Molecular architecture and rates of DNA substitutions of the mitochondrial control region of cracid birds

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 535-545 ◽  
Author(s):  
Sergio L Pereira ◽  
Erwin T Grau ◽  
Anita Wajntal
Keyword(s):  
Control Region ◽  
Mitochondrial Control Region ◽  
High Rate ◽  
Molecular Organization ◽  
Molecular Architecture ◽  
Closely Related Species ◽  
Protein Coding ◽  
Dna Substitution ◽  
Suitable Marker ◽  
Composition Pattern

The control region (CR) plays an important role in replication and transcription in the mitochondrial genome. Its supposedly high rate of DNA substitution makes it a suitable marker for studies of population and closely related species. Three domains can be identified in CR, each having its own characteristics regarding base composition, pattern of variability and rate of DNA substitution. We sequenced the complete CR for 27 cracids, including all 11 genera to characterize its molecular organization, describe patterns of DNA substitution along the gene, and estimate absolute rates of DNA substitution. Our results show that cracid CR organization and patterns of DNA substitution are typical of other birds. Conserved blocks C and B, fused CSB2/3, and a putative segment for bidirectional replication not usually present in birds were identified in cracids. We also suggest a new delimitation for domains to allow better comparisons among CRs at different taxonomic ranking. Our estimates of absolute rates of DNA substitution show that, in general, CR evolves at a rate slower than that of two protein-coding genes (CR, 0.14%–0.3%; ND2, 0.37%–0.47%; and cytochrome b, 0.29%–0.35% per site per million years within genera). Within CR domains, rates within genera ranged from 0.05% to 0.8% per site per million years.Key words: mitochondrial control region, molecular evolution, Cracidae, Aves.

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

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.

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

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.

scholarly journals Complete Mitochondrial Genome of Three Species of the Genus Microtus (Arvicolinae, Rodentia)

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2130
Author(s):  
Luz Lamelas ◽  
Gaël Aleix-Mata ◽  
Michail Rovatsos ◽  
Juan Alberto Marchal ◽  
Teresa Palomeque ◽  
...  
Keyword(s):  
Control Region ◽  
Complete Mitochondrial Genome ◽  
High Rate ◽  
Protein Coding ◽  
Conserved Sequence ◽  
Genetic Features ◽  
Associated Sequences ◽  
Domain Iii ◽  
Domain I ◽  
Rna Genes

The 65 species of the genus Microtus have unusual sex-related genetic features and a high rate of karyotype variation. However, only nine complete mitogenomes for these species are currently available. We describe the complete mitogenome sequences of three Microtus, which vary in length from 16,295 bp to 16,331 bp, contain 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes and a control region. The length of the 13 PCGs and the coded proteins is the same in all three species, and the start and stop codons are conserved. The non-coding regions include the L-strand origin of replication, with the same sequence of 35 bp, and the control region, which varies between 896 bp and 930 bp in length. The control region includes three domains (Domains I, II and III) with extended termination-associated sequences (ETAS-1 and ETAS-2) in Domain I. Domain II and Domain III include five (CSB-B, C, D, E and F) and three (CSB-1, CSB-2, and CSB-3) conserved sequence blocks, respectively. Phylogenetic reconstructions using the mitochondrial genomes of all the available Microtus species and one representative species from another genus of the Arvicolinae subfamily reproduced the established phylogenetic relationships for all the Arvicolinae genera that were analyzed.

scholarly journals Complete Mitochondrial Genome Sequence of Bos Frontalis (Gayal) of Bangladesh

2021 ◽  
Author(s):  
Gautam Kumar Deb ◽  
Razia Khatun ◽  
Shakh Mohammed Jahangir Hossain ◽  
Shamsur Rahaman ◽  
Md. Anamul Bahar Bhuiyan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Related Species ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract Background: Complete mitochondrial genome of Bos frontalis will aid in the investigation of evolutionary links between closely related species. Bos frontalis mitogenome contains 37 genes and a control region. We discover the first complete mitogenome of Bos frontalis found in Bangladesh which was obtained from whole-genome sequencing of Bos frontalis.Results: Bos frontalis mitogenome is 16,347 bp long, with an AT-based nucleotide composition (60.21%). It contains 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region (D-loop). This circular genome starts with ND6(negative strand) and ends at ND5(positive strand). Protein coding genes lost 24 bases and tRNA genes gained 27 bases compared to closely related species. Phylogenetic analysis of the mitochondrial genome of 26 closely related species from 8 congeneric species was conducted by the maximum likelihood method with 1000 bootstrap iteration.Conclusion: Our studied Bos frontalis mitochondrial genome has a similar gene arrangement compared with other Bos species. It has almost the same amount of AT and GC content, but notably the ND6 gene lacks AT skew and GC skew than that of the other two comparing species. PCG’s loss in size might be a continuous process of evolution. The mitochondrial genome is regarded as a critical tool for species identification and monitoring populations of conservation concern.

Molecular population phylogeny of the hazel grouseBonasa bonasiain East Asia inferred from mitochondrial control-region sequences

2002 ◽  
Vol 8 (1) ◽  
pp. 251-259 ◽  
Author(s):  
Yoshiyuki Baba ◽  
Yuzo Fujimaki ◽  
Siegfried Klaus ◽  
Olga Butorina ◽  
Serguei Drovetskii ◽  
...  
Keyword(s):  
East Asia ◽  
Control Region ◽  
Mitochondrial Control Region ◽  
Control Region Sequences

scholarly journals Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1185
Author(s):  
Wenqian Wang ◽  
Huan Zhang ◽  
Jérôme Constant ◽  
Charles R. Bartlett ◽  
Daozheng Qin
Keyword(s):  
Control Region ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Start Codon ◽  
Rrna Genes ◽  
Rich Region ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Rna Genes ◽  
Unpaired Base

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

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