Multiple sequence alignments: Detection and isolation of a new member of Burkholderiaceae-related endofungal bacteria from a new thermophilic species in Mucorales
Authors/Creators
- 1. Sugadaira Research Station, Mountain Science Center, University of Tsukuba
- 2. Tochigi Prefectural Museum
- 3. Ibaraki University College of Agriculture
- 4. Ibaraki University
Description
Methods:
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).
Files:
A. Multiple sequence alignment of the family Burkholderiaceae (Bacterial endosymbiont):
1. Burkholderiaceae_16S_RAW.fasta
Non-aligned dataset of 16S rRNA gene of the family Burkholderiaceae.
2. Burkholderiaceae_16S_aligned.fasta
Aligned dataset of 16S rRNA gene of the family Burkholderiaceae.
B. Multiple sequence alignments of Saksenaea spp. (Fungal host):
1. Sequence_ID.csv
Taxon names, accession numbers, and sequence ID for the concatenated multiple sequence alignment are listed.
2. Saksenaea_ITS_RAW.fasta
Non-aligned dataset of ITS region of Saksenaea spp.
3. Saksenaea_ITS_aligned.fasta
Aligned dataset of ITS region of Saksenaea spp. Only used for ITS phylogeny.
4. Saksenaea_LSU_RAW.fasta
Non-aligned dataset of LSU gene region of Saksenaea spp.
5. Saksenaea_LSU_aligned.fasta
Aligned dataset of LSU gene region of Saksenaea spp. Only used for LSU phylogeny.
6. Saksenaea_tef1_for_concatenated_RAW.fasta
Non-aligned dataset of tef1 gene region of Saksenaea spp.
7. Saksenaea_tef1_for_concatenated_aligned.fasta
Aligned dataset of tef1 gene region of Saksenaea spp. This dataset was used for the phylogeny of tef1 gene region and prepration of a concatenated dataset.
8. Saksenaea_ITS_for_concatenated_RAW.fasta
Non-aligned dataset of ITS region of Saksenaea spp. used for preparation of a concatenated dataset.
9. Saksenaea_ITS_for_concatenated_aligned.fasta
Aligned dataset of ITS region of Saksenaea spp. used for preparation of a concatenated dataset.
10. Saksenaea_LSU_for_concatenated_RAW.fasta
Non-aligned dataset of LSU gene region of Saksenaea spp. used for preparation of a concatenated dataset.
11. Saksenaea_LSU_for_concatenated_aligned.fasta
Aligned dataset of LSU gene region of Saksenaea spp. used for preparation of a concatenated dataset.
12. Saksenaea_ITS_LSU_tef1_concatenated.fasta
Concatenated dataset of three multiple sequence alignments (7, 9, and 11). This concatenated dataset was used for the main phylogeny of Saksenaea spp.
Files
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