Dynamic Nucleotide Mutation Gradients and Control Region Usage in Squamate Reptile Mitochondrial Genomes

Abstract The New World tribe Arini includes 30 genera and represents 148 known species of parrots. A previous phylogenetic study examined nine of those genera and suggested the existence of two groups. Our objective was to better understand the relationships among 14 species from 9 genera belonging to one of those groups. We partially sequenced the 12S and 16S ribosomal DNAs, cytochrome b, cytochrome oxidase I, and control region. We improved our understanding of the phylogenetic relationships among Neotropical parrots by adding both taxa and sequences, but the relationships among the deeper lineages were not well resolved. Our results agree with present classifications that place some species formerly in the genus Ara into three additional genera (Primolius, Orthopsittaca, and Diopsittaca). Additionally, we suggest that (1) D. nobilis and Guarouba guarouba are closely related and the genus Aratinga is not monophyletic; (2) diversification of genera may have occurred during the Miocene, and of species within genera during the Pliocene and Pleistocene; and (3) geologic, climatic, and environmental changes in South America may have been related to that diversification.

Download Full-text

Identification of globally threatened cervids from problematic samples using cytochrome b and control region genes

Conservation Genetics Resources ◽

10.1007/s12686-015-0469-8 ◽

2015 ◽

Vol 7 (3) ◽

pp. 647-650 ◽

Cited By ~ 5

Author(s):

Sangeeta Angom ◽

Sandeep Kumar Gupta ◽

Ajit Kumar ◽

Syed Ainul Hussain

Keyword(s):

Cytochrome B ◽

Control Region ◽

And Control

Download Full-text

Mitochondrial Haplogroups and Control Region Polymorphisms in Age-Related Macular Degeneration: A Case-Control Study

PLoS ONE ◽

10.1371/journal.pone.0030874 ◽

2012 ◽

Vol 7 (2) ◽

pp. e30874 ◽

Cited By ~ 34

Author(s):

Edith E. Mueller ◽

Elena Schaier ◽

Susanne M. Brunner ◽

Waltraud Eder ◽

Johannes A. Mayr ◽

...

Keyword(s):

Macular Degeneration ◽

Control Region ◽

Case Control Study ◽

Case Control ◽

Age Related Macular Degeneration ◽

Mitochondrial Haplogroups ◽

Age Related ◽

And Control ◽

Control Study

Download Full-text

Unraveling the Limits of Mitochondrial Control Region to Estimate the Fine Scale Population Genetic Differentiation in Anadromous FishTenualosa ilisha

Scientifica ◽

10.1155/2016/2035240 ◽

2016 ◽

Vol 2016 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Rashmi Verma ◽

Mahender Singh ◽

Sudhir Kumar

Keyword(s):

Population Structure ◽

Genetic Differentiation ◽

Control Region ◽

Population Genetic ◽

Arabian Sea ◽

Mitochondrial Control Region ◽

Population Genetic Differentiation ◽

First Choice ◽

Scale Population ◽

And Control

The mitochondrial control region has been the first choice for examining the population structure but hypervariability and homoplasy have reduced its suitability. We analysed eight populations using control region for examining the population structure ofHilsa. Although the control region analysis revealed broad structuring between the Arabian Sea and Bay of Bengal (FST 0.0441,p<0.001) it was unable to detect structure among riverine populations. These results suggest that the markers used must be able to distinguish populations and control region has led to an underestimation of genetic differentiation among populations ofHilsa.

Download Full-text

Interpopulation and intrapopulation maternal lineage genetics of the Lanyu pig (Sus scrofa) by analysis of mitochondrial cytochrome b and control region sequences1

Journal of Animal Science ◽

10.2527/jas.2007-0049 ◽

2008 ◽

Vol 86 (10) ◽

pp. 2461-2470 ◽

Cited By ~ 9

Author(s):

Y. N. Jiang ◽

C. Y. Wu ◽

C. Y. Huang ◽

H. P. Chu ◽

M. W. Ke ◽

...

Keyword(s):

Cytochrome B ◽

Control Region ◽

Sus Scrofa ◽

Mitochondrial Cytochrome ◽

Maternal Lineage ◽

Mitochondrial Cytochrome B ◽

And Control

Download Full-text

Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region

10.1101/500330 ◽

2018 ◽

Author(s):

Ji Haishuo ◽

Xu Xiaofeng ◽

Jin Xiufeng ◽

Cheng Zhi ◽

jin Hong ◽

...

Keyword(s):

Steady State ◽

High Resolution ◽

Mitochondrial Genome ◽

Control Region ◽

Transcription Initiation ◽

Tandem Repeats ◽

Mitochondrial Gene ◽

Mitochondrial Genomes ◽

Small Rna Sequencing ◽

Antisense Gene

In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. Most of the new annotations were consistent with the previous annotations which were obtained using PacBio full-length transcripts. Two important findings are that animals transcribe both entire strands of mitochondrial genomes and the tandem repeat in the control region of the E. fullo mitochondrial genome contains the repeated Transcription Initiation Sites (TISs) of the H-strand. In addition, we found that the copy numbers of tandem repeats showed a great diversity within an individual, enriching the fundamental knowledge of mitochondrial biology. This sRNA-seq based method uses 5′ and 3′ end small RNAs to annotate nuclear non-coding and mitochondrial genes at 1 bp resolution and can also be used to identify new steady-state RNAs, particularly long non-coding RNAs (lncRNAs). Animal mitochondrial genomes containing one control region only encode two steady-state lncRNAs, which are the Mitochondrial D-loop 1 (MDL1) and its antisense gene (MDL1AS), while all other reported mitochondrial lncRNAs could be degraded fragments of transient RNAs or random breaks during experimental processing. The high-resolution annotations of mitochondrial genomes can be used to study the phylogenetics and molecular evolution of animals or to investigate mitochondrial gene transcription, RNA processing, RNA maturation and several other related topics.

Download Full-text

Complete mitochondrial genomes of five raptors and implications for the phylogenetic relationships between owls and nightjars

10.7287/peerj.preprints.27478v1 ◽

2019 ◽

Author(s):

Gang Liu ◽

Lizhi Zhou ◽

Guanghong Zhao

Keyword(s):

Control Region ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Stop Codon ◽

Mitochondrial Genomes ◽

Closely Related Species ◽

Protein Coding ◽

Protein Coding Genes ◽

Independent Families ◽

Complete Mitochondrial Genomes

The phylogenetic relationships between owls and nightjars are rather complex and controversial. To clarify these relationships, we determined the complete mitochondrial genomes of Glaucidium cuculoides, Otus scops, Glaucidium brodiei, Caprimulgus indicus, and Strix leptogrammica, and estimated phylogenetic trees based on the complete mitochondrial genomes and aligned sequences from closely related species that were obtained in GenBank. The complete mitochondrial genomes were 17392, 17317, 17549, 17536, and 16307 bp in length. All mitochondrial genomes contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a putative control region. All mitochondrial genomes except for that of Strix leptogrammica contained a pseudo-control region. ATG, GTG, and ATA are generally start codons, whereas TAA is the most frequent stop codon. All tRNAs in the new mtDNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN) , which missing the “DHU” arm. The phylogenetic relationships demonstrated that Strigiformes and Caprimulgiformes are independent orders, and Aegothelidae is a family within Caprimulgiformes. The results also revealed that Accipitriformes is an independent order, and Pandionidae and Sagittariidae are independent families. The results also supported that Apodiformes is polyphyletic, and hummingbirds (family Trochilidae) belong to Apodiformes. Piciformes was most distantly related to all other analyzed orders.

Download Full-text