Abstract
BackgroundThe African buffalo (Syncerus caffer) is an important role player in the savannah ecosystem. It has become a species of relevance because of its role as a wildlife maintenance host for an array of infectious and zoonotic diseases some of which include corridor disease, foot-and-mouth disease and bovine tuberculosis. To date, no complete genome sequence for S. caffer had been available for study and the genomes of other species such as the domestic cow (Bos taurus) had been used as a proxy for any genetics analysis conducted on this species. Here, the high coverage genome sequence of the African buffalo (S. caffer) is presented.ResultsA total of 19,765 genes were predicted and 19,296 genes could be successfully annotated to S. caffer while 469 genes remained unannotated. Moreover, in order to extend a detailed annotation of S. caffer, gene clusters were constructed using twelve additional mammalian genomes. The S. caffer genome contains 10,988 gene clusters, of which 62 are shared exclusively between B. taurus and S. caffer.ConclusionsThis study provides a unique genomic perspective for the S. caffer, allowing for the identification of novel variants that may play a role in the natural history and physiological adaptations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3364-0) contains supplementary material, which is available to authorized users.
Highlights
The African buffalo (Syncerus caffer) is an important role player in the savannah ecosystem
The African buffalo hosts a vast array of nematodes, pathogens and infectious diseases and plays an important role in the maintenance and transmission of economically important livestock diseases such as foot-and-mouth disease (FMD), bovine brucellosis, corridor disease and bovine tuberculosis (BTB) [4, 5]
The total length of the genome assembly equated to 2.68 Gbp and a total of 1235 scaffold contigs made up 90% of the genome assembly and 97.9% of the estimated length (Additional file 2: Table S2)
Summary
The African buffalo (Syncerus caffer) is an important role player in the savannah ecosystem It has become a species of relevance because of its role as a wildlife maintenance host for an array of infectious and zoonotic diseases some of which include corridor disease, foot-and-mouth disease and bovine tuberculosis. Buffalo are of great ecological importance because of their role as bulk feeders in the grazing hierarchy Due to their size they are able to process taller and coarser grasses than most other species [1], playing an important facilitative role for the smaller grazers [2]. They inhabit zones with almost all vegetation types, provided a permanent water source is present. In the absence of a complete reference genome, a related species can be used as a proxy reference to facilitate the identification of various single nucleotide variants (SNVs), but the amount
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