Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii : Combining an Improved Genome with Gene Expression and Chromatin Structure

G3 : Genes - Genomes - Genetics
Sunita SinhaCorey Nislow

Abstract

Extremophilic organisms demonstrate the flexibility and adaptability of basic biological processes by highlighting how cell physiology adapts to environmental extremes. Few eukaryotic extremophiles have been well studied and only a small number are amenable to laboratory cultivation and manipulation. A detailed characterization of the genome architecture of such organisms is important to illuminate how they adapt to environmental stresses. One excellent example of a fungal extremophile is the halophile Hortaea werneckii (Pezizomycotina, Dothideomycetes, Capnodiales), a yeast-like fungus able to thrive at near-saturating concentrations of sodium chloride and which is also tolerant to both UV irradiation and desiccation. Given its unique lifestyle and its remarkably recent whole genome duplication, H. werneckii provides opportunities for testing the role of genome duplications and adaptability to extreme environments. We previously assembled the genome of H. werneckii using short-read sequencing technology and found a remarkable degree of gene duplication. Technology limitations, however, precluded high-confidence annotation of the entire genome. We therefore revisited the H. wernickii genome using long-read, single-molecule sequ...Continue Reading

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Mar 7, 2018·Genes·Cene Gostinčar, Nina Gunde-Cimerman
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Datasets Mentioned

BETA
SRR488142
SRR488143
PRJNA356640

Methods Mentioned

BETA
environmental stresses
RNA-seq

Software Mentioned

bp
subopt
SAMtools
MAFFT
DANPOS2
GSNAP
SMRT Analysis
BLAST
BWA
funannotate

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