Computational protocol: A unique midgut-associated bacterial community hosted by the cave beetle Cansiliella servadeii (Coleoptera: Leptodirini) reveals parallel phylogenetic divergences from universal gut-specific ancestors

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Protocol publication

[…] Sequence chromatograms were visually inspected and sequences were edited and aligned by using MEGA 4.0.2 (http://www.megasoftware.net/).Chimeras were searched with the CHIMERA CHECK program of the Ribosomal Database Project II (http://rdp.cme.msu.edu).A BLASTN GenBank analysis of all the sequences was done through the NCBI website (http://www.ncbi.nlm.nih.gov/) and closely related sequences from the databases were retrieved and added to the alignment. Phylogenetic relationships among newly retrieved gut microbiota sequences to close relatives were estimated using a maximum likelihood analysis (ML) with a GTR+I+G model.The software package DOTUR [] was used to assign sequences to operational taxonomic units (OTUs) for the bacterial identities found in the midgut of C. servadeii. This program assigns sequences to OTUs based on sequence data by using values that are less than the cut-off level, which were at the 97% and 95% identity thresholds. The Chao1 richness estimator [] was also calculated using DOTUR. The richness estimates are reported for 3% difference between sequences.16S rRNA gene sequences of clones from the guts of C. servadeii are accessible under numbers JQ308110 to JQ308155 and from JX463074 to JX463100.The sequences from the culturable microbial community from the midgut and the external tegument are accessible under numbers JQ308156 to JQ308165. […]

Pipeline specifications

Software tools MEGA, BLASTN, DOTUR
Applications Phylogenetics, 16S rRNA-seq analysis