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Alignment of Geomydoecus aurei Clones. Sequence 1: G. aurei COI minicircle is part of the full cox1 minichromosome from louse 1379.16 in Fig 1. This sequence is from a different individual than the clone sequences below it (individual 39.6.J) and was used as a reference to map the other clone sequences. At top, black bars indicate cox1-coding regions, gray bars indicate inverted repeat regions, and pink indicates trnI. In clone sequences, vertical black marks represent differences in nucleotide composition, and horizontal bars indicate presumed insertion/deletion events in the alignment. Clone 12 and clone 19 are the only identical sequences.
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In animals, mitochondrial DNA (mtDNA) typically occurs as a single circular chromosome with 13 protein-coding genes and 22 tRNA genes. The various species of lice examined previously, however, have shown mitochondrial genome rearrangements with a range of chromosome sizes and numbers. Our research demonstrates that the mitochondrial genomes of two...
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... However, it is unknown how stable the mitogenome organization is among individuals (or populations) within a species of louse. Heteroplasmy can also be present in some mitogenomes of lice, either in the form of divergence between homologous genes or multiple chromosomal arrangements within a single individual 13,18,22 . These reported cases suggest heteroplasmy could be much more prevalent in parasitic lice, particularly in lice with fragmented mitogenomes. ...
... We also found evidence for more extreme cases of heteroplasmy, where an individual louse can have multiple types of chromosomes (e.g., a larger chromosome and another, smaller chromosome containing a subset of genes) (Fig. 2). Mitochondrial heteroplasmy has become documented with increasing frequency in many different organisms (including lice 22 ), and can result from a lack of sorting of mitochondrial mutations within the germ line or paternal leakage of mitochondrial DNA 35,36 . The majority of these cases are differences at single sites or in gene lengths, and although there are instances of deleterious heteroplasmic alleles 13,22 , it is seemingly rare for heteroplasmy to result in changes in gene order. ...
... Mitochondrial heteroplasmy has become documented with increasing frequency in many different organisms (including lice 22 ), and can result from a lack of sorting of mitochondrial mutations within the germ line or paternal leakage of mitochondrial DNA 35,36 . The majority of these cases are differences at single sites or in gene lengths, and although there are instances of deleterious heteroplasmic alleles 13,22 , it is seemingly rare for heteroplasmy to result in changes in gene order. ...
The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several species of parasitic lice (Insecta: Phthiraptera) possess fragmented mitogenomes, where the mitochondrial genes are present on separate, circular chromosomes. Nevertheless, the extent, causes, and consequences of this structural variation remain poorly understood. Here, we combined new and existing data to better understand the evolution of mitogenome fragmentation in major groups of parasitic lice. We found strong evidence that fragmented mitogenomes evolved many times within parasitic lice and that the level of fragmentation is highly variable, including examples of heteroplasmic arrangements. We also found a significant association between mitochondrial fragmentation and signatures of relaxed selection. Mitochondrial fragmentation was also associated with changes to a lower AT%, possibly due to differences in mutation biases. Together, our results provide a significant advance in understanding the process of mitogenome fragmentation and provide an important perspective on mitochondrial evolution in eukaryotes. Multiple independent origins of fragmented mitochondrial genome evolution in parasitic lice provide insights into eukaryotic mitochondrial evolution.
... Mitochondrial heteroplasmy has also been occasionally reported to be widespread in some taxon groups (e.g. chewing lice ( Pietan et al. 2016 ), ticks ing rates of susceptibility to mitochondrial mutations during their development, through exposure to oxidative damage ( Santos et al., 2013 ;Shokolenko et al., 2014 ), insufficient repair mechanisms ( Kmiec et al., 2006 ), or errors caused by mitochondrial polymerases during mtDNA replication ( Kennedy et al., 2013 ;Trifunovic et al., 2004 ). However, these mutations are not necessarily heritable ( Ju et al., 2014 ;Pinto and Moraes, 2015 ). ...
Mitochondrial heteroplasmy is the occurrence of more than one type of mitochondrial DNA within a single individual. Although generally reported to occur in a small subset of individuals within a species, there are some instances of widespread heteroplasmy across entire populations. Amphylaeus morosus is an Australian native bee species in the diverse and cosmopolitan bee family Colletidae. This species has an extensive geographical range along the eastern Australian coast, from southern Queensland to western Victoria, covering approximately 2,000 km. Seventy individuals were collected from five localities across this geographical range and sequenced using Sanger sequencing for the mitochondrial cytochrome c oxidase subunit I (COI) gene. These data indicate that every individual had the same consistent heteroplasmic sites but no other nucleotide variation, suggesting two conserved and widespread heteroplasmic mitogenomes. Ion Torrent shotgun sequencing revealed that heteroplasmy occurred across multiple mitochondrial protein-coding genes and is unlikely explained by transposition of mitochondrial genes into the nuclear genome (NUMTs). DNA sequence data also demonstrated a consistent co-infection of Wolbachia across the A. morosus distribution with every individual infected with both bacterial strains. Our data are consistent with the presence of two mitogenomes within all individuals examined in this species and suggest a major divergence from standard patterns of mitochondrial inheritance. Because the host's mitogenome and the Wolbachia genome are genetically linked through maternal inheritance, we propose three possible hypotheses that could explain maintenance of the widespread and conserved co-occurring bacterial and mitochondrial genomes in this species.
... Synthesis of the core subunits (COI, COII, COIII) takes place within the organelle and later they link themselves to the nuclear encoded subunits located at the periphery (Dennerlein and Rehling, 2015) Mitochondrial genome study assists in the understanding of population genetics. As it is known that mitochondrial genes are conserved evolutionarily, therefore it is possible to evaluate related species in terms of their evolution pattern and molecular changes (Pietan et al., 2016). Earlier researches on codon usage pattern of vertebrate and invertebrate mitochondria could reflect on the trends of gene evolution (Uddin et al., 2018). ...
The phenomenon of non-random occurrence of synonymous nucleotide triplets (codons) in the coding sequences of genes is the codon usage bias (CUB). In this study, we used bioinformatic tool kit to analyze the compositional pattern and CUB of mitogenes namely COI, COII and COIII across different orders of reptiles. Estimation of overall base composition in the protein-coding sequences of COI, COII and COIII genes of the reptilian orders revealed an uneven usage of nucleotides. The overall count of A nucleotide was found to be the highest while the overall count of G nucleotide was the least. The CO genes across the three reptilian orders were prominently AT biased. Comparison of the GC proportion at each codon position displayed that GC1 percentage ranked the highest in all the three CO genes of the reptilian orders. SCUO values indicated weaker CUB, while considerable variation of SCUO values existed in the three CO genes across the studied reptiles. Relative synonymous codon usage (RSCU) values indicated that mostly the A ending codons were preferred. Based on the parameters namely neutrality plot, mutational responsive index and translational selection, we could conclude that natural selection was the major evolutionary force in COI, COII and COIII genes in the studied reptilian orders. However, correspondence analysis, parity plot and correlation studies indicated the existence of mutation pressure as well on the CO genes.
... In this study, we characterized the mitochondrial genome of Geomydoecus aurei, a chewing louse (Phthiraptera: Trichodectidae) found on pocket gophers (Rodentia: Geomyidae). One mitochondrial chromosome bearing the cytochrome oxidase c subunit I gene (cox1) and the trnI (isoleucine) gene of this species was previously characterized [17]. Herein, we characterize 11 additional chromosomes bearing the remaining 35 genes expected for an insect. ...
... Pocket gophers (Thomomys bottae) were collected from Socorro County, New Mexico, with the approval from the New Mexico Department of Game and Fish (Permit #3500). Animals were collected using procedures in keeping with guidelines set by the American Society of Mammalogists [23] as described by Pietan et al. [17]. This study was approved by the University of Northern Iowa Institutional Animal Care and Use Committee. ...
... To characterize the mitochondrial chromosome bearing the rrnL gene, DNA was extracted from the same G. aurei specimen used by Pietan et al. [17] to characterize the cox1 chromosome (JWD 39.6; New Mexico: Socorro Co.; 3.5 mi. S La Joya, 34.317, -106.857; ...
Parasitic lice demonstrate an unusual array of mitochondrial genome architectures and gene arrangements. We characterized the mitochondrial genome of Geomydoecus aurei, a chewing louse (Phthiraptera: Trichodectidae) found on pocket gophers (Rodentia: Geomyidae) using reads from both Illumina and Oxford Nanopore sequencing coupled with PCR, cloning, and Sanger sequencing to verify structure and arrangement for each chromosome. The genome consisted of 12 circular mitochondrial chromosomes ranging in size from 1,318 to 2,088 nucleotides (nt). Total genome size was 19,015 nt. All 37 genes typical of metazoans (2 rRNA genes, 22 tRNA genes, and 13 protein-coding genes) were present. An average of 26% of each chromosome was composed of non-gene sequences. Within the non-gene region of each chromosome, there was a 79-nt nucleotide sequence that was identical among chromosomes and a conserved sequence with secondary structure that was always followed by a poly-T region. We hypothesize that these regions may be important in the initiation of transcription and DNA replication, respectively. The G. aurei genome shares 8 derived gene clusters with other chewing lice of mammals, but in G. aurei, genes on several chromosomes are not contiguous.
... To date, no numts from the mitochondrial D-Loop region in the genome have been identified (Liu & Zhao 2007;Hazkani-Covo et al. 2010). However, many studies have reported heteroplasmy of mitochondrial DNA, including the D-Loop region in vertebrates (Wu et al. 2011;Guo et al. 2013;He et al. 2013;Gorkhali et al. 2015) and invertebrate (Gaji c et al. 2016;Pietan et al. 2016). ...
The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.
Lice are six-legged, wingless, insect parasites of mammals and birds and include two main functional groups: blood-sucking lice and chewing lice. However, it is still not clear whether the Chinese red panda Ailurus styani is infested with the parasitic louse. In the present study, we describe a new genus and a species of chewing louse, Pancola ailurus (Phthiraptera: Trichodectidae) based on morphological and molecular datasets. The morphological features showed Pancola is closer to Paratrichodectes. The genetic divergence of cox1 and 12S rRNA among the Pancola ailurus n. sp. and other Trichodectidae lice was 29.7–34.6% and 38.9–43.6%, respectively. Phylogenetic analyses based on the available mitochondrial gene sequences showed that P. ailurus n. sp. is more closely related to Trichodectes canis and Geomydoecus aurei than to Felicola subrostratus and together nested within the family Trichodectidae. This study is the first record of parasitic lice from the endangered Chinese red panda A. styani and highlights the importance of integrating morphological and molecular datasets for the identification and discrimination of new louse species.
