Table 1.
CLIB89 YALI1 sequence read statistics.
Fig 1.
BioNano Irys long-range mapping of CLIB89 YALI1 and comparison to CLIB122 YALI0.
(A) Irys molecules assembled into contigs (coverage indicated as light and dark for lesser and greater coverage, respectively) aligned with the six CLIB89 YALI1 chromosomes (green) show extensions in four chromosome terminal regions. (B) Chromosomal extensions show a repeated pattern of Nt.BspQI nickase sites (vertical grey lines), consistent with tandem, copies of ribosomal (r) RNA-coding sequence. (C) and (D) Alignment of map of Nt.BspQI sites in the CLIB122 YALI0 (upper green bar) and CLIB89 YALI1 assembly (lower green bar) with the physical Nt.BspQI map generated by Irys technology (blue bar) shows they differ by a 71-kb inversion on chromosome B (C) and a 54-kb repeat on chromosome C in CLIB89 YALI1 (D).
Table 2.
Irys CLIB89 YALI1 assembly.
Table 3.
Chromosome assembly lengths.
Table 4.
CLIB89/CLIB122 gene content.
Fig 2.
Y. lipolytica CLIB89 YALI1 annotation pipeline.
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 Yl 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.
Fig 3.
CIRCOS overview of YALI1 gene features.
(A) 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) 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 (http://www.ncbi.nlm.nih.gov/nuccore/NC_002659.1): mismatches (black posts); insertions (green) and deletions (red) relative to the CLIB122 assembly.
Table 5.
Families of transposable elements in CLIB89 and CLIB122.
Fig 4.
The complete Tyl3 Y. lipolytica Ty3/Gypsy element.
(A) Tyl3 was assembled from CLIB89 sequence. Abbreviations are GAG (capsid, CA; and nucleocapsid, NC) and POL (protease, PR; reverse transcriptase, RT; and integrase, IN), Solid triangles represent LTRs, GAG and POL are separated by 324 bp. PBS, primer binding sequence complementary to initiator tRNAMet the presumed primer for minus-strand replication; and PPT, polypurine tract the presumed primer for plus-strand replication. The full-length Tyl3 is adjacent to two tDNA sequences. (B) Full-length S. cerevisiae Ty3 is shown for comparison. Features are similarly abbreviated as in 4A.
Fig 5.
Genomic differences between CLIB89 YALI0 and CLIB122 YALI1 assemblies.
(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).