Open access
Host-Microbial Interactions
25 August 2023

Complete genomes of mutualistic bacterial co-symbionts “Candidatus Sulcia muelleri” and “Candidatus Nasuia deltocephalinicola” of the rice green leafhopper Nephotettix cincticeps


The genomes of obligate bacterial co-symbionts of the green rice leafhopper Nephotettix cincticeps, which is notorious as an agricultural pest, were determined. The streamlined genomes of “Candidatus Sulcia muelleri” and “Candidatus Nasuia deltocephalinicola” exhibited complementary metabolic pathways for synthesizing essential nutrients that contribute to host adaptation.


Mutualistic relationship with endocellular microbial symbionts is indispensable for growth and reproduction of diverse insect species, especially those that rely on nutritionally unbalanced diets like plant sap, vertebrate blood, and woody material (1 - 4). Many plant sap-feeding hemipteran insects belonging to the Auchenorrhyncha harbor bacteriome-associated co-primary symbionts: the ancient obligate endocellular bacterial symbiont “Candidatus Sulcia muelleri,” (hereafter Sulcia) and another microbial partner (5). Despite genome reduction, the co-symbionts retain the capability of synthesizing essential amino acids in a complementary manner, plausibly reflecting their role in nutritional supply to their plant-sucking host insects (6).
Here, we sequenced the genomes of the bacteriome-associated co-symbionts, Sulcia and “Candidatus Nasuia deltocephalinicola,” (hereafter Nasuia), of the rice green leafhopper Nephotettix cincticeps (Hemiptera: Cicadellidae) (7, 8). N. cincticeps is widely found in East Asia and is notorious as a serious pest of rice that vectors such pathogens as rice dwarf virus (9). N. cincticeps used in this study was collected from Kagoshima, Japan, and maintained on rice seedlings. The bacteriome-containing abdomens dissected from 28 adult females were subjected to DNA extraction using Genomic-tip 100/G (QIAGEN). The DNA was fragmented to an average size of 600 bp with a focused ultrasonicator M220 (Covaris). A paired-end library was constructed with a TruSeq DNA PCR-Free Library Prep Kit (Illumina) and sequenced on the Illumina HiSeq platform in a 250-bp paired-end mode. The reads derived from each symbiont were selectively retrieved by mapping to reference bacterial genomes (CP006059-CP006060) (10) using BBmap v39.01 (Bushnell B. and samtools v1.10.2 (11). After removing low-quality reads using Trimmomatic v0.36 (12) with the following parameters: LEADING:30;TRAILING:30;MINLEN:50;ILLUMINACLIP:2:30:10, the reads recruited to the reference genomes were assembled using Unicycler v0.5.0 (13). The finalization of the genomes was manually performed with the aid of Bandage v0.8.1 (14) and IGV v2.15.4 (15). The genome annotation was carried out using DFAST pipeline v 1.2.18 (16) with manual curation.
The complete circular genomes of Sulcia and Nasuia were reconstructed from 223,209 and 23,316 paired reads, corresponding to 580-fold and 103-fold coverage, respectively. The genome of Sulcia was 192,344 bp with 23.7% G + C content. It encoded 186 putative protein-coding sequences (CDS), 30 transfer RNAs, and a single copy of 16S/23S/5S ribosomal RNA operon. The genome of Nasuia was 113,316 bp with 15.5% G + C content. It encoded 133 CDSs, 29 transfer RNAs, and a single ribosomal RNA operon. In Nasuia, the UGA codon was reassigned to tryptophan instead of the stop codon, as seen in other extremely reduced symbiont genomes (6).
Judging from the gene repertoire, Sulcia synthesizes 8 of 10 essential amino acids (Thr, Val, Leu, Ile, Lys, Phe, Trp, and Arg), while Nasuia is responsible for the remaining two (Met and His). It is noteworthy that methionine could be derived from the direct sulfhydrylation pathway (17). These results are consistent with prior studies highlighting the complementary nutritional roles of Sulcia and Nasuia (10, 18 - 21). Our new symbiont genome data will contribute to comparative symbiont genomic studies that provide insight into how sophisticated insect-microbe mutualisms have evolved and diversified.


We thank Hiroaki Noda for his pioneer work on the symbiotic bacteria of N. cincticeps and his kind support. We also would like to thank the staff of Comparative Genomics Laboratory at NIG for supporting genome sequencing.
This study was supported by the JSPS KAKENHI Grants JP17K15399, JP19H02973, and JP16H06279 (PAGS) to M.M. and the JST ERATO Grant JPMJER1902 to T.F.


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Information & Contributors


Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 12Number 919 September 2023
eLocator: e00353-23
Editor: Irene L. G. Newton, Indiana University, Bloomington, Bloomington, Indiana, USA
PubMed: 37623315


Received: 12 May 2023
Accepted: 22 July 2023
Published online: 25 August 2023


  1. endosymbiont
  2. leafhopper
  3. bacteriome

Data Availability

The sequence data have been deposited to DDBJ under the accession numbers AP028057-AP028058 for assemblies and DRR489300-DRR489301 for raw reads.



Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
Author Contributions: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, and Writing – original draft.
Yudai Nishide
Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
Author Contributions: Conceptualization, Resources, and Writing – review and editing.
Atsushi Toyoda
Comparative Genomics Laboratory, National Institute of Genetics (NIG), Mishima, Japan
Author Contributions: Methodology and Writing – review and editing.
School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Japan
Author Contributions: Methodology and Writing – review and editing.
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Japan
Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
Author Contributions: Funding acquisition and Writing – review and editing.


Irene L. G. Newton
Indiana University, Bloomington, Bloomington, Indiana, USA


The authors declare no conflict of interest.

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