scholarly journals Precise annotation of tick mitochondrial genomes reveals multiple STR variation and one transposon-like element

2019 ◽  
Author(s):  
Ze Chen ◽  
Xiaofeng Xu ◽  
Xiaolong Yang ◽  
Zhijun Yu ◽  
Yonghong Hu ◽  
...  
Keyword(s):  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Pcr Amplification ◽  
Mitochondrial Genomes ◽  
Accession Number ◽  
Intraindividual Variation ◽  
Dna Variation ◽  
Genomic Structural Variation ◽  
Repeat Units ◽  
Mitochondrial Gene Order

AbstractIn this study, we used long-PCR amplification combined with Next-Generation Sequencing (NGS) to obtain complete mitochondrial genomes of individual ticks and performed precise annotation of these genomes. These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Based on these annotations, most of our findings were consistent with those from previous studies. Moreover, two important findings were reported for the first time, contributing fundamental knowledge to mitochondrial biology. The first was the discovery of a transposon-like element that may reveal the mechanisms of mitochondrial gene order rearrangement and genomic structural variation. Another finding was that Short Tandem Repeat (STRs) are the dominant variation type causing mitochondrial sequence diversity within an individual tick, insect, mouse and human. Comparisons between interindividual and intraindividual variation showed that polynucleotides and STRs with longer repeat units had the same variation pattern. Particularly, mitochondria containing deleterious mutations can accumulate in cells and deleterious STR mutations irreversibly change the proteins made from their mRNAs. Therefore, we proposed that deleterious STR mutations in mitochondria cause aging and diseases. This finding helped to ultimately reveal the mechanisms of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will give rise to the reconsideration of the importance of STRs and a unified study of STR variation with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mitochondrial genomes. The complete mitochondrial genome sequence of Dermacentor silvarum is available at the NCBI GenBank database under the accession number MN347015 and the raw data is available at the NCBI SRA database under the accession number SRP178347.

scholarly journals Comprehensive Analyses of the Complete Mitochondrial Genome of Figulus binodulus (Coleoptera: Lucanidae)

2020 ◽  
Vol 20 (5) ◽  
Author(s):  
Jungmo Lee ◽  
Jonghyun Park ◽  
Hong Xi ◽  
Jongsun Park
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Mitochondrial Gene Order ◽  
Rna Genes ◽  
Simple Sequence

Abstract Figulus binodulus Waterhouse is a small stag beetle distributed in East Asia. We determined the first mitochondrial genome of F. binodulus of which is 16,261-bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large noncoding region of 1,717 bp. Gene order of F. binodulus is identical to the ancestral insect mitochondrial gene order as in most other stag beetle species. All of 22 tRNAs could be shaped into typical clover-leaf structure except trnSer1. Comparative analyses of 21 Lucanidae mitochondrial genomes was conducted in aspect of their length and AT-GC ratio. Nucleotide diversities analyses provide that cox1 and cox2 in Lucanidae are less diverse than those of Scarabaeoidea. Fifty simple sequence repeats (SSRs) were identified on F. binodulus mitochondrial genome. Comparative analysis of SSRs among five mitochondrial genomes displayed similar trend along with SSR types. Figulus binodulus was sister to all other available family Lucanidae species in the phylogenetic tree.

scholarly journals Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element

2020 ◽  
Author(s):  
Ze Chen ◽  
Yibo Xuan ◽  
Guangcai Liang ◽  
Xiaolong Yang ◽  
Zhijun Yu ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Pcr Amplification ◽  
Mitochondrial Genomes ◽  
Mt Dna ◽  
Dna Variation ◽  
Number Variation ◽  
Short Tandem

Abstract Background: In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotation of these mt genomes. We aimed to: (1) to develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal containing miniscule DNA (e.g. Dermacentor silvarum); (2) to provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) to detect and analyze mt DNA variation within an individual tick.Results: These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and can produce deleterious proteins. Conclusions: We proposed that the accumulation of CNV of STRs in mitochondria may cause aging or diseases. Future tests of the CNV of STRs hypothesis help to ultimately reveal the genetic basis of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.

scholarly journals Initial Phylotranscriptomic Confirmation of Homoplastic Evolution of the Conspicuous Coloration and Bufoniform Morphology of Pumpkin-Toadlets in the Genus Brachycephalus

Toxins ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 816
Author(s):  
Mariana L. Lyra ◽  
Juliane P. C. Monteiro ◽  
Loïs Rancilhac ◽  
Iker Irisarri ◽  
Sven Künzel ◽  
...  
Keyword(s):  
Gene Order ◽  
Convergent Evolution ◽  
Ecological Study ◽  
Mitochondrial Gene ◽  
Mitochondrial Genomes ◽  
Data Sets ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Mitochondrial Gene Order ◽  
Rnaseq Data

The genus Brachycephalus is a fascinating group of miniaturized anurans from the Brazilian Atlantic Forest, comprising the conspicuous, brightly colored pumpkin-toadlets and the cryptic flea-toads. Pumpkin-toadlets are known to contain tetrodotoxins and therefore, their bright colors may perform an aposematic function. Previous studies based on a limited number of mitochondrial and nuclear-encoded markers supported the existence of two clades containing species of pumpkin-toadlet phenotype, but deep nodes remained largely unresolved or conflicting between data sets. We use new RNAseq data of 17 individuals from nine Brachycephalus species to infer their evolutionary relationships from a phylogenomic perspective. Analyses of almost 5300 nuclear-encoded ortholog protein-coding genes and full mitochondrial genomes confirmed the existence of two separate pumpkin-toadlet clades, suggesting the convergent evolution (or multiple reversals) of the bufoniform morphology, conspicuous coloration, and probably toxicity. In addition, the study of the mitochondrial gene order revealed that three species (B. hermogenesi, B. pitanga, and B. rotenbergae) display translocations of different tRNAs (NCY and CYA) from the WANCY tRNA cluster to a position between the genes ATP6 and COIII, showing a new mitochondrial gene order arrangement for vertebrates. The newly clarified phylogeny suggests that Brachycephalus has the potential to become a promising model taxon to understand the evolution of coloration, body plan and toxicity. Given that toxicity information is available for only few species of Brachycephalus, without data for any flea-toad species, we also emphasize the need for a wider screening of toxicity across species, together with more in-depth functional and ecological study of their phenotypes.

scholarly journals Mitochondrial DNA and their nuclear copies in parasitic wasp Pteromalus puparum: A comparative analysis in Chalcidoidea

2018 ◽  
Author(s):  
Zhichao Yan ◽  
Qi Fang ◽  
Yu Tian ◽  
Fang Wang ◽  
Xuexin Chen ◽  
...  
Keyword(s):  
Control Region ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Parasitic Wasp ◽  
Mitochondrial Genomes ◽  
Coding Regions ◽  
Pteromalus Puparum ◽  
Mitochondrial Origin ◽  
Nuclear Degradation

AbstractChalcidoidea (chalcidoid wasps) are an abundant and megadiverse insect group with both ecological and economical importance. Here we report a complete mitochondrial genome in Chalcidoidea from Pteromalus puparum (Pteromalidae). Eight tandem repeats followed by 6 reversed repeats were detected in its 3,308 bp control region. This long and complex control region may explain failures of amplifying and sequencing of complete mitochondrial genomes in some chalcidoids. In addition to 37 typical mitochondrial genes, an extra identical isoleucine tRNA (trnI) was detected. We speculate this recent mitochondrial gene duplication indicates that gene arrangements in chalcidoids are ongoing. A comparison among available chalcidoid mitochondrial genomes, reveals rapid gene order rearrangements overall, and high substitution rate in P. puparum. In addition, we identified 24 nuclear sequences of mitochondrial origin (NUMTs) in P. puparum, summing up to 9,989 bp, with 3,617 bp of these NUMTs originating from mitochondrial coding regions. NUMTs abundance in P. puparum is only one-twelfth of that in its relative, Nasonia vitripennis. Based on phylogenetic analysis, we provide evidence that a faster nuclear degradation rate contributes to the reduced NUMT numbers in P. puparum. Overall, our study shows unusually high rates of mitochondrial evolution and considerable variation in NUMT accumulation in Chalcidoidea.

scholarly journals Complete Mitochondrial Genome of Phoneutria Boliviensis (Araneae, Ctenidae): New Insights Into the Phylogeny and Evolution of Spider

2021 ◽  
Author(s):  
Carlos Fernando Prada ◽  
Lida Marcela Franco ◽  
Felipe Cabarcas
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
High Rate ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Order Analysis ◽  
Phylogeny And Evolution ◽  
The Relationship

Abstract Spiders are the most abundant land predators and megadiverse on earth. In recent years, the mitochondrial genome has been sequenced, mainly for ecological and commercial purposes, reporting some level of rearrangements in this genome. However, there is poor genetic information in several taxonomic families of spiders. The aim of this study was to obtain the sequence of the complete genome of Phoneutria boliviensis and, based on this, extract the mitogenomes of other species of the family Ctenidae from published transcriptomes to perform a comparative study among spider species to determine the relationship between the level of mitochondrial rearrangement and its possible relationship with molecular variability in spiders. Complete mitochondrial genomes of eighteen spiders (including nine Ctenidae species) were obtained by two different methodologies (sequencing and transcriptome extraction). Fifty-eight spider mitochondrial genomes were downloaded from the NCBI database for gene order analysis. After verifying the annotation of each mitochondrial gene, a phylogeny and gene order, analysis from 76 spider mitochondrial genomes was obtained. Our results show a high rate of annotation error in the mitochondrial genomes of spiders published in databases, which could lead to false phylogenetic relationships. Moreover, to provide new mitochondrial genomes in spiders by two different methodologies to obtain them, our analysis identifies six different mitochondrial architectures among all spiders. Translocation or tandem duplication random loss (TDRL) events in tRNA genes were identified to explain the evolution of the spider mitochondrial genome. In addition, our findings provide new insights into spider mitochondrial evolution.

scholarly journals Bird Mitochondrial Gene Order: Insight from 3 Warbler Mitochondrial Genomes

2008 ◽  
Vol 25 (3) ◽  
pp. 475-477 ◽  
Author(s):  
Tiratha Raj Singh ◽  
Ophir Shneor ◽  
Dorothée Huchon
Keyword(s):  
Gene Order ◽  
Mitochondrial Gene ◽  
Mitochondrial Genomes ◽  
Mitochondrial Gene Order

Insect mitochondrial genomics 3: the complete mitochondrial genome sequences of representatives from two neuropteroid orders: a dobsonfly (order Megaloptera) and a giant lacewing and an owlfly (order Neuroptera)

Genome ◽  
2009 ◽  
Vol 52 (1) ◽  
pp. 31-38 ◽  
Author(s):  
Andrew T. Beckenbach ◽  
James Bruce Stewart
Keyword(s):  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Noncoding Region ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Base Pairs ◽  
Major Noncoding Region ◽  
Myrmeleon Immaculatus ◽  
Complete Mitochondrial Genomes

We describe the complete mitochondrial genomes from representatives of two orders of the Neuropterida: a dobsonfly, Corydalus cornutus (Megaloptera: Corydalidae, GenBank Accession No. FJ171323), a giant lacewing Polystoechotes punctatus (Neuroptera: Polystoechotidae, FJ171325), and an owlfly, Ascaloptynx appendiculatus (Neuroptera: Ascalaphidae, FJ171324). The dobsonfly sequence is 15 687 base pairs with a major noncoding (A+T rich) region of approximately 967 bp. The gene content and organization of the dobsonfly is identical to that of most insects. The giant lacewing sequence is 16 036 bp with a major noncoding region of about 1123 bp, while the owlfly sequence is 15 877 bp with a major noncoding region of about 1066 bp. The two Neuroptera sequences include a transposition of two tRNA genes, tRNATrp and tRNACys. These tRNA genes are coded on opposite strands and overlap by seven residues in the standard insect mitochondrial gene arrangement. Thus, the transposition required a duplication of at least the region of overlap. It is likely that the transposition occurred by a duplication of both genes followed by deletion of one copy of each gene. Examination of this region in two other neuropteroid species, a snakefly, Agulla sp. (Raphidioptera: Raphidiidae), and an antlion, Myrmeleon immaculatus (Neuroptera: Myrmeleontidae), shows that the rearrangement is widespread in the order Neuroptera but not present in either of the other two orders of Neuropterida.

scholarly journals Not Frozen in the Ice: large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish

2021 ◽  
Author(s):  
Chiara Papetti ◽  
Massimiliano Babbucci ◽  
Agnes Dettai ◽  
Andrea Basso ◽  
Magnus Lucassen ◽  
...  
Keyword(s):  
Gene Order ◽  
Hot Spot ◽  
Mitochondrial Gene ◽  
Antarctic Fish ◽  
Purifying Selection ◽  
Compositional Bias ◽  
Mitochondrial Genomes ◽  
Notothenioid Fish ◽  
Antarctic Notothenioids ◽  
The Antarctic

Abstract The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analysed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analysing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesised that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

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