scholarly journals Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications

2010 ◽  
Vol 10 (1) ◽  
pp. 141 ◽  
Author(s):  
Yasuhisa Okajima ◽  
Yoshinori Kumazawa
Keyword(s):  
Mitochondrial Genomes ◽  
Gene Rearrangements

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 Gene Rearrangements in the Mitochondrial Genomes of Whiteflies (Hemiptera: Aleyrodinae): Plesiomorphies, Synapomorphies and Autapomorphies

2021 ◽  
Author(s):  
Avas Pakrashi ◽  
VIKAS KUMAR ◽  
Dhirti Banerjee ◽  
Kaomud Tyagi ◽  
C. M. Kalleshwaraswamy
Keyword(s):  
Phylogenetic Analyses ◽  
Species Level ◽  
Individual Species ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Gene Block ◽  
Level Data ◽  
The Family ◽  
Codon Positions ◽  
Complete Mitogenome

Abstract Mitochondrial genome rearrangements have been used for defining historical relationships, but there have been incidences of convergences at different taxonomic levels. Here, we sequenced complete mitogenome of Aleurodicus rugioperculatus (Aleyrodidae: Aleurodicinae) to examine gene rearrangements and phylogenetic relationships within the family Aleyrodidae. We identified five gene blocks (I-V) in the whitefly ancestor that are shared plesiomorphies retained in different whitefly lineages. Gene block I is conserved in all whiteflies except three species (Tetraleurodes acaciae and two Bemisia species). Conversely, we detected 83 derived gene boundaries within the family. Mapping these gene boundaries onto a phylogenetic tree revealed that 16 were symplesiomorphies for two subfamilies; 9 were synapomorphies at different taxonomic levels, and 28 autapomorphies for individual species. Bayesian Inference (BI) and Maximum Likelihood (ML) phylogenetic analyses yielded similar topologies supporting the monophyly of Aleyrodinae and Aleurodicinae. Exclusion of PCG third codon positions from phylogenetic analyses improved both node support and consistency with prior analyses. To understand the significance of gene order convergence on phylogeny of the whiteflies, more species-level data is required.

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 Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2786 ◽  
Author(s):  
Siqi Yuan ◽  
Yun Xia ◽  
Yuchi Zheng ◽  
Xiaomao Zeng
Keyword(s):  
Next Generation Sequencing ◽  
Gene Order ◽  
Illumina Miseq ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Next Generation ◽  
Protein Coding ◽  
Alignment Errors ◽  
Generation Sequencing

Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order,Amolops chunganensisandQuasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome ofA. chunganensisandQ. boulengeriare typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome ofQ. boulengeriis characterized with a tandem duplication oftrnM. Moreover, we utilize 13 protein-coding genes ofA. chunganensis,Q. boulengeriand other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity ofA. chunganensisandQ. boulengeri. In this work, we provide nearly complete mitochondrial genomes ofA. chunganensisandQ. boulengeri.

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.

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