scholarly journals Widespread co-occurrence of two distantly related mitochondrial genomes in individuals of the leaf beetle Gonioctena intermedia

2017 ◽  
Vol 13 (11) ◽  
pp. 20170570 ◽  
Author(s):  
Chedly Kastally ◽  
Patrick Mardulyn
Keyword(s):  
Mitochondrial Genome ◽  
Sanger Sequencing ◽  
Leaf Beetle ◽  
Universal Primers ◽  
Mitochondrial Genomes ◽  
Single Individual ◽  
Sequencing Technologies ◽  
Pcr Products ◽  
Nucleotide Divergence ◽  
Genomic Variant

Mitochondrial genome heteroplasmy—the presence of more than one genomic variant in individuals—is considered only occasional in animals, and most often involves molecules differing only by a few recent mutations. Thanks to new sequencing technologies, a large number of DNA fragments from a single individual can now be sequenced and visualized separately, allowing new insights into intra-individual mitochondrial genome variation. Here, we report evidence from both (i) massive parallel sequencing (MPS) of genomic extracts and (ii) Sanger sequencing of PCR products, for the widespread co-occurrence of two distantly related (greater than 1% nucleotide divergence, excluding the control region) mitochondrial genomes in individuals of a natural population of the leaf beetle Gonioctena intermedia . Sanger sequencing of PCR products using universal primers previously failed to identify heteroplasmy in this population. Its occurrence was detected with MPS data and may have important implications for evolutionary studies. It suggests the need to re-evaluate, using MPS techniques, the proportion of animal species displaying heteroplasmy.

scholarly journals The Complete Mitochondrial Genome of One Breeding Strain of Asian Swamp Eel (Monopterus albus, Zuiew 1793) Using PacBio and Illumina Sequencing Technologies and Phylogenetic Analysis in Synbranchiformes

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1567
Author(s):  
Haifeng Tian ◽  
Qiaomu Hu ◽  
Hongyi Lu ◽  
Zhong Li
Keyword(s):  
Mitochondrial Genome ◽  
Illumina Sequencing ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Sequencing Technologies ◽  
Asian Swamp Eel ◽  
Swamp Eel ◽  
Complete Mitochondrial Genomes

Asian swamp eel (Monopterus albus, Zuiew 1793) is a commercially important fish due to its nutritional value in Eastern and Southeastern Asia. One local strain of M. albus distributed in the Jianghan Plain of China has been subjected to a selection breeding program because of its preferred body color and superiority of growth and fecundity. Some members of the genus Monopterus have been reclassified into other genera recently. These classifications require further phylogenetic analyses. In this study, the complete mitochondrial genomes of the breeds of M. albus were decoded using both PacBio and Illumina sequencing technologies, then phylogenetic analyses were carried out, including sampling of M. albus at five different sites and 14 species of Synbranchiformes with complete mitochondrial genomes. The total length of the mitogenome is 16,621 bp, which is one nucleotide shorter than that of four mitogenomes of M. albus sampled from four provinces in China, as well as one with an unknown sampling site. The gene content, gene order, and overall base compositions are almost identical to the five reported ones. The results of maximum likelihood (ML) and Bayesian inference analyses of the complete mitochondrial genome and 13 protein-coding genes (PCGs) were consistent. The phylogenetic trees indicated that the selecting breed formed the deepest branch in the clade of all Asian swamp eels, confirmed the phylogenetic relationships of four genera of the family Synbranchidae, also providing systematic phylogenetic relationships for the order Synbranchiformes. The divergence time analyses showed that all Asian swamp eels diverged about 0.49 million years ago (MYA) and their common ancestor split from other species about 45.96 MYA in the middle of the Miocene epoch. Altogether, the complete mitogenome of this breed of M. albus would serve as an important dataset for germplasm identification and breeding programs for this species, in addition to providing great help in identifying the phylogenetic relationships of the order Synbranchiformes.

scholarly journals Characterization of Penaeus vannamei mitogenome focusing on genetic diversity

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255291
Author(s):  
Paulo Eduardo T. Soares ◽  
Márcia Danielle A. Dantas ◽  
Rita de Cássia B. Silva-Portela ◽  
Lucymara F. Agnez-Lima ◽  
Daniel Carlos F. Lanza
Keyword(s):  
Mitochondrial Genome ◽  
Low Frequency ◽  
Individual Variability ◽  
Mitochondrial Genomes ◽  
Penaeus Vannamei ◽  
Single Individual ◽  
Variable Regions ◽  
Mitochondrial Markers ◽  
Hypervariable Regions

The diversity of the Penaeus vannamei mitochondrial genome has still been poorly characterized, there are no validated mitochondrial markers available for populational studies, and the heteroplasmy has not yet been investigated in this species. In this study, metagenomic reads extracted from the muscle of a single individual were used to assemble the mitochondrial genome (mtDNA). These data associated with mitochondrial genomes previously described allowed to evaluate the inter-individual variability and heteroplasmy. Comparison among 45 mtDNA control regions led to the detection of conserved and variable segments and the characterization of two hypervariable regions. The analysis of diversity revealed mostly low frequency polymorphisms, and heteroplasmy was found in practically all mitochondrial genes, with a high occurrence of indels. These results indicate that the design of mitochondrial markers for P. vannamei must be done with caution. The mapping of conserved and variable regions and the characterization of heteroplasmy presented here will contribute to increasing the efficiency of mitochondrial markers for population or individual studies.

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.

Co-amplification of mitochondrial pseudogenes in Calomys musculinus (Rodentia, Cricetidae): a source of error in phylogeographic studies

Genome ◽  
2008 ◽  
Vol 51 (1) ◽  
pp. 73-78 ◽  
Author(s):  
Raúl E. González-Ittig ◽  
Cristina N. Gardenal
Keyword(s):  
Single Individual ◽  
Loop Region ◽  
Pcr Product ◽  
Calomys Musculinus ◽  
Pcr Rflp ◽  
Pcr Products ◽  
D Loop ◽  
Nucleotide Divergence ◽  
Source Of Error ◽  
Phylogeographic Study

In a previous phylogeographic study of the rodent Calomys musculinus , 24 haplotypes of the mitochondrial DNA D-loop region were detected using the restriction fragment length polymorphism technique (PCR-RFLP). Seven percent of the individuals showed patterns in which the sum of the sizes of the restriction fragments exceeded the size of the original PCR product. In the present paper we analyze possible causes of these atypical haplotypes. PCR products were cloned, and two or three different clones from a single individual were detected by their RFLP patterns. Nine clones with different restriction patterns were selected for sequence analyses. A maximum parsimony phylogenetic analysis revealed two well-supported paraphyletic groups. One group comprised sequences showing low nucleotide divergence compared with the most common haplotypes detected in the phylogeographic study. The other group was basal to the three species of Calomys other than C. musculinus included in the study; the mutations in the short portion of the cytochrome b gene amplified corresponded to 12 amino acid substitutions. The results suggest that two independent insertions of mtDNA sequences into the nucleus occurred; these sequences would co-amplify in the PCR procedure. Identification of pseudogenes is crucial to obtain reliable reconstruction of the intraspecific genealogy in phylogeographic studies.

scholarly journals Mitochondrial genome evolution in pelagophyte algae

2021 ◽  
Author(s):  
Shannon J Sibbald ◽  
Maggie Lawton ◽  
John M Archibald
Keyword(s):  
Mitochondrial Genome ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
23S Rrna ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Unique Region ◽  
Long Read ◽  
Genomic Studies ◽  
Aureoumbra Lagunensis

Abstract The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756) and five strains of A. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984 and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 base-pairs (bp) (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five A. anophagefferens strains varied slightly in length (42,401 bp—42,621 bp) and were 99.4%-100.0% identical. Gene content and order was highly conserved between the A. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in A. anophagefferens containing DNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. While the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five A. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to non-bloom-forming species.

scholarly journals HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1125
Author(s):  
Sontaga Manyana ◽  
Lilishia Gounder ◽  
Melendhran Pillay ◽  
Justen Manasa ◽  
Kogieleum Naidoo ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Sanger Sequencing ◽  
Clinical Diagnostics ◽  
Treatment Programs ◽  
People Living With Hiv ◽  
Resource Limited Settings ◽  
Gold Standard Method ◽  
Sequencing Technologies ◽  
Resource Limited ◽  
Hiv 1

Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.

The mitochondrial genome organization of a maize fertile cmsT revertant line is generated through recombination between two sets of repeats.

Genetics ◽  
1990 ◽  
Vol 124 (2) ◽  
pp. 423-428 ◽  
Author(s):  
C M Fauron ◽  
M Havlik ◽  
R I Brettell
Keyword(s):  
Mitochondrial Genome ◽  
Genome Organization ◽  
Callus Tissue ◽  
Mitochondrial Genomes ◽  
Normal Type ◽  
Male Sterile ◽  
Sequence Complexity ◽  
Mtdna Organization ◽  
Callus Tissue Culture ◽  
Fertile Revertant

Abstract The mitochondrial genome (mtDNA) organization from a fertile revertant line (V3) derived from the maize cytoplasmic male sterile type T (cmsT) callus tissue culture has been determined. We report that the sequence complexity can be mapped on to a circular "master chromosome" of 705 kb which includes a duplication of 165 kb of DNA when compared to its male sterile progenitor. Associated with this event is also a 0.423-kb deletion, which removed the cmsT-associated urf13 gene. As found for the maize normal type (N) and cmsT mitochondrial genomes, the V3 master chromosome also exists as a multipartite structure generated by recombination through repeated sequences.

scholarly journals Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
J. Robert Macey ◽  
Stephan Pabinger ◽  
Charles G. Barbieri ◽  
Ella S. Buring ◽  
Vanessa L. Gonzalez ◽  
...  
Keyword(s):  
Genomic Organization ◽  
Phylogenetic Analyses ◽  
Genomic Polymorphism ◽  
Sequencing Technologies ◽  
Cold Tolerant ◽  
Long Read ◽  
Sphenodon Punctatus ◽  
Nucleotide Divergence ◽  
Mitochondrial Heteroplasmy ◽  
Transmembrane Regions

AbstractAnimal mitochondrial genomic polymorphism occurs as low-level mitochondrial heteroplasmy and deeply divergent co-existing molecules. The latter is rare, known only in bivalvian mollusks. Here we show two deeply divergent co-existing mt-genomes in a vertebrate through genomic sequencing of the Tuatara (Sphenodon punctatus), the sole-representative of an ancient reptilian Order. The two molecules, revealed using a combination of short-read and long-read sequencing technologies, differ by 10.4% nucleotide divergence. A single long-read covers an entire mt-molecule for both strands. Phylogenetic analyses suggest a 7–8 million-year divergence between genomes. Contrary to earlier reports, all 37 genes typical of animal mitochondria, with drastic gene rearrangements, are confirmed for both mt-genomes. Also unique to vertebrates, concerted evolution drives three near-identical putative Control Region non-coding blocks. Evidence of positive selection at sites linked to metabolically important transmembrane regions of encoded proteins suggests these two mt-genomes may confer an adaptive advantage for an unusually cold-tolerant reptile.

Mitochondrial genome assembly v1

2020 ◽  
Author(s):  
Graham Etherington
Keyword(s):  
Mitochondrial Genome ◽  
Genome Assembly ◽  
De Novo Assembly ◽  
De Novo ◽  
Mitochondrial Genomes

De novo assembly of 49 mustelid whole mitochondrial genomes

scholarly journals Rapid Detection of Phytophthora infestans in Late Blight-Infected Potato and Tomato Using PCR

Plant Disease ◽  
1997 ◽  
Vol 81 (9) ◽  
pp. 1042-1048 ◽  
Author(s):  
C. L. Trout ◽  
J. B. Ristaino ◽  
M. Madritch ◽  
T. Wangsomboondee
Keyword(s):  
Late Blight ◽  
Phytophthora Infestans ◽  
Pcr Amplification ◽  
Accurate Method ◽  
Phytophthora Species ◽  
Universal Primers ◽  
Direct Pcr ◽  
Field Samples ◽  
Pcr Products ◽  
Oomycete Pathogen

Late blight caused by the oomycete pathogen Phytophthora infestans is a devastating disease of potato and tomato worldwide. A rapid and accurate method for specific detection of P. infestans is necessary for determination of late blight in infected fruit, leaves, and tubers. Ribosomal DNA (rDNA) from four isolates of P. infestans representing the four genotypes US1, US6, US7, and US8 was amplified using polymerase chain reaction (PCR) and the universal primers internal transcribed spacer (ITS) 4 and ITS5. PCR products were sequenced using an automated sequencer. Sequences were aligned with published sequences from 5 other Phytophthora species, and a region specific to P. infestans was used to construct a PCR primer (PINF). Over 140 isolates representing 14 species of Phytophthora and at least 13 other genera of fungi and bacteria were used to screen the PINF primer. PCR amplification with primers PINF and ITS5 results in amplification of an approximately 600 base pair product with only isolates of P. infestans from potato and tomato, as well as isolates of P. mirabilis and P. cactorum. P. mirabilis and P. cactorum are not pathogens of potato; however, P. cactorum is a pathogen of tomato. P. infestans and P. cactorum were differentiated by restriction digests of the amplified product. The PINF primer was used with a rapid NaOH lysis technique for direct PCR of P. infestans from infected tomato and potato field samples. The PINF primer will provide a valuable tool for detection of P. infestans in potatoes and tomatoes.

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