Multi-locus (ITS, tef1, tub2) sequence alignments and maximum likelihood tree for Neoscytalidium dimidiatum causing postharvest fruit rot of mandarin in Türkiye

Sequence alignments, partition definition, tree files and figure underlying the multi-locus phylogenetic analysis of Neoscytalidium dimidiatum isolates obtained from mandarin (Citrus reticulata) fruits with postharvest decay collected in retail markets of Mardin Province, south-eastern Türkiye, in 2025. Three representative isolates (NdCf01, NdCf02, NdCf03) were sequenced at the internal transcribed spacer region (ITS) and at partial translation elongation factor 1-alpha (tef1) and β-tubulin (tub2) genes, and analysed with 39 reference strains of Neoscytalidium and of related genera of the Botryosphaeriaceae. Each locus was aligned with MAFFT v7.526 (L-INS-i) and trimmed at both ends to the block covered by at least 90% of the sequences, giving a concatenated matrix of 42 strains and 1,212 characters (ITS 523 bp, tef1 279 bp, tub2 410 bp; 281 variable, 135 parsimony-informative sites). A partitioned maximum likelihood analysis was run in IQ-TREE v3.1.3 with per-locus models selected by ModelFinder under the Bayesian information criterion (ITS K2P, tef1 HKY+F+G4, tub2 TN+F+I), 1,000 ultrafast bootstrap replicates and 1,000 SH-aLRT replicates, rooted with Diplodia seriata CBS 112555. GenBank accession numbers of the sequences generated in this study: NdCf01 – ITS QB053253, tef1 QB058515, tub2 QB058518; NdCf02 – ITS QB053254, tef1 QB058516, tub2 QB058519; NdCf03 – ITS QB053255, tef1 QB058517, tub2 QB058520. The sequences in this deposit are identical to these GenBank records. The deposit contains the unaligned input sequences, the untrimmed and trimmed per-locus alignments, the concatenated matrix and partition file, the ML and consensus trees with SH-aLRT and ultrafast bootstrap support, the full IQ-TREE report and log, a table of all 42 strains with GenBank accession numbers, and the phylogenetic figure in SVG and 600 dpi PNG. Exact command lines, software versions and the random seed are given in README.md, together with a note on how far a multi-threaded IQ-TREE run is repeatable. Species names in the strain table follow the current synonymy of N. dimidiatum; many reference records still carry earlier names in GenBank (N. hyalinum, Scytalidium hyalinum, N. novaehollandiae, N. hylocereum). Note: GenBank record EU673110, sometimes used as an ITS sequence of Lasiodiplodia theobromae CBS 164.96, is a β-tubulin sequence; AY640255 is used here instead. Supplementary data to the manuscript: Tekin, F., Özer, G., Türkkan, M., Türkölmez, Ş. & Derviş, S. Neoscytalidium dimidiatum causing postharvest fruit rot of mandarin in Türkiye, with experimental pathogenicity to selected citrus fruits (in preparation). When the article appears it will be linked from this record under "Related works".