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Pipeline publication

[…] were amplified using LR-N-13398 CGCCTGTTTATCAAAAACAT and LR-J-13007 TTACGCTGTTATCCCTAA under conditions previously described , . Since no comparable P. simplex barcode was available, we also barcoded P. simplex from eight other independent isolations (University of Florida Termite collection accessions FL2476, FL1793, PR348, BA2814, BZ87, GUA615, HN24, and HN700) from Florida, Puerto Rico, Bahamas, Belize, Guatemala, and Honduras (the latter three being new regional and country records for this species). These new barcodes were submitted to GenBank under accessions KC140183-90. These were aligned with all available Paraneotermes and Reticulitermes mt LSU termite barcodes from Genbank using MAFFT , and refined by eye using SeaView . Poorly aligned regions were automatically removed with trimAl using a gap threshold of 0.9 . AIC weight as calculated with the perl script MrAIC.pl was used to determine the evolutionary model that best fit the data, which corresponded to GTR+Γ+I in all cases. For the termite phylogeny, Maximum Likelihood (ML) estimation was carried out using PhyML 3.0 with statistical support inferred from 1000 bootstrap replicates., Whole termite guts were dissected in Trager medium U . Light microscopy was performed on living cells using a Zeiss Axioplan 2 compound microscope using differential interference contrast (DIC) optics. Image capture was carried out using a Canon XL-M1S, from which stills were captured and HD video archived., For scanning electron microscopy (SEM), whole hindgut contents were mounted on a poly-L-lysin coated coverslip, then fixed in 2.5% glutaraldehyde (v/v; final concentration) diluted in Trager's medium U overnight at 4°C. Samples were dehydrated using a graded ethanol series and critical point dried in a Tousimis […]

Pipeline specifications

Software tools MAFFT, SeaView, trimAl, PhyML
Organisms Nitrosomonas sp., Reticulitermes virginicus