Supplemental Material for Franco Ortega et al., 2025
Hibrid genome= ONT + Illumina
Chloroplast and mitochondrial genomes were assembled using CANU (version 2.1.1) and polished using RACON version 1.4.20 and MEDAKA version 1.0.3. (Files=Mitochondria_F.excelsior_2451S.fasta, Chloroplast_F.excelsior_2451S.fasta)
Both chloroplast and mitochondria genomes were annotated using MPI-MP Chlorobox GeSeq tool (Files=Mitochondria_F.excelsior_2451S.annotation.CDS, Mitochondria_F.excelsior_2451S.annotation.gff3, Mitochondria_F.excelsior_2451S.annotation.gtf,Mitochondria_F.excelsior_2451S.annotation.proteins.fasta;Chloroplast_F.excelsior_2451S.annotation.CDS,Chloroplast_F.excelsior_2451S.annotation.gff3, Chloroplast_F.excelsior_2451S.annotation.gtf,Chloroplast_F.excelsior_2451S.annotation.proteins.fasta )
Genome with the reads that did not map against the chloroplast or mitochondria were assembled using CANU. PURGE HAPLOTIGS was used to phase the genome and then it was polished using Illumina reads (ERR1399574; Sollars et al., 2016) with PILON version 1.24 (Walker et al., 2014) (File=F.excelsior_ONT.genome.fasta)
Annotation was done with REPEATMODELER (version 2.1) and REPEATMASKER(version 2.1) to masked the genome and then de-novo gene models were retrieved with BRAKER (version 1.9) using the 5 mRNA-Seq samples previously published and belonging to roots (ERR1399494), cambium (ERR1399492), leaves (mother tree and 2461s, ERR1399495, ERR1399573) and flowers (ERR1399493). TSEBRA with default configuration was used to combine the results of both proteins (viridiplantae) and mRNA-Seq predictions.
GFACS (Version 1.1.2) + ENTAP (Hart et al., 2020) + EGGNOGG (Huerta-Cepas et al., 2019) were used for functional characterization of the gene models. (Files= F.excelsior.annotation.cds, F.excelsior.annotation.pep, F.excelsior_ONT_annotation.gff3, F.excelsior_ONT_annotation.gtf, F.excelsior_ONT_funtional.annotations)
Transposable elements (TE) and tandem repeats were identified using the Extensive de-novo TE Annotator (EDTA) (F.excelsior_ONT.fasta.mod.EDTA.TEanno.gff3)
Methylation was called with nanopolish (version 0.13.2) (File=GSE214553_all_methylation_data_genome_Ash_complete_NEW.tsv.gz, GSE214553_all_methylation_data_genome_Ash_frequency_complete_new.tsv.gz)
Pseudochromosomes against F. pennsylvanica genome (Huff et al., 2022), were created using NTJOIN (version 4.2.1) + NUCMER version 3.1 (Files= contig_to_ntJoin.txt, F.excelsior_ONT_contig_pseudochromosomes.agp, F.excelsior_ONT_contigs_assigned_pseudochromosomes.fa ---> contigs assigned into pseudochromosomes; Files =F.excelsior_ONT_contigs_not_assigned.fa & contigs assigned into pseudochromosomes.agp---> contigs NOT assigned into pseudochromosomes
We remapped the transcriptomic data of a Danish ash population of 182 trees from Harper et al. 2016, aginst this genome. Salmon was also used to obtain TPMs using this genome as reference. We used these outputs to perform associative transcriptomic and idenitiy gene associated markers to ash dieback tolerance.
