Complete Mitochondrial Genome Sequence of Lichtheimia ramosa (syn. Lichtheimia hongkongensis)

Abstract

We report the complete mitochondrial genome sequence of Lichtheimia ramosa (syn. Lichtheimia hongkongensis), the first complete mitochondrial DNA sequence of the genus Lichtheimia. This 31.8-kb mitochondrial genome encodes 11 subunits of respiratory chain complexes, 3 ATP synthase subunits, 25 tRNAs, and small and large rRNAs, with the gene order atp9-cox2-atp6-cox3-cox1-nad2-nad3-cob-nad1-nad6-nad5-nad4l-nad4-atp8.

GENOME ANNOUNCEMENT

Mucormycosis is an opportunistic infection caused by molds of the order Mucorales. The most common species of Mucorales associated with mucormycosis belong to the genera Rhizopus, Rhizomucor, Mucor, and Absidia. Among the Absidia species, the most important species associated with mucormycosis is Absidia corymbifera. According to physiological, phylogenetic, and morphological data, it was proposed that three Absidia species, A. corymbifera, A. blakesleeana, and A. hyalospora, should be reclassified as a separate family, Lichtheimiaceae fam. nov., and the three species renamed Lichtheimia corymbifera, Lichtheimia blakesleeana, and Lichtheimia hyalospora (1, 2). L. blakesleeana was subsequently reduced to a synonym of L. hyalospora (3). Recently, we and others described a novel Lichtheimia species, Lichtheimia ramosa (syn. Lichtheimia hongkongensis), from patients with mucormycosis (4, 5). We also found that a significant number of reported L. corymbifera infections were actually caused by L. ramosa (6). Among the species of Mucorales, the only complete mitochondrial genome sequenced is that of Rhizopus oryzae (7). In this article, we report the complete mitochondrial genome sequence of L. ramosa HKU22.

Mitochondrial DNA (mtDNA) of L. ramosa was purified using the mitochondrial DNA isolation kit, according to the manufacturer’s instructions (PromoKine), and sequenced using random clone libraries, with the nebulized mitochondrial DNA cloned into a modified pBlueScript KS+ vector. Both DNA strands were sequenced by the dideoxy chain-termination method and assembled using CAP3 (http://pbil.univ-lyon1.fr/cap3.php) (8). The putative open reading frames (ORFs) were denoted using Artemis, with the genetic code of mold. Genes were assigned functions through a BLASTp search against fungal mitochondrion-encoded proteins available in the GenBank database. Introns and rRNAs were identified by a BLASTn pairwise comparison of L. ramosa mtDNA with other fungal mitochondrial DNAs. The BLASTn results were viewed through ACT, a DNA sequence comparison viewer based on Artemis, and the exon/intron boundaries were adjusted manually. tRNAs were predicted by tRNAscan-SE 1.21 (http://lowelab.ucsc.edu/tRNAscan-SE/) (9). The core structures of the group I introns were inferred by the program RNAweasel (http://megasun.bch.umontreal.ca/RNAweasel/).

The mtDNA of L. ramosa is a circular DNA molecule of 31,830 bp. The G+C content is 34.1%. Genes are carried by both DNA strands, with the gene order atp9-cox2-atp6-cox3-cox1-nad2-nad3-cob-nad1-nad6-nad5-nad4l-nad4-atp8. Structural genes occupy 57.9% of the genome (39.1% protein-coding exons, 5.8% tRNA genes, and 13.0% rRNA genes), 8.0% is occupied by intergenic spacers, and 1.9% is occupied by introns. The genome contains 11 genes encoding subunits of respiratory chain complexes (cytochrome oxidase subunits I, II, and III [cox1, cox2, and cox3, respectively], apocytochrome b [cob], and the reduced nicotinamide adenine dinucleotide ubiquinone oxireductase subunits [nad1, nad2, nad3, nad4, nad4l, nad5, and nad6]) and three genes encoding ATP synthase subunits (atp6, atp8, and atp9). It also encodes 25 tRNAs and the 23S and 16S rRNAs of the large and small subunits of the ribosome (rnl and rns, respectively). There is one 120-bp ORF, with an unknown function, between nad4 and atp8. The cox1 and cox2 genes contain one group I intron each. Phylogenetically, the mtDNA of L. ramosa is most closely related to that of R. oryzae.

Nucleotide sequence accession number.

The mtDNA sequence is deposited in GenBank with accession no. KJ561171.