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.
Highlights
The oleaginous yeast Yarrowia lipolytica is an industrial model organism for production of biosustainable hydrocarbon-based chemicals [1,2,3,4,5,6]
The CLIB89 genome assembly was designated YALI1 to distinguish it from the previous CLIB122 YALI0 assembly [7]
In order to provide an improved basis for manipulation of strains related to industrial strain CLIB89, we used hybrid, next-generation sequencing coupled with Irys long-range genome mapping to assemble the CLIB89 genome, making it the first Y. lipolytica genome in which single contigs comprise each chromosome
Summary
The oleaginous yeast Yarrowia lipolytica is an industrial model organism for production of biosustainable hydrocarbon-based chemicals [1,2,3,4,5,6]. Y. lipolytica has more traits in common with metazoan cells than other characterized yeasts These include dispersed 5S genes, signal-recognition-particle type 7SL RNA sequence, and a greater fraction of the genome composed of introns and intergenic sequences [7, 8]. Unlike the more widely-studied respiro-fermentative S. cerevisiae, Y. lipolytica is an obligate aerobe It metabolizes a wide range of carbon substrates including lipids, paraffins, oils, glycerol, and acetate and is capable of accumulating a high percentage of cell weight in lipid [1, 13, 14]. This metabolism has recently been tuned for production of hydrocarbon chemicals
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