MSc Thesis Genome Annotation Data for non-Saccharomyces yeast and microalgal species

This repository contains data from my MSc thesis in Bioinformatics and Computational Biology: “Improving the genome annotations of non-Saccharomyces yeast and microalgal species.” The study focuses on generating high-quality genome annotations for: Torulaspora delbrueckii LO544 Lachancea thermotolerans IWBT Y1240 Chlorella sorokiniana These species, with wine-related origins, play important roles in wine fermentation and winery wastewater biotechnology. Despite the availability of genomic data, recent annotation data for these strains is lacking, limiting the exploitation of other omics datasets and their biotechnological potential. This work aimed to address that gap by producing improved genome annotations. The bioinformatics pipeline in this study assembles transcriptomes, evaluates sequencing data quality, and performs structural and functional annotation using MAKER and eggNOG-mapper. It also validates the improved annotations via differential gene expression and functional enrichment to assess biological relevance. Contents Structural Annotations (MAKER): Final consensus GFF3 files Evidence alignments Combined evidence + annotation files BUSCO scores and genome annotation statistics Functional Annotations (eggNOG-mapper): XLSX reports with predicted protein names, PFAM domains, GO terms, KEGG pathways and modules, and COG functional categories Validation Analysis (only tested on the Torulaspora delbrueckii strain): Differential gene expression (DESeq2 results) DEG visualizations GO and KEGG enrichment graphs Significance These resources provide a foundation for future experimental and bioinformatics research aimed at leveraging the biotechnological applications of non-Saccharomyces yeasts and microalgal species.