16S rDNA sequencing data for characterizing the endosymbionts of leaf curl plum aphid ( Brachycaudus helichrysi) clones

# 16S rDNA sequencing data for characterizing the endosymbionts of leaf curl plum aphid ( Brachycaudus helichrysi) clones [https://doi.org/10.5061/dryad.zpc866tgn](https://doi.org/10.5061/dryad.zpc866tgn) The data set contains raw reads resulting from the illumina sequencing of a fragment of 16S rDNA gene on a world wide Brachycaudus helichrysi sampling. A total of 102 individuals, representative of six *B. helichrysi* clones and the diversity of their geographic distribution were used for characterising bacterial endosymbionts. Using DNA extracts from the same individuals utilised for microsatellite genotyping in Piffaretti et al. (2013) or Popkin et al. (2017), we amplified a 251 bp portion of the V4 region of the 16S rRNA gene (Mizrahi-Man et al. 2013) and used targeted sequencing of indexed bacterial fragments on a MiSeq (Illumina) platform (Kozich et al. 2013) following the protocol described in Jousselin et al. (2016). Each DNA sample was amplified twice (replicates were conducted on distinct 96-well microplates). We also used negative controls (DNA extraction and PCR controls conducted on blank templates) to filter out bacterial contamination during laboratory procedures. A total of 216 PCR products (comprising DNA extracts and controls) were obtained, pooled, and then separated by gel electrophoresis. Bands based on the expected size of the PCR products were excised from the gel, purified with a PCR clean-up and gel extraction kit (Macherey-Nagel), and quantified with the Kapa Library Quantification Kit (Kapa Biosystems). Paired-end sequencing of the DNA pool was carried out on a MISEQ (Illumina) FLOWCELL with a 500-cycle Reagent Kit v2 (Illumina). Sequencing reads of DNA extraction and PCR controls are also provided ## Description of the data and file structure Sequencing Reads are demultiplexed by individuals. Each fast.gz file corresponds to the sequencing of a pcr product: extension "L001_R1_001" corresponds to sequencing using forward primers, and extension "L001_R2_001" corresponds to the sequencing using reverse primer. PCR protocol is described above. Each individual has been amplified twice (i.e. file extension "-BIS" corresponds to a PCR replicate . Sample description (i.e sample name with collection details : date of collection, host plant association, clone identify, locality) is given in a table attached to this submission (and also Appendix S3 of the paper). ## Code/Software FROGS pipeline (Escudié et al. 2018) have been used to generate an abundance table of symbiont lineages across samples given as a supplemntary material of the paper. References Escudié, F., Auer, L., Bernard, M., Mariadassou, M., Cauquil, L., Vidal, K., Maman, S., Hernandez-Raquet, G., Combes, S. and Pascal, G. 2018. FROGS: find, rapidly, OTUs with galaxy solution. - Bioinformatics 34: 1287–1294. Jousselin, E., Clamens, A.-L., Galan, M., Bernard, M., Maman, S., Gschloessl, B., Duport, G., Meseguer, A. S., Calevro, F. and Coeur D’Acier, A. 2016. Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus. - Mol Ecol Resour 16: 628–640. Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. and Schloss, P. D. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. - Appl Environ Microbiol 79: 5112–5120. Mizrahi-Man, O., Davenport, E. R. and Gilad, Y. 2013. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. - PLoS One 8: e53608. Piffaretti, J., Clamens, A.-L., Vanlerberghe-masutti, F., Gupta, R. K., Call, E., Halbert, S. and Jousselin, E. 2013a. Regular or covert sex defines two lineages and worldwide superclones within the leaf-curl plum aphid (*Brachycaudus helichrysi*, Kaltenbach). - Mol Ecol 22: 3916–3932. Popkin, M., Piffaretti, J., Clamens, A.-L., Qiao, G.-X., Chen, J., Vitalis, R., Vanlerberghe-Masutti, F., Gupta, R. K., Lamaari, M., Langella, O. and others 2017. Large-scale phylogeographic study of the cosmopolitan aphid pest *Brachycaudus helichrysi* reveals host plant associated lineages that evolved in allopatry. - Biological Journal of the Linnean Society 120: 102–114.