Browsing by Subject "Genome, Mitochondrial"

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Open Access
An Exploration into Fern Genome Space.
(Genome Biol Evol, 2015-08-26) Wolf, PG; Sessa, EB; Marchant, DB; Li, F; Rothfels, CJ; Sigel, EM; Gitzendanner, MA; Visger, CJ; Banks, JA; Soltis, DE
Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.
Open Access
Mitochondrial mutations in adenoid cystic carcinoma of the salivary glands.
(PLoS One, 2009-12-30) Mithani, Suhail K; Shao, Chunbo; Tan, Marietta; Smith, Ian M; Califano, Joseph A; El-Naggar, Adel K; Ha, Patrick K
BACKGROUND: The MitoChip v2.0 resequencing array is an array-based technique allowing for accurate and complete sequencing of the mitochondrial genome. No studies have investigated mitochondrial mutation in salivary gland adenoid cystic carcinomas. METHODOLOGY: The entire mitochondrial genome of 22 salivary gland adenoid cystic carcinomas (ACC) of salivary glands and matched leukocyte DNA was sequenced to determine the frequency and distribution of mitochondrial mutations in ACC tumors. PRINCIPAL FINDINGS: Seventeen of 22 ACCs (77%) carried mitochondrial mutations, ranging in number from 1 to 37 mutations. A disproportionate number of mutations occurred in the D-loop. Twelve of 17 tumors (70.6%) carried mutations resulting in amino acid changes of translated proteins. Nine of 17 tumors (52.9%) with a mutation carried an amino acid changing mutation in the nicotinamide adenine dinucleotide dehydrogenase (NADH) complex. CONCLUSIONS/SIGNIFICANCE: Mitochondrial mutation is frequent in salivary ACCs. The high incidence of amino acid changing mutations implicates alterations in aerobic respiration in ACC carcinogenesis. D-loop mutations are of unclear significance, but may be associated with alterations in transcription or replication.
Open Access
Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.
(Mol Phylogenet Evol, 2010-10) Nabholz, Benoit; Jarvis, Erich D; Ellegren, Hans
Classically, the mitochondrial genome is sequenced by a series of amplicons using conserved PCR primers. Here we show how shot-gun transcriptome sequencing can be used to obtain the complete set of protein-coding genes from the mtDNA of four passerine bird species. With these sequences, we address the still unresolved basal Passerida relationships (Aves: Passeriformes). Our analysis suggests a new hypothesis for the basal relationships of Passerida, namely a clade grouping Sylvioidea and Passeroidea, with Paridae and Muscicapidae as successive sister groups to this clade. This study demonstrates the usefulness of next-generation sequencing transcriptome sequencing for obtaining new mtDNA genomes.