Genomic and transcriptomic insights into Trichomonascus vanleenenianus, a xylan-degrading yeast isolated from saproxylic insect larvae

Abstract Studying microbial biodiversity offers enormous potential for improving the valorisation of plant biomass, particularly in conversion processes. Microorganisms, such as bacteria, fungi, yeasts and algae, play an essential role in degrading plant biomass and can be exploited to maximise the conversion of organic matter into valuable products. Of particular importance is the ability to use yeast strains that can degrade and utilise xylan. We sequenced and annotated the genome of a new strain of Trichomonascus vanleenenianus isolated from the gut of a saproxylic insect larva that exhibits this capacity. The genome of strain L1-24 (= CLIB 3782) was assembled into 116 nuclear scaffolds totaling 14.9 Mb. Comparative genomics analysis revealed that this species is phylogenetically closely related to the species Blastobotrys mokoenaii, Blastobotrys malaysiensis and Blastobotrys illinoisensis. Genome analysis revealed characteristics including a large number of spliceosomal introns (2,362 in the CDS of 1,706 genes and 176 in the UTRs) and the presence of all 5S rRNA genes arranged in tandem with tRNA genes. Protein prediction identified a total of 192 carbohydrate-active enzymes, many of which potentially act on plant cell wall polymers. Like the three other closely related species, T. vanleenenianus possesses the complete enzymatic repertoire necessary for the hydrolysis of xylan, including a key functional GH11 endoxylanase that is unique to these four species. Transcriptomic analysis in the presence of xylan revealed the induction of at least five xylan-degrading genes, including one coding for a protein belonging to the GH5_22 subfamily, as well as several transporters that could specialise in the uptake of xylooligosaccharides by yeast. Finally, monitoring xylan degradation and sugar uptake was performed using a fluorescent reporter protein under the control of the XYL1 promoter.