DOI: 10.5281/zenodo.6303649
title: Multiple sequence alignments: Detection and isolation of a new member of Burkholderiaceae-related endofungal bacteria from a new thermophilic species in Mucorales

description: <strong>Methods:</strong><br> Nucleotide sequences were aligned independently for each region using MAFFT v7.212 (Katoh and Standley, 2013). The obtained alignment blocks were subject to Gblocks 0.91b (Castresana, 2000) to remove poorly aligned positions with the relaxed selection setting described in Talavera & Castresana (2007) using the following parameters (-t = d -b2 = 9 -b3 = 10 -b4 = 5 -b5 = h). After automatically removing gaps, the alignment blocks were viewed using MEGA 6.06 software (Tamura et al., 2013) and poorly aligned positions at either end of the alignments were removed manually. Multiple sequence alignment of 16S rRNA gene of the family Burkholderiaceae was prepared for the phylogeny of a bacterial endosymbiont. Multiple sequence alignments of ITS, LSU, and tef1 genes of Saksenaea spp. (Mucorales) were separately prepared for the phylogeny of a fungal host. Concatenated dataset of these genes were also prepared. All nucleotide sequences were retrieved from GenBank (See "Sequence_ID.csv" and taxon names of each alignment). <strong>Files:</strong> <strong>A. Multiple sequence alignment of the family <em>Burkholderiaceae</em> (Bacterial endosymbiont):</strong> <strong>1. Burkholderiaceae_16S_RAW.fasta</strong> Non-aligned dataset of 16S rRNA gene of the family <em>Burkholderiaceae</em>. <strong>2. Burkholderiaceae_16S_aligned.fasta</strong> Aligned dataset of 16S rRNA gene of the family <em>Burkholderiaceae</em>. <strong>B. Multiple sequence alignments of <em>Saksenaea</em> spp. (Fungal host):</strong> <strong>1. Sequence_ID.csv</strong> Taxon names, accession numbers, and sequence ID for the concatenated multiple sequence alignment are listed. <strong>2. Saksenaea_ITS_RAW.fasta</strong> Non-aligned dataset of ITS region of <em>Saksenaea</em> spp. <strong>3. Saksenaea_ITS_aligned.fasta</strong> Aligned dataset of ITS region of<em> Saksenaea</em> spp. Only used for ITS phylogeny. <strong>4. Saksenaea_LSU_RAW.fasta</strong> Non-aligned dataset of LSU gene region of <em>Saksenaea</em> spp. <strong>5. Saksenaea_LSU_aligned.fasta</strong> Aligned dataset of LSU gene region of <em>Saksenaea</em> spp. Only used for LSU phylogeny. <strong>6. Saksenaea_tef1_for_concatenated_RAW.fasta</strong> Non-aligned dataset of tef1 gene region of<em> Saksenaea</em> spp. <strong>7. Saksenaea_tef1_for_concatenated_aligned.fasta</strong> Aligned dataset of tef1 gene region of <em>Saksenaea</em> spp. This dataset was used for the phylogeny of tef1 gene region and prepration of a concatenated dataset. <strong>8. Saksenaea_ITS_for_concatenated_RAW.fasta</strong> Non-aligned dataset of ITS region of <em>Saksenaea</em> spp. used for preparation of a concatenated dataset. <strong>9. Saksenaea_ITS_for_concatenated_aligned.fasta</strong> Aligned dataset of ITS region of <em>Saksenaea</em> spp. used for preparation of a concatenated dataset. <strong>10. Saksenaea_LSU_for_concatenated_RAW.fasta</strong> Non-aligned dataset of LSU gene region of <em>Saksenaea </em>spp. used for preparation of a concatenated dataset. <strong>11. Saksenaea_LSU_for_concatenated_aligned.fasta</strong> Aligned dataset of LSU gene region of <em>Saksenaea</em> spp. used for preparation of a concatenated dataset. <strong>12. Saksenaea_ITS_LSU_tef1_concatenated.fasta</strong> Concatenated dataset of three multiple sequence alignments (7, 9, and 11). This concatenated dataset was used for the main phylogeny of <em>Saksenaea </em>spp.