DOI: 10.5061/dryad.zpc866tgn
title: 16S rDNA sequencing data for characterizing the endosymbionts of leaf curl plum aphid ( Brachycaudus helichrysi) clones

description: Asexual lineages often exhibit broad distributions and can thrive in
 extreme habitats compared to their sexual counterparts. Several hypotheses
 can be proposed to explain this pattern. Asexual lineages could be
 versatile genotypes with wide environmental tolerance, enabling their
 dispersal and persistence across large geographic areas. Alternatively,
 asexual genotypes could be ecological specialists that thrive in specific
 environments and outcompete relatives colonizing distantly related areas
 with similar conditions in the process. Several aphid species feature
 widespread obligate asexual lineages, commonly known as “superclones”. Yet
 it is often unknown whether these clones are widespead ecological
 generalists or  successful specialists. To explore these
 hypotheses, we examined climatic niche differentiation among six globally
 distributed obligate asexual lineages of the cosmopolitan aphid pest,
 Brachycaudus helichrysi. To insure that we were investigating the aphid
 genotype niche and not a by-product of their association with
 endosymbionts mediating thermal tolerance, we first verified that clones
 hosted similar endosymbiont communities. Subsequently, we conducted
 multivariate analyses on clone occurrence data on a worldwide scale. Our
 results revealed that despite their global distribution, B. helichrysi
 superclones occupy different climatic niches. This study represents the
 first evidence that aphid superclones distribution can be mediated by
 distinctive ranges of climatic tolerance.
description: This data results from the sequencing of a 251 bp fragment of the
 16S rDNA bacterial gene amplified in a worldwide sample of the leaf curl
 plum aphid pest (<em>Brachycaudus helichrysi</em>). The table
 with collection details is also attached to this data
 submission. A total of 102 individuals, representative
 of six aphid clones and the diversity of their geographic distribution
 were used for characterising bacterial endosymbionts. Using DNA extracts
 from the individuals utilised for microsatellite genotyping in Piffaretti
 et al. (2013), 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).
 Briefly, 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. After
 purification of PCR products 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). We first applied sequence ﬁltering criteria
 following Illumina’s quality control procedure. We then merged paired
 sequences into contigs with FLASH V.1.2.11 (Magoč and Salzberg 2011) and
 trimmed primers with CUTADAPT v.1.9.1 (Martin 2011). We then used the
 FROGS pipeline (Escudié et al. 2018)to generate an abundance table of
 symbiont lineages across samples. 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
 (<em>Brachycaudus helichrysi</em>, Kaltenbach). - Mol Ecol 22:
 3916–3932.
description: # 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.