Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes

2018 ◽  
Vol 15 (1) ◽  
pp. 83-95 ◽  
Author(s):  
Tom Hartmann ◽  
An-Chiang Chu ◽  
Martin Middendorf ◽  
Matthias Bernt
Keyword(s):  
Tandem Duplication ◽  
Random Loss

TANDEM DUPLICATION RANDOM LOSS EVENTS INFLUENCED TO GENE ORDER CHANGES IN BAIKALIAN AMPHIPODS

2018 ◽  
Author(s):  
E.A. SIROTININA ◽  
◽  
E.V. ROMANOVA ◽  
D. YU. SHERBAKOV ◽  
◽  
...  
Keyword(s):  
Gene Order ◽  
Tandem Duplication ◽  
Random Loss

scholarly journals Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11402
Author(s):  
Dan-Na Yu ◽  
Pan-Pan Yu ◽  
Le-Ping Zhang ◽  
Kenneth B. Storey ◽  
Xin-Yan Gao ◽  
...  
Keyword(s):  
Family Relationships ◽  
Phylogenetic Relationships ◽  
Tandem Duplication ◽  
Rapid Evolution ◽  
Morphological Characters ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Random Loss ◽  
Suitable Marker ◽  
And Inversion

Background The phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera. Methods Mitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups. Results Among these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata.

scholarly journals "Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 84 ◽  
Author(s):  
Jianfeng Ren ◽  
Xiao Liu ◽  
Guofan Zhang ◽  
Bin Liu ◽  
Ximing Guo
Keyword(s):  
Tandem Duplication ◽  
Mitochondrial Genomes ◽  
Random Loss

scholarly journals Finding All Sorting Tandem Duplication Random Loss Operations

2009 ◽  
pp. 301-313
Author(s):  
Matthias Bernt ◽  
Ming-Chiang Chen ◽  
Daniel Merkle ◽  
Hung-Lung Wang ◽  
Kun-Mao Chao ◽  
...  
Keyword(s):  
Tandem Duplication ◽  
Random Loss

scholarly journals Finding all sorting tandem duplication random loss operations

2011 ◽  
Vol 9 (1) ◽  
pp. 32-48 ◽  
Author(s):  
Matthias Bernt ◽  
Kuan-Yu Chen ◽  
Ming-Chiang Chen ◽  
An-Chiang Chu ◽  
Daniel Merkle ◽  
...  
Keyword(s):  
Tandem Duplication ◽  
Random Loss
Sign in / Sign up

Export Citation Format

Share Document