DOI: 10.5061/dryad.v15dv427f
title: Genome sequence assembly and annotation of MATA and MATB strains of <em>Yarrowia lipolytica</em>

description: Yeast is commonly utilized in molecular and cell biology research, and
 Yarrowia lipolytica is favored by bio-engineers due to its ability to
 produce copious amounts of lipids, chemicals, and enzymes for industrial
 applications. Y. lipolytica is a dimorphic yeast that can proliferate in
 aerobic and hydrophobic environments conducive to industrial use. However,
 there is limited knowledge about the basic molecular biology of this
 yeast, including how the genome is duplicated and how gene silencing
 occurs. Genome sequences of Y. lipolytica strains have offered insights
 into the genetic basis of this yeast species and have facilitated the
 development of new industrial applications. Although previous studies have
 reported the genome sequence of a few Y. lipolytica strains, it is of
 value to have more precise sequences and annotation, particularly for
 studies of the biology of this yeast. To further study and characterize
 the molecular biology of this microorganism, a high-quality reference
 genome assembly and annotation has been produced for two related Y.
 lipolytica strains of the opposite mating type, MATA (E122) and MATB
 (22301-5). The combination of short-read and long-read sequencing of
 genome DNA and short-read and long-read sequencing of transcript cDNAs
 allowed the genome assembly and a comparison with a distantly related
 Yarrowia strain.
description: # Genome sequence assembly and annotation of MATA and MATB strains of
 *Yarrowia lipolytica* Two related *Yarrowia lipolytica* strains of
 opposite mating type were obtained from Richard A. Rachubunski, University
 of Alberta, Canada, and single clones were isolated and used for both
 genome and transcript sequencing. The strains were 22301-5 (MATB) and E122
 (MATA, alternatively called CLIB120) (5, 28, 29)  (Figure 1). E122 is
 MATA, ura3-302, leu2-270, lys8-11, and is related to the MATB strain E150
 (CLIB122 and is the current DNA sequence reference strain (6, 23)*.*
 Strain 22301-5 is MATB, his-1, uras-302, leu2-270. ### Files and variables
 #### File: yarrowia_lipolytica-22301-5.fasta **Description:** Strain
 22301-5 Genome assembly #### File: yarrowia_lipolytica-E122.fasta
 **Description:** Strain E122 Genome assembly #### File:
 yarrowia_lipolytica-E122.gff Description: Strain E122 Transcriptome
 assembly and annotation. Full structural gene annotation in GFF3 format
 (genes, exons, CDS) #### File: yarrowia_lipolytica-22301-5.gff
 Description: Strain 22301-5 Transcriptome assembly and annotation. Full
 structural gene annotation in GFF3 format (genes, exons, CDS) #### File:
 yarrowia_lipolytica-22301-5.AED_filter_1.gff Description: Strain 22301-5
 Filtered GFF with high-confidence gene models (AED ≤ 1). #### File:
 yarrowia_lipolytica-E122.AED_filter_1.gff Description: Strain E122
 Filtered GFF with high-confidence gene models (AED ≤ 1). #### File:
 yarrowia_lipolytica-22301-5.evd.cdna.fasta Description: Strain 22301-5
 FASTA of spliced cDNA (transcripts including UTRs). #### File:
 yarrowia_lipolytica-E122.evd.cdna.fasta Description: Strain E122 FASTA of
 spliced cDNA (transcripts including UTRs). #### File:
 yarrowia_lipolytica-22301-5.evd.cds.fasta Description: Strain 22301-5
 FASTA of coding sequences (CDS only). #### File:
 yarrowia_lipolytica-E122.evd.cds.fasta Description: Strain E122 FASTA of
 coding sequences (CDS only). #### File:
 yarrowia_lipolytica-22301-5.evd.protein.fasta Description: Strain 22301-5
 FASTA of translated protein sequences. #### File:
 yarrowia_lipolytica-E122.evd.protein.fasta Description: Strain E122 FASTA
 of translated protein sequences. #### File:
 yarrowia_lipolytica-22301-5.evd.protein.interproscan.tsv Description:
 Strain 22301-5 InterProScan results: protein domain/function annotations.
 #### File: yarrowia_lipolytica-E122.evd.protein.interproscan.tsv
 Description: Strain E122 InterProScan results: protein domain/function
 annotations. #### File:
 yarrowia_lipolytica-22301-5.fasta.mod.EDTA.intact.gff3 Description:
 Strain 22301-5 GFF3 of intact transposable elements (TEs) identified by
 EDTA. #### File: yarrowia_lipolytica-E122.fasta.mod.EDTA.intact.gff3
 Description: Strain E122 GFF3 of intact transposable elements (TEs)
 identified by EDTA. #### File:
 yarrowia_lipolytica-22301-5.fasta.mod.EDTA.TEanno.gff3 Description:
 Strain 22301-5 GFF3 of all annotated TE features (both intact and
 fragmented). #### File:
 yarrowia_lipolytica-E122.fasta.mod.EDTA.TEanno.gff3 Description:
 Strain E122 GFF3 of all annotated TE features (both intact and
 fragmented). #### File:
 yarrowia_lipolytica-22301-5.fasta.mod.EDTA.TEanno.sum Description:
 Strain 22301-5 Summary statistics of TE annotations (counts, lengths,
 classes). #### File: yarrowia_lipolytica-E122.fasta.mod.EDTA.TEanno.sum
 Description: Strain E122 Summary statistics of TE annotations (counts,
 lengths, classes). #### File:
 yarrowia_lipolytica-22301-5.fasta.mod.EDTA.TElib.fa Description:
 Strain 22301-5 Custom TE library (consensus sequences of identified
 repeats). #### File: yarrowia_lipolytica-E122.fasta.mod.EDTA.TElib.fa
 Description: Strain E122 Custom TE library (consensus sequences of
 identified repeats). #### File:
 yarrowia_lipolytica-22301-5.fasta.mod.MAKER.masked Description:
 Strain 22301-5 Genome sequence with repeats masked (soft-masked by MAKER
 using EDTA TE annotations). #### File:
 yarrowia_lipolytica-E122.fasta.mod.MAKER.masked Description: Strain E122
 Genome sequence with repeats masked (soft-masked by MAKER using EDTA TE
 annotations). #### File: repeatLib.fungi.fa Description: Custom fungal
 repeat library in FASTA format (used for repeat masking). #### File:
 yarrowia_lipolytica-22301-5_core_2_87_1.repeat_report Description:
 Strain 22301-5 RepeatMasker output report summarizing repeat content
 (type, count, coverage). #### File:
 yarrowia_lipolytica-E122_core_2_87_1.repeat_report Description:
 Strain E122 RepeatMasker output report summarizing repeat content (type,
 count, coverage). #### File:
 yarrowia_lipolytica-22301-5_repeat_feature.gene.overlap.txt Description:
 Strain 22301-5 TE-related genes overlapping repeat element #### File:
 yarrowia_lipolytica-E122_repeat_feature.gene.overlap.txt Description:
 Strain E122 TE-related genes overlapping repeat element. #### File:
 yali_id.system_name.orthologs.csv Description: CSV file containing
 ortholog relationships between *Yarrowia lipolytica* genes and genes from
 other species or strains; includes gene IDs and matched orthologs. ##
 Code/software Genome and transcriptome data, as well as gff3 annotation
 files can all be viewed using a genome browser. (e.g. IGV). The remaining
 files can be opened in a text editor/viewer or excel.