Open access
28 June 2018

Genome Sequence of the Soybean Cyst Nematode (Heterodera glycines) Endosymbiont “Candidatus Cardinium hertigii” Strain cHgTN10


In this study, we present the genome sequence of the “Candidatus Cardinium hertigii” strain cHgTN10, an endosymbiotic bacterium of the plant-parasitic nematode Heterodera glycines. This is the first genome assembly reported for an endosymbiont directly sequenced from a tylenchid nematode.


The soybean cyst nematode (SCN [Heterodera glycines]) causes more economic loss to soybean (Glycine max) than any other biotic pathogen of this important crop (1). Although an abundance of molecular studies have highlighted the nematode’s interaction with its primary host, soybean, little is known about the molecular interactions between the SCN and its Cardinium endosymbiont. Molecular cloning studies of the 16S RNA and gyrB genes within an SCN endosymbiont identified the bacterium as “Candidatus Paenicardinium endonii,” thereafter taxonomically reassigned to “Candidatus Cardinium hertigii” group B (2, 3).
DNA was extracted from surface-sterilized second-stage juveniles of H. glycines population TN10 (Hg type 0) cultured on the susceptible soybean cultivar Essex on soil in the greenhouse. Genomic DNA was extracted using a standard proteinase K protocol (4). PacBio RS II and Illumina TruSeq DNA libraries were prepared from the extracted DNA. The PacBio library was sequenced on 20 single-molecule real-time (SMRT) cells. The Illumina DNA library was sequenced as paired ends (2 × 260) on the Illumina HiSeq 2500 platform. The PacBio reads were assembled with the Canu (version 1.4) long-read assembler (5). The resultant metagenomic assembly was error corrected with Pilon (version 1.22) (6) using the Illumina reads aligned with the BWA-MEM (version 0.7.15) alignment algorithm (7). For the identification of potential endosymbiont contigs within the endosymbiont-nematode metagenome assembly, a BlobTools (version (8) database was built with BWA-MEM alignments to the contigs, and the results from the contigs were aligned to the UniProt uniref100 database with the DIAMOND (version 0.9.10) (9) aligner, using the blastx parameter. Additionally, previously identified 16S RNA (GenBank accession no. DQ314214) and gyrB (GenBank accession no. DQ314215) genes for “Ca. Cardinium hertigii” were aligned with blastn, and H. glycines RNA sequencing (RNA-seq) reads from NCBI BioProject no. PRJNA415980 (10) were aligned with TopHat (version 2.1.1) (11). All contigs identified as bacterial by BlobTools were manually inspected for the presence of RNA splicing. A single 1.2-Mb contig was identified as the “Ca. Cardinium hertigii” chromosome sequence based upon the following 4 supporting criteria: (i) had a predicted circular link to itself, (ii) was taxonomically identified as bacterial, (iii) contained the “Ca. Cardinium hertigii” gyrB and 16S RNA alignments, and (iv) did not show evidence of RNA splicing. This contig was circularized using Circlator (version 1.5.1) (12) and subsequently error corrected using 2 passes through Quiver and 2 additional passes through Pilon. The resultant 1.2-Mb genome assembly is reported here.
Gene prediction with Prokka (version 1.13) (13) resulted in 973 protein-coding genes and 37 tRNAs. BLASTP alignments of the predicted cHgTN10 proteins to the NCBI NR database (accessed 8 February 2018) resulted in 770 (79%) cHgTN10 predicted proteins with a bit score greater than 60, of which 594 (61%) proteins had a highest scoring blastp alignment to 1 of the 2 previously reported “Ca. Cardinium hertigii” strains, cEper1 and cBtQ1 (14, 15). Functional annotation with InterProScan (16) resulted in the identification of several proteins and protein domains similar to those of “Ca. Cardinium hertigii,” including the following: Ankyrin repeats, ABC transporters, permeases, a WH2 motif, and DEAD box helicase, as reported for cEper1 (14).

Accession number(s).

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. CP029619. The version described in this paper is the first version, CP029619.1.


This work was funded by the North Central Soybean Research Program.


Wrather A, Koenning S. 2009. Effects of diseases on soybean yields in the United States 1996 to 2007. Plant Health Progress.
Noel GR, Atibalentja N. 2006. “Candidatus Paenicardinium endonii”, an endosymbiont of the plant-parasitic nematode Heterodera glycines (Nemata: Tylenchida), affiliated to the phylum Bacteroidetes. Int J Syst Evol Microbiol 56:1697–1702.
Nakamura Y, Kawai S, Yukuhiro F, Ito S, Gotoh T, Kisimoto R, Yanase T, Matsumoto Y, Kageyama D, Noda H. 2009. Prevalence of Cardinium bacteria in planthoppers and spider mites and taxonomic revision of “Candidatus Cardinium hertigii” based on detection of a new Cardinium group from biting midges. Appl Environ Microbiol 75:6757–6763.
Bekal S, Domier LL, Gonfa B, McCoppin NK, Lambert KN, Bhalerao K. 2014. A novel flavivirus in the soybean cyst nematode. J Gen Virol 95:1272–1280.
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736.
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963.
Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv arXiv:1303.3997 [q-bio.GN].
Laetsch DR, Blaxter ML. 2017. BlobTools: interrogation of genome assemblies. F1000Res 6:1287.
Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60.
Gardner M, Dhroso A, Johnson N, Davis EL, Baum TJ, Korkin D, Mitchum MG. 2018. Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. Sci Rep 8:2505.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36.
Hunt M, De Silva N, Otto TD, Parkhill J, Keane JA, Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol 16:294.
Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069.
Penz T, Schmitz-Esser S, Kelly SE, Cass BN, Muller A, Woyke T, Malfatti SA, Hunter MS, Horn M. 2012. Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii. PLoS Genet 8:e1003012.
Santos-Garcia D, Rollat-Farnier P-A, Beitia F, Zchori-Fein E, Vavre F, Mouton L, Moya A, Latorre A, Silva FJ. 2014. The genome of Cardinium cBtQ1 provides insights into genome reduction, symbiont motility, and its settlement in Bemisia tabaci. Genome Biol Evol 6:1013–1030.
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. 2005. InterProScan: protein domains identifier. Nucleic Acids Res 33:W116–W120.

Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 6Number 2628 June 2018
eLocator: 10.1128/genomea.00624-18


Received: 30 May 2018
Accepted: 2 June 2018
Published online: 28 June 2018



Kurt C. Showmaker
Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
Kimberly K. O. Walden
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
Christopher J. Fields
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
Kris N. Lambert
Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
Matthew E. Hudson
Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA


Address correspondence to Kurt C. Showmaker, [email protected].

Metrics & Citations


Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.


If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.

View Options

Figures and Media






Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy