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

Abstract

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.

Keywords: Bacterial endosymbionts; Cardinium; Genomic analysis; Sogatella furcifera.

Fig. 1

Phylogenomic tree for Cardinium. a Phylogenetic tree of 47 species. Phylogenetic tree reconstruction was done with a concatenated alignment of 16 orthologous single copy genes related to replication/recombination/repair, translation/ribosomal structure/biogenesis and post-translational modification/protein turnover. The Cardinium endosymbiont cSfur of Sogatella furcifera is displayed in bold. Species of different orders are displayed in different colors. Chorobaculum tepidum was used as an outgroup. Triangles represent collapsed branches of the same order. b Phylogenetic tree for Cardinium from different arthropod species based on gyrB gene. Phylogenetic relationship among different Cardinium supergroups are shown. The taxon names are the Cardinium endosymbionts’ hosts names and the geneinfo (gi) numbers of the corresponding gyrB genes. Cardinium cSfur falls in the clade of Cardinium endosymbionts of the planthopper, belonging to the group A. Amoebophilus asiaticus 5a2 was used as an outgroup. Bootstrap values over 50 are displayed

Fig. 2

Synteny and redundancy of the three Cardinium genomes. a Synteny of the three Cardinium genomes at the protein level. b Mummer plot showing the repeats of the genomes with a minimum length of 500 bp

Fig. 3

a Euler diagram of orthologous clusters. Euler diagram representing the core genome, the strain-specific orthologous clusters and the orthologous clusters shared only bye two Cardinium genomes. b Percentages of core, dispensable, and specific genes in three Cardinium genomes. The box of the core genome set is displayed in red; the genes with the highest (524) numerical values in all three genomes belong to the core genome, especially cBtQ1, which accounts for approximately 79.64%. The box of the strain-specific set is shown in yellow, the Cardinium cSfur has the most strain-specific genes, accounting for 24.66%

Fig. 4

Syntenic blocks between Cardinium cSfur genome and Cardinium cEper1 and cBtQ1 plasmids. The genes marked in the same color are homologous, with pCher being the plasmid of Caridnium cEper1 and pcBtQ1 that of Cardinium cBtQ1

Fig. 5

Gene distributions of 17 species in Cytophagales. a Percentage relative abundances of gene clusters in Cytophagales. The values are centered and scaled in the row direction. Two main COG clusters (left) are observed: highly retained categories (U, J, L, D, O, M, I, Z) and low retained categories free-living bacteria (latter 13). b Percentages of 4 categories in Cytophagales. Compared with the free-living bacteria, the host-dependent endosymbionts have higher percentages of genes related tothe information storage and processing (green), with lower percentages of genes involved in metabolism (blue). J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; B: Chromatin structure and dynamics; C: Energy production and conversion; G: Carbohydrate transport and metabolism; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; P: Inorganic ion transport and metabolism; Q: Secondary metabolite biosynthesis, transport and catabolism; D: Cell cycle control, cell division, chromosome partitioning; V: Defense mechanisms; T: Signal transduction mechanisms; M: Cell wall/membrane biogenesis; N: Cell motility; Z: Cytoskeleton; U: Intracellular trafficking and vesicular transport; O: Post-translational modification, protein turnover andchaperones; R: General function prediction only; S: Function unknown. Aas: Amoebophilus asiaticus 5a2; cBtQ1: Cardinium cBtQ1; cEper1: Cardinium cEper1; cSfur: Cardinium cSfur; lby: Leadbetterella byssophila DSM 17132; bbd: Belliella baltica DSM 15883; mtt: Marivirga tractuosa DSM 4126; dfe: Dyadobacter fermentans DSM 18053; sli: Spirosoma linguale DSM 74; eol: Emticicia oligotrophica DSM 17448; rsi: Runella slithyformis DSM 19594; cmr: Cyclobacterium marinum DSM 745; evi: Echinicola vietnamensis DSM 17526; hsw: Hymenobacter swuensis DY53; fae: Fibrella aestuarina BUZ 2; gm03586: Algoriphagus machipongonensis PR1

Fig. 6

HGT in the Cardinium cSfur genome. a Percentages of nearest neighbors of the 25 genes encoding non-transposases acquired by HGT in Cardinium cSfur genome. b Phylogenetic tree of the genes related to biotin biosynthesis. Ten species harboring all the 6 genes were chosen, the 6 encoding proteins of each genome were concatenated in order and aligned with MAFFT, and then phylogenetic trees were reconstructed using the software MEGA6. c Genes related to glycolysis in the Cardinium cSfur genome and the highest identity between each gene and its homologous ones inside (red) or outside (green) of the Bacteroides phylum (IB or IOB). d The 15 genes encoding transposases aquired by the event of HGT in the Caridnium cSfur genome, the genes marked in the same color are homologous

Fig. 7

Gliding genes profile, PorSS system and PCR confirmation of Cardinium cSfur existence. a Distribution of gld and spr orthologs in the Cytophagias. The genes gldKLMN and sprAET also encode the PorSS system. b Duplication of gldJ and the following 5 genes in the Cardinium cSfur genome. c PCR confirmation of Cardinium cSfur existence in different tissues of S. furcifera. PCR of a fragment of 16S rDNA (766 bp) and gyrB (575 bp) gene of different tissues of female and male adults. MG: malpighian tubule, OV/TE: ovary/testis, SG: salivary gland, MT: midgut, FB: fat body, R: rest of body, control: negative control without DNA template

Fig. 8

Genome size comparison and evaluation of evolutionary relationships between Cardinium and their hosts. a Comparison of genome sizes and GC content of selected endosymbiotic bacteria. P-endosymbionts are marked in red, S-endosymbionts in orange, and Cardinium cSfur is specially marked in green. Cr, Carsonella ruddii DC; Pa, Portiera aleyrodidarum BT-B-HRs; Rp, Riesia pediculicola; Ba, Buchnera aphidicola str. Sg; Bc, Baumannia cicadellinicola; Bf, Blochmannia floridanus; Wg, Wigglesworthia glossinidia; Sc, Spiroplasma chrysopicola; Hd, Hamiltonella defensa 5AT; aas, Amoebophilus asiaticus 5a2; Ri, Regiella insecticola R5.15; Ss, Serratia symbiotica str. Tucson; An, Arsenophonus nasoniae; Sg, Sodalis glossinidius. b Comparisons of the evolutionary relationships between Cardinium strains and their different insect hosts. The host tree is based on the mitochondria gene COXI sequence, while the endosymbiont Cardinium tree is based on gyrB