Integrated data-driven reannotation of the Kluyveromyces marxianus genome reveals an expanded protein coding repertoire

Many new biotechnology applications make use of non-traditional yeast species that possess characteristics and traits that are advantageous in specific settings. To a large extent, this is possible because of advances in molecular and genomic technologies that provide opportunities to study and manipulate the genomes of diverse yeasts. There remains, however, a substantial gap between what we know about well-studied models versus emerging industrial yeast species. In this study, we applied a multi-faceted omics analysis to better understand organisation of protein coding gene expression in Kluyveromyces marxianus , a yeast widely used in food and industrial biotechnology. We combined advanced transcriptomic techniques for mapping 5' and 3' ends of RNA transcripts with ribosome profiling to explore the transcriptional and translational landscapes of this yeast. This allowed us to improve the genome annotation and identify over 300 un-annotated or mis-annotated genes. We discovered numerous examples of novel proteoforms due to use of alternative transcription or translation start sites, many genes with translated upstream open reading frames (uORFs), and a novel case of programmed ribosomal frameshifting. Only some of newly discovered features are shared with distant species, for example, being present in Saccharomyces cerevisiae orthologs. The exploration of shared and unique features may provide an insight into the evolution of gene regulation in pre- and post- WGD yeasts. The processed data has been made available on the GWIPS-viz and Trips-Viz browsers, thus providing an accurate data-driven annotation of transcripts and their protein coding regions along with quantitative information on their transcription and translation. ### Competing Interest Statement Pavel Baranov (P.V.B.) and Audrey Michel (A.M.) are co-founders of RiboMaps Ltd, a company which provides ribosome profiling as a service