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Insights into genome evolution, pan-genome, and phylogenetic implication through mitochondrial genome sequence of Naegleria fowleri species
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Insights into genome evolution, pan-genome, and phylogenetic implication through mitochondrial genome sequence of Naegleria fowleri species
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Journal Article
Insights into genome evolution, pan-genome, and phylogenetic implication through mitochondrial genome sequence of Naegleria fowleri species
2022
Overview
In the current study, we have systematically analysed the mitochondrial DNA (mtDNA) sequence of
Naegleria fowleri
(
N. fowleri)
isolate AY27, isolated from Karachi, Pakistan. The
N. fowleri
isolate AY27 has a circular mtDNA (49,541 bp), which harbours 69 genes (46 protein-coding genes, 21 tRNAs and 2 rRNAs). The pan-genome analysis of
N. fowleri
species showed a B
pan
value of 0.137048, which implies that the pan-genome is open. KEGG classified core, accessory and unique gene clusters for human disease, metabolism, environmental information processing, genetic information processing and organismal system. Similarly, COG characterization of protein showed that core and accessory genes are involved in metabolism, information storages and processing, and cellular processes and signaling. The
Naegleria
species (n = 6) formed a total of 47 gene clusters; 42 single-copy gene clusters and 5 orthologous gene clusters. It was noted that 100% genes of
Naegleria
species were present in the orthogroups. We identified 44 single nucleotide polymorphisms (SNP) in the
N. fowleri
isolate AY27 mtDNA using
N. fowleri
strain V511 as a reference. Whole mtDNA phylogenetic tree analysis showed that
N. fowleri
isolates AY27 is closely related to
N. fowleri
(Accession no. JX174181.1). The ANI (Average Nucleotide Identity) values presented a much clear grouping of the
Naegleria
species compared to the whole mtDNA based phylogenetic analysis. The current study gives a comprehensive understanding of mtDNA architecture as well as a comparison of
Naegleria
species (
N. fowleri
and
N. gruberi
species) at the mitochondrial genome sequence level.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
