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Data from: The complete mitochondrial genome of Laetiporus ailaoshanensis (Laetiporaceae, Basidiomycota): features, evolution, and phylogeny

Ma, Jinxin1

Published May 11, 2026 on Dryad. https://doi.org/10.5061/dryad.xsj3tx9v4

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Abstract

This study selected the mitochondrial genomes of 46 species. Using the MAFFT version 7.471 software [1], the protein-coding genes (PCGs) of these mitochondrial genomes were extracted and aligned. The alignments were refined with MACSE version 2 [2] and trimmed using Gblocks [3]. The resulting gene alignments were concatenated, and PartitionFinder version 2.1.1 [4] was used to determine the best partitioning schemes and evolutionary models. Phylogenetic relationships were constructed using MrBayes version 3.2 and IQ-TREE, employing Bayesian inference (BI) and maximum likelihood (ML) methods [5, 6]. All analyses were performed within the PhyloSuite platform [7], and the resulting phylogenetic trees were annotated and visualized using the iTOL web tool (https://itol.embl.de/) [8].

1. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772−80. https://doi.org/10.1093/molbev/mst010.

2. Ranwez V, Douzery EJP, Cambon C, Chantret N, Delsuc F. MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons. Mol Biol Evol. 2018;35(10):2582−4. https://doi.org/10.1093/molbev/msy159.

3. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56(4):564−77. https://doi.org/10.1080/10635150701472164.

4. Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 2017;34(3):772−3. https://doi.org/10.1093/molbev/msw260.

5. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61(3):539−42. https://doi.org/10.1093/sysbio/sys029.

6. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268−74. https://doi.org/10.1093/molbev/msu300.

7. Zhang D, Gao FL, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 2020;20(1):348−55. https://doi.org/10.1111/1755-0998.13096.

8. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2010;49(W1):W293−6. https://doi.org/10.1093/nar/gkab301.