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

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 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 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.

scholarly journals A new mitochondrial gene order in the banded cusk-eel Raneya brasiliensis (Actinopterygii, Ophidiiformes)

2018 ◽  
Vol 4 (1) ◽  
pp. 1-4 ◽  
Author(s):  
Amir Fromm ◽  
Stephen D. Atkinson ◽  
Gema Alama-Bermejo ◽  
Paulyn Cartwright ◽  
Jerri L. Bartholomew ◽  
...  
Keyword(s):  
Gene Order ◽  
Mitochondrial Gene ◽  
Mitochondrial Gene Order

scholarly journals A novel mitochondrial gene order in shorebirds (Scolopacidae, Charadriiformes)

2010 ◽  
Vol 57 (1) ◽  
pp. 411-416 ◽  
Author(s):  
Yvonne I. Verkuil ◽  
Theunis Piersma ◽  
Allan J. Baker
Keyword(s):  
Gene Order ◽  
Mitochondrial Gene ◽  
Mitochondrial Gene Order
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