Assembled transcriptomes from two <i>Hanseniaspora </i>species:<i> H. occidentalis</i> var. <i>occidentalis </i>and<i> H. uvarum</i>

Triplicate cultures of Hanseniaspora occidentals var. occidentals and Hanseniaspora uvarum were grown for 18 hours in 20 ml rich YPD medium (yeast extract, peptone, 2% glucose) in a room-temperature shaker at 250 rpm. Cell pellets were flash-frozen and stored at -80oC. mRNA was isolated using the NEBNext Poly(A) mRNA Magentic Isolation Module (NEB) with the NEBNext Ultra II Directional RNA Library Prep kit (NEB). One of the three H. occidentals var. occidentals libraries failed, leaving only two replicates for sequencing. Sequencing was performed at the University of Wisconsin-Madison Biotechnology Center. Paired-end reads were trimmed and deduplicated using fastp v.0.20.1. A guided assembly was conducted using HISAT2 v2.2.1 to align the sequence reads against their respective reference draft genomes, both of which were retrieved from the Y1000+ Project. The resulting alignment files were processed through Stringtie v2.2.1 for transcript annotation from their respective reference species annotation files, followed by extracting the protein-coding sequences from the reference genomes of each replicate annotation file into FASTA files using TransDecoder v5.5.0. Codon usage data was calculated using DAMBE v7.3.32 Files H_occ-YPD-replicate-1.CDS.fasta - Hanseniaspora occidentals var. occidentals assembled transcriptome replicate 1H_occ-YPD-replicate-2.CDS.fasta - Hanseniaspora occidentals var. occidentals assembled transcriptome replicate 2H_uv-YPD-replicate-1.CDS.fasta - Hanseniaspora uvarum assembled transcriptome replicate 1H_uv-YPD-replicate-2.CDS.fasta - Hanseniaspora uvarum assembled transcriptome replicate 2H_uv-YPD-replicate-3.CDS.fasta - Hanseniaspora uvarum assembled transcriptome replicate 3H_occ-YPD-replicate-1.CDS.count.out - Hanseniaspora occidentals var. occidentals transcriptome codon counts replicate 1H_occ-YPD-replicate-2.CDS.count.out - Hanseniaspora occidentals var. occidentals transcriptome codon counts replicate 2H_uv-YPD-replicate-1.CDS.count.out - Hanseniaspora uvarum transcriptome codon counts replicate 1H_uv-YPD-replicate-2.CDS.count.out - Hanseniaspora uvarum transcriptome codon counts replicate 2H_uv-YPD-replicate-3.CDS.count.out - Hanseniaspora uvarum transcriptome codon counts replicate 3The codon transcriptome counts have 1 transcript per row and 1 codon per column. The numbers are the raw counts for each codon in that transcript