Computational protocol: Diversity of culturable bacteria including Pantoea in wild mosquito Aedes albopictus

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Protocol publication

[…] Both strands of 16S rDNA amplified from isolates representative of each ARDRA profile were sequenced at Biofidal-DTAMB (FR Bio-Environment and Health, Lyon, France). Sequences were manually curated and assembled from forward and reverse primer-generated sequences. Curated sequences were then compared to available bacterial sequences in GenBank using the BLASTn program in the National Center for Biotechnology Information (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The Ribosomal Database Project II Chimera Check was used (http://wdcm.nig.ac.jp/RDP/html/analyses.html) to discard any chimeric sequences.Phylogenetic analyses were performed on a set of Pantoea sequences. Sequences of 16S rRNA genes from Pantoea isolates from mosquitoes were compared to all available sequences of Pantoea retrieved from GenBank that originated from other insect species and environments. Sequences were aligned using ClustalW then corrected manually using Bioedit software []. The resulting alignment was used to construct a maximum-likelihood tree using Seaview v.4.2.12. (http://pbil.univ-lyon1.fr/software/seaview.html). The tree topology was tested by bootstrap analysis with 1,000 resamplings. […]

Pipeline specifications

Software tools BLASTN, Clustal W, BioEdit, SeaView
Databases WDCM
Application Phylogenetics
Organisms Aedes albopictus