service USDA, Beltsville, MD, USA Full list of author information is available at the end of the article. - Another method con- sists of verifying the allelic state of the last common an- cestor (LCA) or the allele within current populations that least differs from the LCA [10].. - In a cat- tle study of Utsunomiya et al. - Therefore, the goal of this study is to fill this gap and to determine a fixed set of AA in cattle by using out- group species in the Bovinae subfamily, namely gaur, yak, bison, wisent, banteng, and gayal sequences. - In addition, we scanned the list of AA for physical regions linked to conserved and mutated traits in taurine and zebu cattle.. - Four prin- cipal components (PC) explained and 17.7% of the variance for first, second, third, and fourth PC, respectively. - In concordance with the principal component analysis, 13 yak individuals are sit- uated together in the top clade of the tree. - Banteng-gaur-gayal share a clade together, however, variations in the order within these three species exist in trees inferred from different chromosomes [see Add- itional file 1]. - Using allele frequency over all individuals in outgroup, we defined ~ 32.4 million variants that are fixed across 29 chromo- somes as AA corresponding to 1.2% of the total genome.. - GC content percentage of ances- tral alleles is 58%, which is higher than the GC content of the reference genome. - Windows with high ancestral allele counts in taurine and zebu cattle. - We counted AA by non-overlapping windows of 10 Kb in taurine and zebu cattle separately. - Figures 4 and 5 present the distribution of AA on chromosome 27 for taurine and zebu, respectively (The distribution of AA for all chromosomes can be found in Additional file 2).. - Peaks of high ancestral alleles count regions in contrast with background averages number of ancestral alleles are clearly distinguished in chromosome in taurine cattle and in zebu cattle [see Add- itional file 2].. - Windows without the occurrence of ancestral alleles We found 3306 windows without AA in taurine and 2189 windows in zebu. - The highest ratio of windows with null AA counts to total windows was 2.9% on chromosome 29 in taurine and the lowest is 0.14% in chromosome 25 of zebu cattle (Fig. - In taurine cattle, 65% of windows without AA are due to the latter reason, while in zebu it is 46%.. - Annotation of scanning windows with high number of ancestral alleles. - We annotated each scanning window passing the re- spective threshold of top 0.1%, corresponding to 255 re- gions in taurine and 258 regions in zebu across 29 chromosomes. - 3 Intersection of defined ancestral alleles (in millions) from three lineages. - Annotation of scanning windows without ancestral alleles There were 713 windows in taurine with protein coding genes, while in zebu 121 windows were found. - There are 42 GO terms defined for taurine and 7 GO terms for zebu. - 4 Distribution of ancestral count in taurine chr 29. - 5 Distribution of ancestral count in zebu chr 29. - In taurine cattle, apart from terms related to immune system process and cellular function, there are GO terms exclusive to taurine cattle that are related to production traits. - Regions without AA in zebu were mainly related to 5 GO terms in domain of immune response and one term related to cellular process of transmembrane transport.. - It is dominated by metabolism terms in taurine and immune response in zebu.. - We used subsets of all vari- ants per chromosome to comply with maximum 50,000 markers/sequences per output of the analysis as directed. - Defining AA by only a single lineage was not an option since any of the current lineages could have undergone independent evolutionary events and might have di- verged from the initial ancestral state. - Using the same data- set, we infered the ancestral alleles several times result- ing in the same list of alleles as we strictly considered only variants with fixed allele (100% frequency) in each species. - Although, we used the best dataset available in terms size, sequence read quality, and coverage for the outgroup species, additional re-sequencing data of the outgroup species might have slightly modified the de- fined ancestral alleles as the frequency for those fixed al- leles might be changed by new individuals. - However, as Table 1 GO terms of genes indicated by high count ancestral alleles. - 8 GO terms for regions without ancestral alleles (taurine-left. - Ancestral allele counts within scanning windows in taurine and zebu cattle var- ied in the genome. - We took two extreme ends of the oc- currence distribution. - highest count and second is windows without ancestral allele count. - In taurine high count regions, DEFB7 and DEFB3 are within this term, while regions without AA in zebu are DEFB6, LOC781146, DEFB1, DEFB3.. - Within this scope, more GO terms found in taurine cattle compared to zebu possibly due to more intensive selection for production traits. - Skin inflammatory response by high secretion of granulocytes and T-lymphocytes in taurine is not neces- sary could cease tick invasion. - We inferred ancestral alleles by combining fixed alleles in three lineages of cattle outgroups. - Regions conserving more primitive functions indicated by high count ances- tral alleles were linked to lipid metabolism in taurine and zebu. - Meanwhile, regions undergone mutation indi- cated by no preserved ancestral alleles were found more. - These regions were linked to pro- duction traits in taurine and robustness traits in zebu.. - Workflow of the ancestral analysis pipeline is shown in Fig. - Then, we set four components to reduce dimension of the whole inde- pendent variants and plotted the species based on the first two components.. - R functions for calling the ancestral allele in this study are provided in https://. - Given ancestral allele denotes as p(A AA ) with fre- quency of 1 for A allele, ϑ is calculated by subtract p(A AA ) from x. - We then excluded regions that are fall in the intergenic, downstream and upstream of known genes, leaving only regions that overlapping with functional genes. - 9 Workflow of the ancestral allele analysis. - Distribution of ancestral allele in all chromosomes of taurine and zebu. - Annotation of regions without ancestral alleles Additional file 4. - AA: Ancestral allele. - Defined cattle ancestral alleles is available at https://tinyurl.com/cattle-aa.. - Daetwyler HD, Capitan A, Pausch H, Stothard P, Binsbergen R, Brøndum R, et al. - 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Chapter 10 - structural genomic variation in the human genome. - Rohde K, Keller M, la Cour Poulsen L, Ronningen T, Stumvoll M, Tonjes A, et al. - Porto-Neto LR, Sonstegard TS, Liu GE, Bickhart DM, Da Silva MV, Machado MA, et al. - Variation in the mutation rate across mammalian genomes. - Park SDE, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, et al. - Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.. - Impact of including growth, carcass and feed efficiency traits in the breeding goal for combined milk and beef production systems.. - Cole JB, Wiggans GR, Ma L, Sonstegard TS, Lawlor TJ, Crooker BA, et al.. - comparing taurine and zebu cattle. - Pérez O ’ Brien AM, Utsunomiya YT, Mészáros G, Bickhart DM, Liu GE, Van Tassell CP, et al. - Franzin AM, Maruyama SR, Garcia GR, Oliveira RP, Ribeiro JMC, Bishop R, et al. - Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, et al. - Wu D-D, Ding X-D, Wang S, Wójcik JM, Zhang Y, Tokarska M, et al. - 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investigation of ancestral alleles in the Bovinae subfamily;
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