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Background   Sogatella furcifera  is a migratory pest that damages rice plants and causes severe economic losses. Due to its ability to annually migrate long distances,  S. furcifera  has emerged as a major pest of rice in several Asian countries. Symbiotic relationships of inherited bacteria with terrestrial arthropods have significant implications. The genus  Cardinium  is present in many types of arthropods, where it influences some host characteristics. We present a report of a newly identified strain of the bacterial endosymbiont  Cardinium  cSfur in  S. furcifera .    Result  From the whole genome of  S. furcifera  previously sequenced by our laboratory, we assembled the whole genome sequence of  Cardinium  cSfur. The sequence comprised 1,103,593 bp with a GC content of 39.2%. The phylogenetic tree of the Bacteroides phylum to which  Cardinium  cSfur belongs suggests that  Cardinium  cSfur is closely related to the other strains ( Cardinium  cBtQ1 and cEper1) that are members of the Amoebophilaceae family. Genome comparison between the host-dependent endosymbiont including  Cardinium cSfur  and free-living bacteria revealed that the endosymbiont has a smaller genome size and lower GC content, and has lost some genes related to metabolism because of its special environment, which is similar to the genome pattern observed in other insect symbionts.  Cardinium  cSfur has limited metabolic capability, which makes it less contributive to metabolic and biosynthetic processes in its host. From our findings, we inferred that, to compensate for its limited metabolic capability,  Cardinium  cSfur harbors a relatively high proportion of transport proteins, which might act as the hub between it and its host. With its acquisition of the whole operon related to biotin synthesis and glycolysis related genes through HGT event,  Cardinium  cSfur seems to be undergoing changes while establishing a symbiotic relationship with its host.    Conclusion  A novel bacterial endosymbiont strain ( Cardinium  cSfur) has been discovered. A genomic analysis of the endosymbiont in  S. furcifera  suggests that its genome has undergone certain changes to facilitate its settlement in the host. The envisaged potential reproduction manipulative ability of the new endosymbiont strain in its  S. furcifera  host has vital implications in designing eco-friendly approaches to combat the insect pest.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5078-y) contains supplementary material, which is available to authorized users.

Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host