Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'

2002 ◽  
Vol 16 (3) ◽  
pp. 345 ◽  
Author(s):  
M. Dowton ◽  
L. R. Castro ◽  
A. D. Austin
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Gene Rearrangement ◽  
Mitochondrial Gene ◽  
Molecular Data ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Genome Organisation ◽  
Rearrangement Mechanism ◽  
Molecular Characters

Mitochondrial gene rearrangements are the latest tool in the arsenal of phylogeneticists for investigating historical relationships. They are complex molecular characters that may provide more reliable evidence of ancestry than comparative molecular data. Here we review the phylogenetic utility of mitochondrial gene rearrangements, and find that despite isolated incidences of convergence, derived gene order appears highly congruent with phylogenies produced from other sources of data. We calculate that the chance of two mitochondrial genomes sharing the same derived genome organisation is only 1/2664, but caution that this ignores the possibility that the (as yet uncharacterised) gene rearrangement mechanism may greatly increase the chance of convergence. Broader taxonomic surveys of mitochondrial genome organisation will lead to a more realistic indication of the historical incidence of convergence in genome organisation.

scholarly journals Linear Mitochondrial genome in Anthozoa (Cnidaria): A case study in Ceriantharia

2018 ◽  
Author(s):  
Sergio N Stampar ◽  
Michael B Broe ◽  
Jason Macrander ◽  
Adam M Reitzel ◽  
Marymegan Daly
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Mitochondrial Gene ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Gene Sequences ◽  
Phylogenetic Placement ◽  
Organellar Genome ◽  
Linear Mitochondrial Genome

Sequences and structural attributes of mitochondrial genomes have played a key role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia ("tube anemones") remains one of the most enigmatic groups in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both ceriantharian species studied, the mitochondrial gene sequences could not be assembled into a circular genome. Instead, our analyses suggest both species have fragmented mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The number of fragments and the variation in gene order between species is much greater in Ceriantharia than among Medusozoa. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other anthozoan groups.

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 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 Linear Mitochondrial genome in Anthozoa (Cnidaria): A case study in Ceriantharia

2018 ◽  
Author(s):  
Sergio N Stampar ◽  
Michael B Broe ◽  
Jason Macrander ◽  
Adam M Reitzel ◽  
Marymegan Daly
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Mitochondrial Gene ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Gene Sequences ◽  
Phylogenetic Placement ◽  
Organellar Genome ◽  
Linear Mitochondrial Genome

Sequences and structural attributes of mitochondrial genomes have played a key role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia ("tube anemones") remains one of the most enigmatic groups in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both ceriantharian species studied, the mitochondrial gene sequences could not be assembled into a circular genome. Instead, our analyses suggest both species have fragmented mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The number of fragments and the variation in gene order between species is much greater in Ceriantharia than among Medusozoa. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other anthozoan groups.

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 Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kun Zhang ◽  
Kehua Zhu ◽  
Yifan Liu ◽  
Hua Zhang ◽  
Li Gong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Tandem Duplication ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Muraenesox Cinereus ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

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.

scholarly journals The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ying-ying Ye ◽  
Jing Miao ◽  
Ya-hong Guo ◽  
Li Gong ◽  
Li-hua Jiang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Phylogenetic Studies ◽  
Gc Skew ◽  
Strong Bootstrap Support

AbstractThe complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

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.

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