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

<div><p><i>Yarrowia lipolytica</i>, 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 <i>Y</i>. <i>lipolytica</i> 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 <i>de novo</i> annotated assembly of the chromosomal genome of an industrially-relevant strain, W29/CLIB89, determined by hybrid next-generation sequencing. For the first time, each <i>Y</i>. <i>lipolytica</i> 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 <i>Y</i>. <i>lipolytica</i> 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 <i>Y</i>. <i>lipolytica</i> 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.</p></div

CIRCOS overview of YALI1 gene features.

<p><b>(A)</b> Chromosomal genes. Outer ring, chromosomes. First mapping track [RNA polymerase II (POL2)-transcribed genes]: LINE retroelements (outward light grey posts), overlapping genes on both strands (inward blue posts), POL2 less than 1 kb (blue rings), POL2 between 1 kb and 5 kb (light green rings), POL2 between 5 kb and 10 kb (green rings), and POL2 > 10 kb (red rings). The next inner track (POL3 and POL2 ncRNA genes), tRNA (green), rRNA (orange), and ncRNA genes (dark yellow). <b>(B)</b> Mitochondrial genes. Transcripts from exons (longer spanning light blue wedges); transcripts from introns (narrower and taller overlapping wedges); CDS (gray); tDNA (purple); and rDNA (yellow). Outer track shows variants comparison with the CLIB122 assembly (<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_002659.1" target="_blank">http://www.ncbi.nlm.nih.gov/nuccore/NC_002659.1</a>): mismatches (black posts); insertions (green) and deletions (red) relative to the CLIB122 assembly.</p

Families of transposable elements in CLIB89 and CLIB122.

<p>Families of transposable elements in CLIB89 and CLIB122.</p

CLIB89 YALI1 sequence read statistics.

<p>CLIB89 YALI1 sequence read statistics.</p

Genomic differences between CLIB89 YALI0 and CLIB122 YALI1 assemblies.

<p>(A) Circos diagram illustrating the sequence variation between CLIB122 YALI0 and CLIB89 YALI1 and the locations of annotated TE. Outer circle: TE in both assemblies are represented by colored bars projected outward (CLIB89 YALI1) or inward (CLIB122 YALI0) from the chromosome ideograms: Ylli (blue), Mutyl (purple), Ylt1 (red), LTRyl1 (green), LTRylt7 (orange), LTRyl8 (maroon), LTRyl9 (gold), Tyl3 (yellow), Tyl6 (grey). Inner circles: The black track indicates the mismatch density between corresponding regions between CLIB89 and CLIB122 in each chromosome. The green and orange tracks represent insertions and deletions respectively relative to the CLIB122 YALI0 reference genome assembly. (B) Mismatch density of TE and flanking iLoci of allelic compared to nonallelic elements. The mismatch density (mismatch/kb) of each individual element and flanking iloci is shown. Mean and median (red and black horizontal bars, respectively); near and far outliers (black and white circles, respectively).</p

Chromosome assembly lengths.

<p>Chromosome assembly lengths.</p

CLIB89/CLIB122 gene content.

<p>CLIB89/CLIB122 gene content.</p

<i>Y</i>. <i>lipolytica</i> CLIB89 YALI1 <i>a</i>nnotation pipeline.

<p>YALI1 Annotations were derived from a combination of three automated annotation pipelines and a set of manual Blast searches. The three pipelines consist of mapping existing <i>Yl</i> annotations from CLIB122 YALI0 (NCBI RefSeq) to the CLIB89 YALI1 sequence; synteny and homology predictions (YGAP); and fungal HMM predictions (Snowy Owl). Loci of identified features were merged, checked for consistency, selected for CDS based on size and RNA-Seq support, and vetted through NCBI's Sequin upload service to produce the final set of gene features. Contributions and agreements for CDS features from the three automated pipelines are shown in the Venn diagram to the lower right.</p