scholarly journals Establishment of a near-contiguous genome sequence of the citric acid producing yeast Yarrowia lipolytica DSM 3286 with resolution of rDNA clusters and telomeres

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Tobias Luttermann ◽  
Christian Rückert ◽  
Daniel Wibberg ◽  
Tobias Busche ◽  
Jan-Philipp Schwarzhans ◽  
...  
Keyword(s):  
Yarrowia Lipolytica ◽  
Genome Sequence ◽  
Fine Tuning ◽  
Rdna Cluster ◽  
Large Size ◽  
Long Reads ◽  
Genome Assemblies ◽  
Yeast Yarrowia Lipolytica ◽  
Shed Light ◽  
Specific Cluster

Abstract Yarrowia lipolytica is an oleaginous yeast that is particularly suitable for the sustainable production of secondary metabolites. The genome of this yeast is characterized by its relatively large size and its high number of different rDNA clusters located in its telomeric regions. However, due to the presence of long repetitive elements in the sub-telomeric regions, rDNA clusters and telomeres are missing in current genome assemblies of Y. lipolytica. Here, we present the near-contiguous genome sequence of the biotechnologically relevant strain DSM 3286. We employed a hybrid assembly strategy combining Illumina and nanopore sequencing reads to integrate all six rDNA clusters as well as telomeric repeats into the genome sequence. By fine-tuning of DNA isolation and library preparation protocols, we were able to create ultra-long reads that not only contained multiples of mitochondrial genomes but also shed light on the inter- and intra-chromosomal diversity of rDNA cluster types. We show that there are ten different rDNA units present in this strain that additionally appear in a predefined order in a cluster. Based on single reads, we also demonstrate that the number of rDNA repeats in a specific cluster varies from cell to cell within a population.

scholarly journals Chromosome-scale genome assembly of the high royal jelly-producing honeybees

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Lianfei Cao ◽  
Xiaomeng Zhao ◽  
Yanping Chen ◽  
Cheng Sun
Keyword(s):  
Genome Sequence ◽  
Genetic Basis ◽  
Royal Jelly ◽  
Repetitive Sequences ◽  
Chromosome Inversion ◽  
Protein Coding ◽  
Long Reads ◽  
Alignment Analysis ◽  
Shed Light ◽  
Selection Of

AbstractA high royal jelly-producing strain of honeybees (HRJHB) has been obtained by successive artificial selection of Italian honeybees (Apis mellifera ligustica) in China. The HRJHB can produce amounts of royal jelly that are dozens of times greater than their original counterparts, which has promoted China to be the largest producer of royal jelly in the world. In this study, we generated a chromosome-scale of the genome sequence for the HRJHB using PacBio long reads and Hi-C technique. The genome consists of 16 pseudo-chromosomes that contain 222 Mb of sequence, with a scaffold N50 of 13.6 Mb. BUSCO analysis yielded a completeness score of 99.3%. The genome has 12,288 predicted protein-coding genes and a rate of 8.11% of repetitive sequences. One chromosome inversion was identified between the HRJHB and the closely related Italian honeybees through whole-genome alignment analysis. The HRJHB’s genome sequence will be an important resource for understanding the genetic basis of high levels of royal jelly production, which may also shed light on the evolution of domesticated insects.

scholarly journals Whole-Genome Sequencing and De Novo Assembly of Malassezia pachydermatis Isolated from the Ear Canal of a Dog with Otitis

2021 ◽  
Vol 10 (21) ◽  
Author(s):  
S. D’Andreano ◽  
J. Viñes ◽  
O. Francino
Keyword(s):  
Genome Sequencing ◽  
Genome Sequence ◽  
De Novo Assembly ◽  
De Novo ◽  
Whole Genome ◽  
Ear Canal ◽  
Malassezia Pachydermatis ◽  
Content Type ◽  
Long Reads ◽  
Genome Assemblies

We have de novo assembled the genome sequence of Malassezia pachydermatis isolated from a canine otitis sample with Nanopore-only long reads. With 99× coverage and 8.23 Mbp, the genome sequence was assembled in 10 contigs, with 6 of them corresponding to chromosomes, improving the scaffolding of previous genome assemblies for the species.

scholarly journals Draft Genome Sequence of the Dimorphic Yeast Yarrowia lipolytica Strain W29

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Kyle R. Pomraning ◽  
Scott E. Baker
Keyword(s):  
Small Molecules ◽  
Yarrowia Lipolytica ◽  
Genome Sequence ◽  
Industrial Production ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Lipolytica Strain ◽  
Dimorphic Yeast ◽  
Ascomycete Yeast ◽  
Yeast Yarrowia Lipolytica

Here, we present the draft genome sequence of the dimorphic ascomycete yeast Yarrowia lipolytica strain W29 (ATCC 20460). Y. lipolytica is a commonly employed model for the industrial production of lipases, small molecules, and more recently for its ability to accumulate lipids.

scholarly journals Genome Sequence of the Oleaginous Yeast Yarrowia lipolytica H222

2019 ◽  
Vol 8 (4) ◽  
Author(s):  
Hugo Devillers ◽  
Cécile Neuvéglise
Keyword(s):  
Yarrowia Lipolytica ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Oleaginous Yeast ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Content Type ◽  
Yeast Yarrowia Lipolytica

Here, we report the genome sequence of the oleaginous yeast Yarrowia lipolytica H222. De novo genome assembly shows three main chromosomal rearrangements compared to that of strain E150/CLIB122.

scholarly journals Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Jean-Marc Aury ◽  
Benjamin Istace
Keyword(s):  
Single Molecule ◽  
Direct Consequence ◽  
High Quality ◽  
Sequencing Errors ◽  
Coding Regions ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Long Read ◽  
Genome Assemblies

Abstract Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. In the case of diploid genomes, the consensus of a given gene can be a mixture between the two haplotypes and can lead to premature stop codons. Several methods have been developed to polish genome assemblies using short reads and generally, they inspect the nucleotide one by one, and provide a correction for each nucleotide of the input assembly. As a result, these algorithms are not able to properly process diploid genomes and they typically switch from one haplotype to another. Herein we proposed Hapo-G (Haplotype-Aware Polishing Of Genomes), a new algorithm capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.

scholarly journals Psychrotrophic yeast Yarrowia lipolytica NCYC 789 mediates the synthesis of antimicrobial silver nanoparticles via cell-associated melanin

AMB Express ◽  
2013 ◽  
Vol 3 (1) ◽  
pp. 32 ◽  
Author(s):  
Mugdha Apte ◽  
Devashree Sambre ◽  
Shital Gaikawad ◽  
Swanand Joshi ◽  
Ashok Bankar ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Yarrowia Lipolytica ◽  
Yeast Yarrowia Lipolytica

scholarly journals Stable isotope and chemical inhibition analyses suggested the existence of a non-mevalonate-like pathway in the yeast Yarrowia lipolytica

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sivamoke Dissook ◽  
Tomohisa Kuzuyama ◽  
Yuri Nishimoto ◽  
Shigeru Kitani ◽  
Sastia Putri ◽  
...  
Keyword(s):  
Yarrowia Lipolytica ◽  
Oleaginous Yeast ◽  
Isoprenoid Biosynthesis ◽  
Mep Pathway ◽  
Authentic Standard ◽  
Chemical Inhibition ◽  
Chromatographic Peaks ◽  
Methyl Erythritol Phosphate ◽  
Limiting Condition ◽  
Yeast Yarrowia Lipolytica

AbstractMethyl erythritol phosphate (MEP) is the metabolite found in the MEP pathway for isoprenoid biosynthesis, which is known to be utilized by plants, algae, and bacteria. In this study, an unprecedented observation was found in the oleaginous yeast Yarrowia lipolytica, in which one of the chromatographic peaks was annotated as MEP when cultivated in the nitrogen limiting condition. This finding raised an interesting hypothesis of whether Y. lipolytica utilizes the MEP pathway for isoprenoid biosynthesis or not, because there is no report of yeast harboring the MEP pathway. Three independent approaches were used to investigate the existence of the MEP pathway in Y. lipolytica; the spiking of the authentic standard, the MEP pathway inhibitor, and the 13C labeling incorporation analysis. The study suggested that the mevalonate and MEP pathways co-exist in Y. lipolytica and the nitrogen limiting condition triggers the utilization of the MEP pathway in Y. lipolytica.

scholarly journals Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica

2017 ◽  
Vol 16 (1) ◽  
Author(s):  
Thomas Beneyton ◽  
Stéphane Thomas ◽  
Andrew D. Griffiths ◽  
Jean-Marc Nicaud ◽  
Antoine Drevelle ◽  
...  
Keyword(s):  
Yarrowia Lipolytica ◽  
High Throughput ◽  
High Throughput Screening ◽  
Yeast Yarrowia Lipolytica
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