The emergence of
Anaplasma bovis
or
A. bovis
-like infection in humans from China and the United States of America has raised concern about the public health importance of this pathogen. Although
A. bovis
has been detected in a wide range of ticks and mammals in the world, no genome of the pathogen is available up to now, which has prohibited us from better understanding the genetic basis for its pathogenicity. Here we describe an
A. bovis
genome from metagenomic sequencing of an infected goat in China.
Anaplasma bovis
had the smallest genome of the genus
Anaplasma
, and relatively lower GC content. Phylogenetic analysis of single-copy orthologue sequence showed that
A. bovis
was closely related to
A. platys
and
A. phagocytophilum
, but relatively far from intraerythrocytic
Anaplasma
species.
Anaplasma bovis
had 116 unique orthogroups and lacked 51 orthogroups in comparison to other
Anaplasma
species. The virulence factors of
A. bovis
were significantly less than those of
A. phagocytophilum
, suggesting less pathogenicity of
A. bovis
. When tested by specific PCR assays,
A. bovis
was detected in 23 of 29 goats, with an infection rate up to 79.3% (95% CI: 64.6% ∼94.1%). The phylogenetic analyses based on partial 16S rRNA,
gltA
and
groEL
genes indicated that
A. bovis
had high genetic diversity. The findings of this study lay a foundation for further understanding of the biological characteristics and genetic diversity of
A. bovis
, and will facilitate the formulation of prevention and control strategies.