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The complete mitochondrial genome of Engyodontium album and comparative analyses with Ascomycota mitogenomes.

ABSTRACT: Engyodontium album is a widespread pathogen that causes different kinds of dermatoses and respiratory tract diseases in humans and animals. In spite of its perniciousness, the basic genetic and molecular background of this species remains poorly understood. In this study, the mitochondrial genome sequence of E. album was determined using a high-throughput sequencing platform. The circular mitogenome was found to be 28,081 nucleotides in length and comprised of 17 protein-coding genes, 24 tRNA genes, and 2 rRNA genes. The nucleotide composition of the genome was A+T-biased (74.13%). Group-II introns were found in the nad1, nad5, and cob genes. The most frequently used codon of protein-coding genes was UAU. Isoleucine was identified as the most common amino acid, while proline was the least common amino acid in protein-coding genes. The gene-arrangement order is nearly the same when compared with other Ascomycota mitogenomes. Phylogenetic relationships based on the shared protein-coding genes revealed that E. album is closely related to the Cordycipitaceae family, with a high-confidence support value (100%). The availability of the mitogenome of E. album will shed light on the molecular systematic and genetic differentiation of this species.

SUBMITTER: Yuan XL

PROVIDER: S-EPMC5738615 | biostudies-literature | 2017 Oct-Dec

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome of Engyodontium album and comparative analyses with Ascomycota mitogenomes.

Yuan Xiao-Long XL Mao Xin-Xin XX Liu Xin-Min XM Cheng Sen S Zhang Peng P Zhang Zhong-Feng ZF

Genetics and molecular biology 20171023 4

Engyodontium album is a widespread pathogen that causes different kinds of dermatoses and respiratory tract diseases in humans and animals. In spite of its perniciousness, the basic genetic and molecular background of this species remains poorly understood. In this study, the mitochondrial genome sequence of E. album was determined using a high-throughput sequencing platform. The circular mitogenome was found to be 28,081 nucleotides in length and comprised of 17 protein-coding genes, 24 tRNA ge ...[more]

PMID: 29064513

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Project description:Mitochondrial genomes comprise a small but critical component of the total DNA in eukaryotic organisms. They encode several key proteins for the cell's major energy producing apparatus, the mitochondrial respiratory chain. Additionally, their nucleotide and amino acid sequences are of great utility as markers for systematics, molecular ecology and forensics. Their characterization through nucleotide sequencing is a fundamental starting point in mitogenomics. Methods to amplify complete mitochondrial genomes rapidly and efficiently from microgram quantities of tissue of single individuals are, however, not always available. Here we validate two approaches, which combine long-PCR with Roche 454 pyrosequencing technology, to obtain two complete mitochondrial genomes from individual amphibian species.We obtained two new xenopus frogs (Xenopus borealis and X. victorianus) complete mitochondrial genome sequences by means of long-PCR followed by 454 of individual genomes (approach 1) or of multiple pooled genomes (approach 2), the mean depth of coverage per nucleotide was 9823 and 186, respectively. We also characterised and compared the new mitogenomes against their sister taxa; X. laevis and Silurana tropicalis, two of the most intensely studied amphibians. Our results demonstrate how our approaches can be used to obtain complete amphibian mitogenomes with depths of coverage that far surpass traditional primer-walking strategies, at either the same cost or less. Our results also demonstrate: that the size, gene content and order are the same among xenopus mitogenomes and that S. tropicalis form a separate clade to the other xenopus, among which X. laevis and X. victorianus were most closely related. Nucleotide and amino acid diversity was found to vary across the xenopus mitogenomes, with the greatest diversity observed in the Complex 1 gene nad4l and the least diversity observed in Complex 4 genes (cox1-3). All protein-coding genes were shown to be under strong negative (purifying selection), with genes under the strongest pressure (Complex 4) also being the most highly expressed, highlighting their potentially crucial functions in the mitochondrial respiratory chain.Next generation sequencing of long-PCR amplicons using single taxon or multi-taxon approaches enabled two new species of Xenopus mtDNA to be fully characterized. We anticipate our complete mitochondrial genome amplification methods to be applicable to other amphibians, helpful for identifying the most appropriate markers for differentiating species, populations and resolving phylogenies, a pressing need since amphibians are undergoing drastic global decline. Our mtDNAs also provide templates for conserved primer design and the assembly of RNA and DNA reads following high throughput "omic" techniques such as RNA- and ChIP-seq. These could help us better understand how processes such mitochondrial replication and gene expression influence xenopus growth and development, as well as how they evolved and are regulated.

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The complete mitochondrial genome of Engyodontium album and comparative analyses with Ascomycota mitogenomes.

Publications

The complete mitochondrial genome of Engyodontium album and comparative analyses with Ascomycota mitogenomes.

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