Mitochondrial genomes within bark lice (Insecta: Psocodea: Psocomorpha) reveal novel gene rearrangements containing phylogenetic signal

2021 ◽  
Author(s):  
Oscar Fernando Saenz Manchola ◽  
Stephany Virrueta Herrera ◽  
Lorenzo Mario D'Alessio ◽  
Kazunori Yoshizawa ◽  
Alfonso Neri García Aldrete ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Novel Gene ◽  
Bark Lice

scholarly journals Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, Hoplobatrachus tigerinus and Euphlyctis hexadactylus, from Bangladesh

2010 ◽  
Vol 85 (3) ◽  
pp. 219-232 ◽  
Author(s):  
Mohammad Shafiqul Alam ◽  
Atsushi Kurabayashi ◽  
Yoko Hayashi ◽  
Naomi Sano ◽  
Md. Mukhlesur Rahman Khan ◽  
...  
Keyword(s):  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Novel Gene ◽  
Hoplobatrachus Tigerinus ◽  
Complete Mitochondrial Genomes

scholarly journals Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1134
Author(s):  
Fei Ye ◽  
Hu Li ◽  
Qiang Xie
Keyword(s):  
Gene Rearrangement ◽  
Hot Spot ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Deep Understanding ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Current View ◽  
Novel Gene ◽  
Spot Group

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

Complete Mitogenome of Threespot Flounder Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae) and Study on the Mechanism of Gene Rearrangement in 13 Bothids

2019 ◽  
Author(s):  
Hairong Luo ◽  
Xiaoyu Kong ◽  
Shixi Chen ◽  
Wei Shi
Keyword(s):  
Gene Rearrangement ◽  
Structural Diversity ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Significant Evidence ◽  
Rearrangement Process ◽  
Genomic Scale ◽  
Complete Mitogenome ◽  
Shed Light ◽  
High Diversity

Abstract Background: The mitochondrial genomes (mitogenomes) of 12 bothids (Pleuronectiformes) from eight genera have been obtained. From the data, the genomic-scale and various gene rearrangements revealed the high diversity of variation in these mitogenomes. Results: A total of 18170 bp of Grammatobothus polyophthalmus mitogenome was determined including 37 genes and two control regions (CRs). Genes encoded by L-strand were grouped to an eight-genes cluster (Q-A-C-Y-S1-ND6-E-P) except for the tRNA-N, other genes encoded by H-strand were grouped together (F-12S … CytB-T) except for the tRNA-D that was translocated to inside of the eight-genes cluster. The mitogenome of G. polyophthalmus and that of 12 known bothids possessed the similar genomic-scale rearrangements with the only differences in the various combinations of CR, tRNA-D and eight-genes cluster, and the shuffling of tRNA-V. Based on the structure character of all 13 bothid mitogenomes, the Dimer-Mitogenome and Non-Random Loss (DMNR) model was fitted to account for all these rearrangements. And the translocation of tRNA-D occurring after the DMNR process in 10 of 13 bothid mitogenomes was confirmed. The striking finding was that each of degenerated genes existing in the gene rearrangement process in 13 bothids had their counterparts of intergenic spaces. Conclusions: The result of corresponding relationship between degenerated genes and intergenic spaces provided the significant evidence to support the possibility of the DMNR model, as well as, the existing of dimeric mitogenome in mitochondrion. The findings of this study were rare phenomenona in teleost fish, which not only promoted the understanding of mitogenome structural diversity, but also shed light on studying of mitochondrial rearrangement and replication.

scholarly journals Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10017
Author(s):  
Raden Pramesa Narakusumo ◽  
Alexander Riedel ◽  
Joan Pons
Keyword(s):  
Amino Acid ◽  
Phylogenetic Signal ◽  
Mitochondrial Protein ◽  
Amino Acid Sequences ◽  
Mitochondrial Genomes ◽  
Length Variation ◽  
Codon Site ◽  
Protein Coding ◽  
Large Variability ◽  
Molecular Features

Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.

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