scholarly journals Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration

Life ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 171
Author(s):  
Xuhua Xia
Keyword(s):  
Rapid Evolution ◽  
Nucleotide Composition ◽  
Mitochondrial Genes ◽  
Phylogenetic Position ◽  
Standard Genetic Code ◽  
Nucleotide Level ◽  
Synonymous Codons ◽  
Genetic Codes ◽  
User Friendly ◽  
Phylogenetic Noise

Recovering deep phylogeny is challenging with animal mitochondrial genes because of their rapid evolution. Codon degeneration decreases the phylogenetic noise and bias by aiming to achieve two objectives: (1) alleviate the bias associated with nucleotide composition, which may lead to homoplasy and long-branch attraction, and (2) reduce differences in the phylogenetic results between nucleotide-based and amino acid (AA)-based analyses. The discrepancy between nucleotide-based analysis and AA-based analysis is partially caused by some synonymous codons that differ more from each other at the nucleotide level than from some nonsynonymous codons, e.g., Leu codon TTR in the standard genetic code is more similar to Phe codon TTY than to synonymous CTN codons. Thus, nucleotide similarity conflicts with AA similarity. There are many such examples involving other codon families in various mitochondrial genetic codes. Proper codon degeneration will make synonymous codons more similar to each other at the nucleotide level than they are to nonsynonymous codons. Here, I illustrate a “principled” codon degeneration method that achieves these objectives. The method was applied to resolving the mammalian basal lineage and phylogenetic position of rheas among ratites. The codon degeneration method was implemented in the user-friendly and freely available DAMBE software for all known genetic codes (genetic codes 1 to 33).

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

scholarly journals COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences

2019 ◽  
Vol 11 (12) ◽  
pp. 3523-3528 ◽  
Author(s):  
Jérôme Bourret ◽  
Samuel Alizon ◽  
Ignacio G Bravo
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Null Hypothesis ◽  
Similarity Index ◽  
Bimodal Distribution ◽  
Added Value ◽  
Complete Analysis ◽  
Coding Sequences ◽  
Synonymous Codons ◽  
User Friendly

Abstract Codon Usage Preferences (CUPrefs) describe the unequal usage of synonymous codons at the gene, chromosome, or genome levels. Numerous indices have been developed to evaluate CUPrefs, either in absolute terms or with respect to a reference. We introduce the normalized index COUSIN (for COdon Usage Similarity INdex), that compares the CUPrefs of a query against those of a reference and normalizes the output over a Null Hypothesis of random codon usage. The added value of COUSIN is to be easily interpreted, both quantitatively and qualitatively. An eponymous software written in Python3 is available for local or online use (http://cousin.ird.fr). This software allows for an easy and complete analysis of CUPrefs via COUSIN, includes seven other indices, and provides additional features such as statistical analyses, clustering, and CUPrefs optimization for gene expression. We illustrate the flexibility of COUSIN and highlight its advantages by analyzing the complete coding sequences of eight divergent genomes. Strikingly, COUSIN captures a bimodal distribution in the CUPrefs of human and chicken genes hitherto unreported with such precision. COUSIN opens new perspectives to uncover CUPrefs specificities in genomes in a practical, informative, and user-friendly way.

scholarly journals Phylogenetic Position and Peculiar Genetic Traits of a Midgut Bacterial Symbiont of the Stinkbug Parastrachia japonensis

2010 ◽  
Vol 76 (13) ◽  
pp. 4130-4135 ◽  
Author(s):  
Takahiro Hosokawa ◽  
Yoshitomo Kikuchi ◽  
Naruo Nikoh ◽  
Xian-Ying Meng ◽  
Mantaro Hironaka ◽  
...  
Keyword(s):  
Uric Acid ◽  
Phylogenetic Analyses ◽  
Posterior Part ◽  
Nucleotide Composition ◽  
Bacterial Symbiont ◽  
Phylogenetic Position ◽  
Tsetse Flies ◽  
Genetic Traits ◽  
Molecular Phylogenetic ◽  
Close Relatives

ABSTRACT The stinkbug Parastrachia japonensis (Hemiptera: Parastrachiidae) is known for its prolonged prereproductive nonfeeding period, maternal care of eggs in an underground nest, and maternal collection and provisioning of food (fruits) for nymphs. A previous study suggested that a bacterial symbiont is involved in uric acid recycling in this insect during the nonfeeding period, but the identity of this symbiont has not been determined. Here we characterized a novel bacterial symbiont obtained from P. japonensis. Molecular phylogenetic analyses based on 16S rRNA, gyrB, and groEL gene sequences consistently indicated that this symbiont constituted a distinct lineage in the Gammaproteobacteria that has no close relatives but is allied with gut symbionts of acanthosomatid and plataspid stinkbugs, as well as with endocellular symbionts of sharpshooters, tsetse flies, and aphids. The symbiont genes had a remarkably AT-biased nucleotide composition and exhibited significantly accelerated molecular evolution. The symbiont genome was extremely reduced; its size was estimated to be 0.85 Mb. These results suggest that there has been an intimate host-symbiont association over evolutionary time. The symbiont was localized in swollen crypts in a posterior part of the midgut, which was a specialized symbiotic organ. The possibility that the symbiont is involved in uric acid recycling is discussed. The designation “Candidatus Benitsuchiphilus tojoi” is proposed for the symbiont.

Characterization of the complete mitochondrial genome of Metastrongylus salmi (M. salmi) derived from Tibetan pigs in Tibet, China

2018 ◽  
Vol 63 (2) ◽  
pp. 280-286 ◽  
Author(s):  
Kun Li ◽  
Muhammad Shahzad ◽  
Hui Zhang ◽  
Khalid Mehmood ◽  
Xiong Jiang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Translation Termination ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Tibetan Pigs ◽  
Translation Termination Codon ◽  
Rna Genes

AbstractThe present study was designed to determine and analyze themtgenomes ofMetastrongylus salmi(M.salmi), and reveal the phylogenetic relationships of this parasite usingmtDNA sequences. Results showed that the completemtgenome ofM.salmiwas 13722 bp containing 12 protein-coding genes (cox1-3, nad1-6, nad4L, atp6 and cytb), 22 transfer RNA genes, and 2 ribosomal RNA genes (rrnL and rrnS). The overall A+T content was 73.54% and the nucleotide composition was A (23.52%), C (6.14%), G (19.60%), T (50.02%), and N (UCAG) (0.73%). A total of 4237 amino acids are encoded from the Tibetan isolates ofM. salmi mtgenomes. The ATA was predicted as the most common starting codon with 41.7% (5/12 protein genes); and 11 of the 12 protein genes were found to have a TAG or TAA translation termination codon. By clustering together the phylogenetic trees of TibetanM.salmiand AustrianM.salmi, theM.salmiisolated from Tibetan pigs was found to be highly homological with that stemmed from Austrian one. This information provides meaningful insights into the phylogenetic position of theM.salmiChina isolate and represents a useful resource for selecting molecular markers for diagnosis and population studies.

scholarly journals The Complete Nucleotide Sequence of the Mitochondrial Genome of the Lungfish (Protopterus dolloi) Supports Its Phylogenetic Position as a Close Relative of Land Vertebrates

Genetics ◽  
1996 ◽  
Vol 142 (4) ◽  
pp. 1249-1263
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Nucleotide Sequence ◽  
Mitochondrial Genome ◽  
Dna Sequence ◽  
Gene Order ◽  
Complete Nucleotide Sequence ◽  
Mitochondrial Genes ◽  
Phylogenetic Position ◽  
African Lungfish ◽  
Protopterus Dolloi ◽  
Land Vertebrates

Abstract The complete DNA sequence (16,646 bp) of the mitochondrial genome of the African lungfish, Protopterus dolloi, was determined. The evolutionary position of lungfish as possibly the closest living relative among fish of land vertebrates made its mitochondrial DNA sequence particularly interesting. Its mitochondrial gene order conforms to the consensus vertebrate gene order. Several sequence motifs and secondary structures likely involved in the regulation of the initiation of replication and transcription of the mitochondrial genome are conserved in the lungfish and are more similar to those of land vertebrates than those of ray-finned fish. A novel feature discovered is that the putative origin of L-strand replication partially overlaps the adjacent tRNAcys. The phylogenetic analyses of genes coding for tRNAs and proteins confirm the intermediate phylogenetic position of lungfish between ray-finned fishes and tetrapods. The complete nucleotide sequence of the African lungfish mitochondrial genome was used to estimate which mitochondrial genes are most appropriate to elucidate deep branch phylogenies. Only a combined set of either protein or tRNA mitochondrial genes (but not each gene alone) is able to confidently recover the expected phylogeny among vertebrates that have diverged up to but not over ~400 mya.

Many alternative and theoretical genetic codes are more robust to amino acid replacements than the standard genetic code

2019 ◽  
Vol 464 ◽  
pp. 21-32 ◽  
Author(s):  
Paweł Błażej ◽  
Małgorzata Wnętrzak ◽  
Dorota Mackiewicz ◽  
Przemysław Gagat ◽  
Paweł Mackiewicz
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Standard Genetic Code ◽  
Genetic Codes

scholarly journals Switch in Codon Bias and Increased Rates of Amino Acid Substitution in the Drosophila saltans Species Group

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 339-350 ◽  
Author(s):  
Francisco Rodríguez-Trelles ◽  
Rosa Tarrío ◽  
Francisco J Ayala
Keyword(s):  
Rapid Evolution ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Species Group ◽  
Effective Population ◽  
Recombination Rates ◽  
Mutation Pressure ◽  
Saltans Group ◽  
Codon Use ◽  
Population Numbers

Abstract We investigated the nucleotide composition of five genes, Xdh, Adh, Sod, Per, and 28SrRNA, in nine species of Drosophila (subgenus Sophophora) and one of Scaptodrosophila. The six species of the Drosophila saltans group markedly differ from the others in GC content and codon use bias. The GC content in the third codon position, and to a lesser extent in the first position and the introns, is higher in the D. melanogaster and D. obscura groups than in the D. saltans group (in Scaptodrosophila it is intermediate but closer to the melanogaster and obscura species). Differences are greater for Xdh than for Adh, Sod, Per, and 28SrRNA, which are functionally more constrained. We infer that rapid evolution of GC content in the saltans lineage is largely due to a shift in mutation pressure, which may have been associated with diminished natural selection due to smaller effective population numbers rather than reduced recombination rates. The rate of GC content evolution impacts the rate of protein evolution and may distort phylogenetic inferences. Previous observations suggesting that GC content evolution is very limited in Drosophila may have been distorted due to the restricted number of genes and species (mostly D. melanogaster) investigated.

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