DOI: 10.5061/dryad.0k6djhb89
title: Data from: Repeated loss of function at HD mating-type genes and of recombination suppression without mating-type locus linkage in anther-smut fungi

description: A wide diversity of mating systems occur in nature, with frequent
 evolutionary transitions in mating-compatibility mechanisms. Basidiomycete
 fungi typically have two mating-type loci controlling mating
 compatibility, HD and PR, usually residing on different chromosomes. In
 Microbotryum anther-smut fungi, there have been repeated events of linkage
 between the two mating-type loci through chromosome fusions, leading to
 large non-recombining regions. By generating high-quality genome
 assemblies, we found that two sister Microbotryum species parasitizing
 Dianthus plants, M. superbum and M. shykoffianum, as well as the distantly
 related M. scorzonarae, have their HD and PR mating-type loci on different
 chromosomes, but with the PR mating-type chromosome fused with part of the
 ancestral HD chromosome. Furthermore, progressive extensions of
 recombination suppression have generated evolutionary strata. In all three
 species, rearrangements suggest the existence of a transient stage of
 HD-PR linkage by whole chromosome fusion, and, unexpectedly, the HD genes
 lost their function. In M. superbum, multiple natural diploid strains were
 homozygous, and the disrupted HD2 gene was hardly expressed. Mating tests
 confirmed that a single genetic factor controlled mating compatibility
 (i.e. PR) and that haploid strains with identical HD alleles could mate
 and produce infectious hyphae. The HD genes have therefore lost their
 function in the control of mating compatibility in these Microbotryum
 species. While the loss of function of PR genes in mating compatibility
 has been reported in a few basidiomycete fungi, these are the first
 documented cases for the loss of mating-type determination by HD genes in
 heterothallic fungi. The control of mating compatibility by a single
 genetic factor is beneficial under selfing and can thus be achieved
 repeatedly, through evolutionary convergence in distant lineages,
 involving different genomic or similar pathways.
description: <strong>Read mapping and
 quantification</strong> Reference genome matching
 reads were obtained with bbduk from bbmap [Ref:https://sourceforge.net/projects/bbmap/] with deffault options for quality and adapter trimming. Matching reads were mapped back to the reference genome with STAR 2.7.11a [Ref:https://doi.org/10.1093/bioinformatics/bts635] with the deffault options for paired end reads. Reads with inserts larger than 5 kbp were filtered out. Read counts by transcript feature were obtained with featureCounts from subread 2.0.2 suite [Ref:https://doi.org/10.1093/bioinformatics/btt656].  <strong>Trans-specific polymorphism</strong> Gene trees were obtained with IQ-TREE 2.2.6 based on macse v2.05 codon-based alignments. Gene trees were midpoint rooted with gotree [Ref:https://doi.org/10.1093/nargab/lqab075] and subtrees containing the <em>M. shykoffianum</em> and <em>M. superbum</em> A1 alleles recovered with nw_clade from Newick utils [Ref: https://doi.org/10.1093/bioinformatics/btq243]. If the subtree contains a single branch connecting only two tips it means that A1 alleles were recovered as monophyletic (i.e. displaying transpecific polymorphism), we repeated the procedure for the A2 alleles and counted the number trees showing full (both alleles recovered as monophyletic clades) or partial (either A1 or A2 were recovered as monophyletic) transpecific polymorphism. Gene trees in which neither A1 nor A2 were recovered as monophyletic were collated as "Other" topologies, often following the species phylogeny (i.e. alternative alleles from the same species clustered together, <em>M. superbum</em> and <em>M. shykoffianum</em> being recovered as sister clades).
description: # Data from: Repeated loss of function at HD mating-type genes and of
 recombination suppression without mating-type locus linkage in anther-smut
 fungi ## Data description This repository includes three types of data
 associated with [Lucotte et al.,
 2025](https://doi.org/10.1101/2024.03.03.583181). 1. Genome assemblies and
 annotation. 2. RNAseq quantification to explore HD expression. 3. Gene
 trees to explore transpecific polymorphism in non recombining regions. ##
 Files and variables ### FILES #### File: MPbarcode50.fa **Description:**
 Whole genome assembly in fasta format obtained with flye from ONT reads of
 an haploid sample. #### File: Mscorzo-A1\_renamed.fa **Description:**
 Whole genome assembly in fasta format obtained with canu from ONT reads of
 an haploid sample. #### File: Mscorzo-A2\_renamed.fa **Description:**
 Whole genome assembly in fasta format obtained with canu from ONT reads of
 an haploid sample. #### File: Mv-cat-C212-A1.fa **Description:** Whole
 genome assembly in fasta format obtained with hifiasm from HiFi reads of a
 diploid sample (haplotype 2). #### File: Mv-cat-C212-A2.fa
 **Description:** Whole genome assembly in fasta format obtained with
 hifiasm from HiFi reads of a diploid sample (haplotype 1). #### File:
 Mv-sup-1065-A1.fa **Description:** Whole genome assembly in fasta format
 obtained with canu from HiFi reads of an haploid sample. #### File:
 Mv-sup-1065-A2.fa **Description:** Whole genome assembly in fasta format
 obtained with canu from HiFi reads of an haploid sample. #### File:
 Mv-lyc-1064\_impuntedMAT\_region\_gene.gtf **Description:** General
 Transfer Format (gtf). Nine columns, tab separated #### File:
 MPbarcode50\_tsebra.gtf **Description:** General Transfer Format (gtf).
 Nine columns, tab separated #### File:
 featurecounts\_noLinsert\_a1a2\_mated\_48-1\_on\_Mv-lyc-1064-A2\_A1impMAT
 **Description:** Fractional read mapping per gene feature. Seven columns,
 tab separated. #### File:
 featurecounts\_noLinsert\_a1a2\_mated\_48-2\_on\_Mv-lyc-1064-A2\_A1impMAT
 **Description:** Fractional read mapping per gene feature. Seven columns,
 tab separated. #### File: featurecounts\_noLinsert\_A\_on\_MPbarcode50flye
 **Description:** Fractional read mapping per gene feature. Seven columns,
 tab separated. #### File: featurecounts\_noLinsert\_B\_on\_MPbarcode50flye
 **Description:** Fractional read mapping per gene feature. Seven columns,
 tab separated. #### File: featurecounts\_noLinsert\_C\_on\_MPbarcode50flye
 **Description:** Fractional read mapping per gene feature. Seven columns,
 tab separated. #### File: gene\_trees **Description:** Two columns file
 with stratum imputation and gene tree in newick format #### File:
 speciestree.tre **Description:** Newick format ### DATA DESCRIPTION Each
 `*gtf` has nine tab separated columns as follows, see [GFF/GTF
 specification](https://www.ensembl.org/info/website/upload/gff.html) 1.
 **seqname** - name of the chromosome or scaffold; chromosome names can be
 given with or without the 'chr' prefix. 2. **source** - name of
 the program that generated this feature, or the data source (database or
 project name) 3. **feature** - feature type name, e.g. Gene, Variation,
 Similarity 4. **start** - Start position* of the feature, with sequence
 numbering starting at 1. 5. **end** - End position* of the feature, with
 sequence numbering starting at 1. 6. **score** - A floating point value.
 7. **strand** - defined as + (forward) or - (reverse). 8. **frame** - One
 of '0', '1' or '2'. '0' indicates
 that the first base of the feature is the first base of a codon,
 '1' that the second base is the first base of a codon, and so
 on.. 9. **attribute** - A semicolon-separated list of tag-value pairs,
 providing additional information about each feature. Each `featurecounts*`
 file has seven tab separate columns as follows. Command used is recorded
 in the first row, columns names are defined in the second row and data
 starts at the third row. 1. **Geneid** - Gene/transcript identifier as in
 the **attribute** column of the `gtf` file 2. **Chr** - Assembled
 pseudomolecule identifier as in the **seqname** column of the `gtf` file
 3. **Start** - Semicolon separated list of CDS features **start**
 positions 4. **End** - Semicolon separated list of CDS features **end**
 positions 5. **Strand** - defined as + (forward) or - (reverse) 6.
 **Length** - Sum length of the CDS features associated to the same
 **Geneid** 7. \ - Total fractional read counts across the
 feature ## Code/software #### Genome assembly * `Mscorzo-A[12]_renamed.fa
 canu 1.7b` with default parameters on ONT reads * `Mv-cat-C212-A[12].fa
 hifiasm 0.16.1-r375` with default parameters on HiFi reads *
 `Mv-sup-1065-A[12].fa canu 2.2` with `-pacbio-hifi` parameter on HiFi
 reads * `MPbarcode50.fa flye 2.9.4-b1799` with `-g 48.7m -i 3 --nano-raw`
 parameters on ONT reads #### Genome annotation Whole genome shotgun
 assemblies were annotated with Braker2 based on RNAseq or conserved
 proteins evidence and combined with TSEBRA. Genome annotation workflow
 correspond to **Step I** described
 [here](https://github.com/QuentinRougemont/EASYstrata?tab=readme-ov-file#operations-of-step-i-te-and-gene-prediction). #### RNAseq quantification Fractional read counts per transcript feature were summarized with `featureCounts` from `subread` package, based on `STAR 2.7.11a` read alignments. Specific commands are recorded at the first row of each `featurecounts*` file. #### Phylogenetic trees Species (concatenation of monocopy genes alignments) and individual gene trees were obtained with `IQTree2 2.2.6` and processed as described in the methods section of this repository (`gotree` and `newick_utils`). ## Access information Other publicly accessible locations of the data: * Additional custom scripts are available at [https://github.com/eliselucotte/MicrobotryumOnDianthus](https://github.com/eliselucotte/MicrobotryumOnDianthus) * Additional data, including SRA with WGS and RNAseq reads, can be found at GenBank associated to BioProjects [PRJNA1169769](https://www.ncbi.nlm.nih.gov/bioproject/1169769), [PRJNA1206992](https://www.ncbi.nlm.nih.gov/bioproject/1206992) and [PRJNA1206994](https://www.ncbi.nlm.nih.gov/bioproject/1206994) Data was derived from the following sources: * Previously obtained RNAseq data is available at BioProject [PRJNA246470](https://www.ncbi.nlm.nih.gov/bioproject/246470)