Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity

Abstract

Yarrowia lipolytica, an oleaginous yeast, is capable of accumulating significant cellular mass in lipid making it an important source of biosustainable hydrocarbon-based chemicals. In spite of a similar number of protein-coding genes to that in other Hemiascomycetes, the Y. lipolytica genome is almost double that of model yeasts. Despite its economic importance and several distinct strains in common use, an independent genome assembly exists for only one strain. We report here a de novo annotated assembly of the chromosomal genome of an industrially-relevant strain, W29/CLIB89, determined by hybrid next-generation sequencing. For the first time, each Y. lipolytica chromosome is represented by a single contig. The telomeric rDNA repeats were localized by Irys long-range genome mapping and one complete copy of the rDNA sequence is reported. Two large structural variants and retroelement differences with reference strain CLIB122 including a full-length, novel Ty3/Gypsy long terminal repeat (LTR) retrotransposon and multiple LTR-like sequences are described. Strikingly, several of these are adjacent to RNA polymerase III-transcribed genes, which are almost double in number in Y. lipolytica compared to other Hemiascomycetes. In addition to previously-reported dimeric RNA polymerase III-transcribed genes, tRNA pseudogenes were identified. Multiple full-length and truncated LINE elements are also present. Therefore, although identified transposons do not constitute a significant fraction of the Y. lipolytica genome, they could have played an active role in its evolution. Differences between the sequence of this strain and of the existing reference strain underscore the utility of an additional independent genome assembly for this economically important organism.

Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica

“…Custom Matlab scripts were used to design each sgRNA in the library based on a recent assembly of the Y. lipolytica PO1f parent strain genome, W29 (Magnan et al, 2016). sgRNAs were designed for all non-redundant protein coding sequences.…”

Stress-Induced Expression is Enriched for Evolutionarily Young Genes in Diverse Budding Yeasts

“…To test for a relationship between differential expression and gene age, we stratified the proteincoding genes of K. marxianus and Y. lipolytica using the same sorting concept described above for S. cerevisiae (Supplemental Figure 4). The only modification to these sorting approaches was the elimination of the whole-genome duplication group, as neither of these species has undergone a recent whole-genome duplication 29,30 .…”

Characterization of threeYarrowia lipolyticastrains in respect to different cultivation temperatures and metabolite secretion

“…Paired reads were trimmed with BBDuk (version 37.25) using qtrim=rl, trimq=20, minlength=20. Then the reads were mapped against CLIB89 (Magnan et al 2016) For variant calling a minimum coverage with five reads and minimum variant frequency of 0.9 (with p-value ≦ 10 -6 ) were set. Variant calling was not performed in regions with high coverage which were defined with coverage > (mean + 2*sdv).…”

“…Currently, a strong research focus lies on the natural isolates H222, W29, including its derivatives from the Po1 series and CBS6142-2 (Beopoulos et al 2010;Bredeweg et al 2017) . High quality genomic sequences are likewise analyzed and provided just for a couple of strains (Devillers et al 2016 ;Magnan et al 2016 ;Pomraning and Baker 2015 ;Liu and Alper 2014 ;Dujon et al 2004) . Efforts to overcome this restricted view were recently made by ( Egermeier et al 2017 ).…”