![]() Briefly, the short reads from Ion PGM were corrected using SPADES 3.11 ( Bankevich et al. Genome assembly was performed using Flye 2.3.3 assembler ( Kolmogorov et al. We obtained 10.8 M reads (mean length 216 bp) from Ion PGM, and 129 K reads from MinION (mean length 8.3 kb), accounting for approximately 165-fold and 75-fold genome coverage, respectively. The libraries were enriched in an Ion 318™ Chip v2 using Ion Chef (ThermoFisher Scientific), and subsequent sequencing was performed in the Ion PGM System (ThermoFisher Scientific). Briefly, the barcoded library of 400 base-reads was prepared after fragmentation of 100 ng of the DNA using the Ion Xpress™ Plus Fragment Library Kit (ThermoFisher Scientific, Waltham, MA, USA). The library for the Ion semiconductor sequencing was prepared as described previously ( Panthee et al. Library Preparation and Ion PGM Sequencing ![]() The sequence reads were obtained with MinKNOW software using the 48-h protocol and live base-calling. The adapted library was purified using Agencourt AMPure XP (Beckman Coulter Inc.) and applied to a primed FLO-MIN106 R9.4 SpotON Flow Cell attached to MinION (Oxford Nanopore Technologies). The DNA was then ligated to the adapter using NEB Blunt/TA Ligase Master Mix (NEB). Briefly, 1 µg genomic DNA was end-prepped using the NEBNext End repair/dA-tailing Module (New England Biolabs, Inc., Ipswich, MA, USA) and the DNA was cleaned up using Agencourt AMPure XP (Beckman Coulter Inc., Brea, CA, USA). ![]() The library preparation for Oxford Nanopore sequencing was performed using the manufacturer’s recommended protocol-1D Genomic DNA by ligation for the SQK-LSK108 kit (Oxford Nanopore Technologies, Oxford, UK). Library Preparation and Oxford Nanopore Sequencing DNA ExtractionĬ andida albicans TIMM1768 was cultured on YPD medium, and the genomic DNA from 300 µl of culture broth was isolated with a Qiagen DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) using zymolyase for cell lysis. 9FEF27, Eiken Chemical Co., Ltd., Japan). The minimum inhibitory concentration of antifungal agents was determined based on CLSI M27-A3 using a commercial kit (cat. Materials and Methods Strain and Minimum Inhibitory Concentration Assay Annotation and comparative analysis revealed 424 genes with a potential role in pathogenesis. The 14.4-Mb TIMM1768 genome was assembled into eight chromosomes and one mitochondrion. albicans TIMM1768 by combining Oxford Nanopore long reads and Ion PGM short reads. Because the availability of the genome is essential for genome mining, here, we sequenced the genome of C. Further, MinION has a low capital cost, produces data in real-time, and is portable. The Oxford Nanopore Technologies third-generation sequencer MinION is a new sequencing technology that offers ultra-long reads and can be particularly beneficial for resolving repeat-rich regions. Although this has greatly advanced genomic and transcriptomic studies, fungal genome assembly remains challenging, due in part to the high repeat content. The last decade has seen significant development in next-generation sequencers that produce high-throughput short reads. One approach to elucidate this phenotype is to mine the genome sequence for the genes with a potential pathogenic role, such as virulence factors and proteases. Despite noteworthy progress in elucidating TIMM1768 pathogenicity, the genetic element responsible for its high pathogenicity has yet to be identified. Hyphal growth is associated with its virulence and N-acetylglucosamine (GlcNAc), an inducer of the hyphal growth, leads to severe colonization in the oral and gastrointestinal models of TIMM1768 candidiasis ( Mizutani et al. albicans genome sequence and functional genomic approaches ( Anderson and Bennett 2016).Ĭandida albicans TIMM1768 is a highly virulent strain isolated from the feces of a candidiasis patient. Global studies were recently facilitated by the availability of the C. albicans virulence studies were performed by the functional elucidation of a few candidate genes. Enhancing our understanding of the biological and pathogenic features of the fungus will significantly advance the discovery of novel approaches to counteract the infections caused by this organism. Recently, there has been a tremendous rise in the fungal infections caused by candida ( Odds 2010). Candida albicans, de novo assembly, genomics, pathogenesis, MinION sequencing IntroductionĬandida albicans, a fungus usually present in the gastrointestinal tract, mouth, and genital tract of human beings as a part of the human microbiome, is capable of causing both superficial and systemic infections, especially in patients with compromised immune function.
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