| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| Buchnera aphidicola strain CjNOSY1 | This study | N/A |
| Arsenophonus sp. strain CjNOSY1 | This study | N/A |
| Hamiltonella defensa strain CjNOSY1 | This study | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| RNase A (17,500 U) | Qiagen | Cat#19101 |
| Proteinase K (2 mL) | Qiagen | Cat#19131 |
| DAPI | Dojindo Laboratories | Cat#340-07971 |
| Hoechst 33342 | Thermo Fisher Scientific | Cat#H3570 |
| Alexa Fluor™ 594 phalloidin | Thermo Fisher Scientific | Cat#A12381 |
| FM™ 4-64FX | Thermo Fisher Scientific | Cat#F34653 |
| Critical commercial assays | ||
| DNeasy Blood & Tissue Kit (250) | Qiagen | Cat#69506 |
| Quick-16S NGS Library Prep Kit | Zymo Research | Cat#D6400 |
| TruSeq DNA PCR-Free Low Throughput Library Prep Kit (24 samples) | Illumina | Cat#20015962 |
| Genomic-tip 20/G | Qiagen | Cat#10223 |
| Ligation Sequencing Kit | Oxford Nanopore Technologies | Cat#SQK-LSK110 |
| Deposited data | ||
| Ceratovacuna japonica strain NOSY1 Nanopore genome sequencing data | This study | Accession number: DRR379965 |
| Ceratovacuna japonica strain NOSY1 Illumina genome sequencing data | This study | Accession number: DRR379966 |
| Ceratovacuna japonica strain NOSY1 mtDNA, complete genome | This study | Accession number: LC722794 |
| Buchnera aphidicola (Ceratovacuna japonica) strain CjNOSY1 genome | This study | Accession number: AP026065 (chromosome), AP026066 (pLeu), AP026067 (pTrp) |
| Arsenophonus sp. (Ceratovacuna japonica) strain CjNOSY1 genome | This study | Accession number: AP026064 |
| Candidatus Hamiltonella defensa (Ceratovacuna japonica) strain CjNOSY1 | This study | Accession number: AP026068 |
| 16S rRNA amplicon sequencing data of Ceratovacuna japonica | This study | Accession number: DRA014323 |
| Predicted protein-coding genes, amino acid sequences, and annotations | This study | Figshare: 10.6084/m9.figshare.c.6026333 |
| Scripts for analyses | This study | GitHub: https://github.com/shigenobulab/21shunta_cjsym_msprep |
| Experimental models: Organisms/strains | ||
| Ceratovacuna japonica strain NOSY1 | This study | N/A |
| Oligonucleotides | ||
| For primer sequences, please see Table S8 | This study | N/A |
| For probe sequences, please see Table S8 | This study | N/A |
| Software and algorithms | ||
| MAFFT version 7.490 | Katoh et al. (2002) | https://mafft.cbrc.jp/alignment/software/ |
| QIIME2 version 2020.8 | Bolyen et al. (2019) | https://qiime2.org/ |
| dada2 | Callahan et al. (2016) | https://benjjneb.github.io/dada2/dada-installation.html |
| naïve Bayes classifier | Bokulich et al. (2018) | N/A |
| Primer3Plus | Untergasser et al. (2007) | https://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi |
| Guppy version 4.3.4 | Oxford Nanopore Technologies | https://github.com/nanoporetech |
| Raven version 1.5.0 | Vaser and Šikić (2021) | https://github.com/lbcb-sci/raven |
| BLAST version 2.12.0 | Altschul et al. (1990) | https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download |
| DIAMOND version 2.0.5 | Buchfink et al. (2015) | https://github.com/bbuchfink/diamond |
| BlobTools version version 1.1.1 | Laetsch and Blaxter (2017) | https://github.com/DRL/blobtools |
| minimap2 version 2.17-r941 | Li (2018) | https://github.com/lh3/minimap2 |
| Racon version 1.4.20 | Vaser et al. (2017) | https://github.com/isovic/racon |
| medaka version 1.4.1 | Oxford Nanopore Technologies | https://github.com/nanoporetech/medaka |
| cutadapt version 2.10 | Martin (2011) | https://github.com/marcelm/cutadapt |
| Bowtie2 version 2.4.2 | Langmead and Salzberg (2012) | https://github.com/BenLangmead/bowtie2 |
| Pilon version 1.24 | Walker et al. (2014) | https://github.com/broadinstitute/pilon |
| JBrowse2 version 2.1.0 | Hershberg et al. (2021) | https://jbrowse.org/jb2/download/ |
| Prokka version 1.14.6 | Seemann (2014) | https://github.com/tseemann/prokka |
| eggNOG-mapper version 2.1.3 | Huerta-Cepas et al. (2017), 2019 | https://github.com/eggnogdb/eggnog-mapper |
| KEGG mapper | Kanehisa and Sato (2020) | https://www.genome.jp/kegg/mapper/ |
| circlize version 0.4.15 | Gu et al. (2014) | https://cran.r-project.org/web/packages/circlize/index.html |
| gggenes version 0.4.1 | Wilkins and Kurtz (2019) | https://github.com/wilkox/gggenes |
| TrimAL version 1.4.rev15 | Capella-Gutiérrez et al. (2009) | https://vicfero.github.io/trimal/ |
| ModelTest-NG version 0.1.6 | Darriba et al. (2020) | https://github.com/ddarriba/modeltest |
| RAxML-NG version 1.0.3 | Kozlov et al. (2019) | https://github.com/amkozlov/raxml-ng |
| OrthoFinder version 2.5.2 | Emms and Kelly (2019) | https://github.com/davidemms/OrthoFinder |
| FigTree version 1.4.4 | Institute of Evolutionary Biology, University of Edinburgh, Edinburgh | http://tree.bio.ed.ac.uk/software/figtree/ |
| Jalview version 2.11.0 | Waterhouse et al. (2009) | http://www.jalview.org/getdown/release/ |
| FIJI | Schindelin et al. (2012) | https://imagej.net/software/fiji/ |
| R version 4.2.0 | R Core Team (2021) | https://www.r-project.org/ |
| ggplot2 version 3.3.6 | Wickham, 2016 | https://ggplot2.tidyverse.org/ |
| Python version 3.9.1 | Python Software Foundation | https://www.python.org/ |
Official websites use .gov
A
.gov website belongs to an official
government organization in the United States.
Secure .gov websites use HTTPS
A lock (
) or https:// means you've safely
connected to the .gov website. Share sensitive
information only on official, secure websites.