scholarly journals Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3901 ◽  
Author(s):  
Zachary R. Hanna ◽  
James B. Henderson ◽  
Anna B. Sellas ◽  
Jérôme Fuchs ◽  
Rauri C.K. Bowie ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Genome Sequences ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Strix Occidentalis Caurina ◽  
Control Regions

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226–19,522 nt in length and included copies of all mitochondrial genes except tRNAPro, ND6, and tRNAGlu. Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes.

scholarly journals Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region

2017 ◽  
Author(s):  
Zachary R Hanna ◽  
James B Henderson ◽  
Anna B Sellas ◽  
Jérôme Fuchs ◽  
Rauri C. K. Bowie ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Genome Sequences ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Northern Spotted Owl ◽  
Strix Occidentalis Caurina

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts).

scholarly journals Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region

2017 ◽  
Author(s):  
Zachary R Hanna ◽  
James B Henderson ◽  
Anna B Sellas ◽  
Jérôme Fuchs ◽  
Rauri C. K. Bowie ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Genome Sequences ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Northern Spotted Owl ◽  
Strix Occidentalis Caurina

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts).

scholarly journals Comparison of the mitochondrial genomes of the Old and New World strains of the legume pod borer, Maruca vitrata (Lepidoptera: Crambidae)

2017 ◽  
Vol 37 (03) ◽  
pp. 125-136
Author(s):  
Tolulope A. Agunbiade ◽  
Brad S. Coates ◽  
Weilin Sun ◽  
Mu-Rou Tsai ◽  
Maria Carmen Valero ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
New World ◽  
De Novo ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Maruca Vitrata ◽  
Mitochondrial Genomes ◽  
Old World ◽  
Pod Borer ◽  
Legume Pod Borer

Abstract Maruca vitrata (Fabricius, 1787) is a cryptic pantropical species of Lepidoptera that are comprised of two unique strains that inhabit the American continents (New World strain) and regions spanning from Africa through to Southeast Asia and Northern Australia (Old World strain). In this study, we de novo assembled the complete mitochondrial genome sequence of the New World legume pod borer, M. vitrata, from shotgun sequence data generated on an Illumina HiSeq 2000. Phylogenomic comparisons were made with other previously published mitochondrial genome sequences from crambid moths, including the Old World strain of M. vitrata. The 15,385 bp M. vitrata (New World) sequence has an 80.7% A+T content and encodes the 13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes in the typical orientation and arrangement of lepidopteran mitochondrial DNAs. Mitochondrial genome-wide comparison between the New and Old World strains of M. vitrata detected 476 polymorphic sites (4.23% nucleotide divergence) with an excess of synonymous substitution as a result of purifying selection. Furthermore, this level of sequence variation suggests that these strains diverged from ~1.83 to 2.12 million years ago, assuming a linear rate of short-term substitution. The de novo assemblies of mitochondrial genomes from next-generation sequencing (NGS) reads provide readily available data for similar comparative studies.

scholarly journals The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum

2018 ◽  
Vol 4 ◽  
Author(s):  
Helen E. Robertson ◽  
Philipp H. Schiffer ◽  
Maximilian J. Telford
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Limited Support ◽  
Cell Layers

Abstract The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14 247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.

scholarly journals SMART: Statistical Mitogenome Assembly with Repeats

2019 ◽  
Author(s):  
Fahad Alqahtani ◽  
Ion I. Măndoiu
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Complete Mitochondrial Genome ◽  
Bootstrap Support ◽  
Mitochondrial Genomes ◽  
Genome Sequences ◽  
Genome Database ◽  
Sequencing Technologies ◽  
Likelihood Model ◽  
Low Coverage

AbstractBy using next-generation sequencing technologies it is possible to quickly and inexpensively generate large numbers of relatively short reads from both the nuclear and mitochondrial DNA contained in a biological sample. Unfortunately, assembling such whole-genome sequencing (WGS) data with standard de novo assemblers often fails to generate high quality mitochondrial genome sequences due to the large difference in copy number (and hence sequencing depth) between the mitochondrial and nuclear genomes. Assembly of complete mitochondrial genome sequences is further complicated by the fact that many de novo assemblers are not designed for circular genomes, and by the presence of repeats in the mitochondrial genomes of some species.In this paper we describe the Statistical Mitogenome Assembly with Repeats (SMART) pipeline for automated assembly of complete circular mitochondrial genomes from WGS data. SMART uses an efficient coverage-based filter to first select a subset of reads enriched in mtDNA sequences. Contigs produced by an initial assembly step are filtered using BLAST searches against a comprehensive mitochondrial genome database, and used as “baits” for an alignment-based filter that produces the set of reads used in a second de novo assembly and scaffolding step. In the presence of repeats, the possible paths through the assembly graph are evaluated using a maximum-likelihood model. Additionally, the assembly process is repeated a user-specified number of times on re-sampled subsets of reads to select for annotation the reconstructed sequences with highest bootstrap support.Experiments on WGS datasets from a variety of species show that the SMART pipeline produces complete circular mitochondrial genome sequences with a higher success rate than current state-of-the art tools, even from low coverage WGS data. The pipeline is available through an easy-to-use web interface at https://neo.engr.uconn.edu/?tool_id=SMART.

Seven complete mitochondrial genome sequences of bushtits (Passeriformes, Aegithalidae,Aegithalos): the evolution pattern in duplicated control regions

2015 ◽  
Vol 26 (3) ◽  
pp. 350-356 ◽  
Author(s):  
Xiaoyang Wang ◽  
Yuan Huang ◽  
Nian Liu ◽  
Jing Yang ◽  
Fumin Lei
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Genome Sequences ◽  
Evolution Pattern ◽  
Control Regions

scholarly journals Highly rearranged mitochondrial genome in Nycteria parasites (Haemosporidia) from bats

2016 ◽  
Vol 113 (35) ◽  
pp. 9834-9839 ◽  
Author(s):  
Gregory Karadjian ◽  
Alexandre Hassanin ◽  
Benjamin Saintpierre ◽  
Guy-Crispin Gembu Tungaluna ◽  
Frederic Ariey ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mitochondrial Genome ◽  
Evolutionary History ◽  
Complete Mitochondrial Genome ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
History Of ◽  
Generation Sequencing ◽  
Complete Mitochondrial Genomes

Haemosporidia parasites have mostly and abundantly been described using mitochondrial genes, and in particular cytochrome b (cytb). Failure to amplify the mitochondrial cytb gene of Nycteria parasites isolated from Nycteridae bats has been recently reported. Bats are hosts to a diverse and profuse array of Haemosporidia parasites that remain largely unstudied. There is a need to obtain more molecular data from chiropteran parasites. Such data would help to better understand the evolutionary history of Haemosporidia, which notably include the Plasmodium parasites, malaria’s agents. We use next-generation sequencing to obtain the complete mitochondrial genome of Nycteria parasites from African Nycteris grandis (Nycteridae) and Rhinolophus alcyone (Rhinolophidae) and Asian Megaderma spasma (Megadermatidae). We report four complete mitochondrial genomes, including two rearranged mitochondrial genomes within Haemosporidia. Our results open outlooks into potentially undiscovered Haemosporidian diversity.

scholarly journals The complete mitochondrial genome sequences of Japanese earthworms Metaphire hilgendorfi and Amynthas yunoshimensis (Clitellata: Megascolecidae)

2021 ◽  
Vol 6 (3) ◽  
pp. 965-967
Author(s):  
Akira Seto ◽  
Hayato Endo ◽  
Yukio Minamiya ◽  
Masaru Matsuda
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Genome Sequences
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