THE FIRST MITOCHONDRIAL GENOME FROM A HEMIUROID (DIDYMODICLINUS SP. FROM PUERTO RICO) HIGHLIGHTS PHYLOGENETIC VOLATILITY.
Description
Alignments of mitochondrial and nuclear DNA markers for phylogenetic analyses to identify a juvenile didymozoid trematode.
Files
Steps to reproduce
Sequence selection - DNA sequences were retrieved from Didymozoidae taxa available in GenBank selecting for the following minimum lengths: 28S ≥ 800bp 18S ≥ 1000bp CO1 (barcoding and post-barcoding) ≥ 400bp ITS2 ≥ 300bp Mitogenome and operon sequences were selected based on availability at the time of analysis. Sequences were aligned using ClustalOmega 1.2.2 (Sievers et al., 2011). Mitogenome, operon, 18S, and all CO1 regions were stripped entirely of gaps. 28S and ITS2 alignments are available without gaps stripped and with partially stripped gaps using the tool BMGE (Criscuolo and Gribaldo, 2010) with default parameters. All steps were performed through Geneious Prime (Huelsenbeck and Ronquist, 2001) except BMGE trimming. BMGE (v2.0) was run via command line using the guide provided by Criscuolo and Gribaldo (2011) in the following link: https://gensoft.pasteur.fr/docs/BMGE/1.12/BMGE_doc.pdf Sample command format showcased below java -jar BMGE.jar -i input.fasta -o output.fasta -t DNA
Institutions
- University of Puerto Rico Mayaguez Research and Development Center