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Manee MM, Al-Shomrani BM, Alqahtani FH. Mitochondrial DNA of the Arabian Camel Camelus dromedarius. Animals (Basel) 2024; 14:2460. [PMID: 39272245 PMCID: PMC11394021 DOI: 10.3390/ani14172460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/21/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
The Camelidae family, ranging from southwest Asia to north Africa, South America, and Australia, includes key domesticated species adapted to diverse environments. Among these, the Arabian camel (Camelus dromedarius) is vital to the cultural and economic landscape of the Arabian Peninsula. This review explores the mitochondrial DNA of the dromedary camel, focusing on the D-loop region to understand its genetic diversity, maternal inheritance, and evolutionary history. We aim to investigate the unique characteristics of Arabian camel mtDNA, analyze the D-loop for genetic diversity and maternal lineage patterns, and explore the implications of mitochondrial genomic studies for camel domestication and adaptation. Key findings on mtDNA structure and variation highlight significant genetic differences and adaptive traits. The D-loop, essential for mtDNA replication and transcription, reveals extensive polymorphisms and haplotypes, providing insights into dromedary camel domestication and breeding history. Comparative analyses with other camelid species reveal unique genetic signatures in the Arabian camel, reflecting its evolutionary and adaptive pathways. Finally, this review integrates recent advancements in mitochondrial genomics, demonstrating camel genetic diversity and potential applications in conservation and breeding programs. Through comprehensive mitochondrial genome analysis, we aim to enhance the understanding of Camelidae genetics and contribute to the preservation and improvement of these vital animals.
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Affiliation(s)
- Manee M Manee
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Advanced Agricultural and Food Technologies Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Badr M Al-Shomrani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Advanced Agricultural and Food Technologies Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Fahad H Alqahtani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Advanced Agricultural and Food Technologies Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
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Skorupski J. Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. Genes (Basel) 2022; 13:genes13010125. [PMID: 35052465 PMCID: PMC8774856 DOI: 10.3390/genes13010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023] Open
Abstract
In this paper, a complete mitochondrial genome of the critically endangered European mink Mustela lutreola L., 1761 is reported. The mitogenome was 16,504 bp in length and encoded the typical 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and harboured a putative control region. The A+T content of the entire genome was 60.06% (A > T > C > G), and the AT-skew and GC-skew were 0.093 and −0.308, respectively. The encoding-strand identity of genes and their order were consistent with a collinear gene order characteristic for vertebrate mitogenomes. The start codons of all protein-coding genes were the typical ATN. In eight cases, they were ended by complete stop codons, while five had incomplete termination codons (TA or T). All tRNAs had a typical cloverleaf secondary structure, except tRNASer(AGC) and tRNALys, which lacked the DHU stem and had reduced DHU loop, respectively. Both rRNAs were capable of folding into complex secondary structures, containing unmatched base pairs. Eighty-one single nucleotide variants (substitutions and indels) were identified. Comparative interspecies analyses confirmed the close phylogenetic relationship of the European mink to the so-called ferret group, clustering the European polecat, the steppe polecat and the black-footed ferret. The obtained results are expected to provide useful molecular data, informing and supporting effective conservation measures to save M. lutreola.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-91-444-16-85
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
- The European Mink Centre, 71-415 Szczecin, Poland
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Urantówka AD, Kroczak A, Strzała T, Zaniewicz G, Kurkowski M, Mackiewicz P. Mitogenomes of Accipitriformes and Cathartiformes Were Subjected to Ancestral and Recent Duplications Followed by Gradual Degeneration. Genome Biol Evol 2021; 13:evab193. [PMID: 34432018 PMCID: PMC8435663 DOI: 10.1093/gbe/evab193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2021] [Indexed: 11/25/2022] Open
Abstract
The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus, as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14-47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
| | - Tomasz Strzała
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Grzegorz Zaniewicz
- Department of Vertebrate Ecology and Zoology, Avian Ecophysiology Unit, University of Gdańsk, Poland
| | - Marcin Kurkowski
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
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Urantówka AD, Kroczak A, Mackiewicz P. New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves. BMC Genomics 2020; 21:874. [PMID: 33287726 PMCID: PMC7720580 DOI: 10.1186/s12864-020-07284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. RESULTS Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. CONCLUSIONS The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
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Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D. Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications. Genome Biol Evol 2019; 11:2824-2849. [PMID: 31580435 PMCID: PMC6795242 DOI: 10.1093/gbe/evz209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/29/2022] Open
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.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
| | - Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Dorota Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
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Jiang L, Peng L, Tang M, You Z, Zhang M, West A, Ruan Q, Chen W, Merilä J. Complete mitochondrial genome sequence of the Himalayan Griffon, Gyps himalayensis (Accipitriformes: Accipitridae): Sequence, structure, and phylogenetic analyses. Ecol Evol 2019; 9:8813-8828. [PMID: 31410282 PMCID: PMC6686361 DOI: 10.1002/ece3.5433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 11/12/2022] Open
Abstract
This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein-coding genes, 22 tRNA coding genes, two rRNA-coding genes, a control region (CR), and an extra pseudo-control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5' end of the domain I region, a long continuous poly-C sequence was found. Two tandem repeats were found in the pseudo-control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein-coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Liqing Peng
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Min Tang
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
| | - Andrea West
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVicAustralia
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
| | - Wei Chen
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty Biological & Environmental SciencesUniversity of HelsinkiHelsinkiFinland
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Mitochondrial DNA D-Loop Diversity of the Helmeted Guinea Fowls in Kenya and Its Implications on HSP70 Gene Functional Polymorphism. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7314038. [PMID: 30539018 PMCID: PMC6258102 DOI: 10.1155/2018/7314038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/28/2018] [Indexed: 11/18/2022]
Abstract
We analyzed variations in 90 mitochondrial DNA (mtDNA) D-loop and heat shock protein 70 (HSP70) gene sequences from four populations of domesticated helmeted Guinea fowls (70 individuals) and 1 population of wild helmeted Guinea fowls (20 individuals) in Kenya in order to get information about their origin, genetic diversity, and traits associated with heat stress. 90 sequences were assigned to 25 distinct mtDNA and 4 HSP70 haplotypes. Most mtDNA haplotypes of the domesticated helmeted Guinea fowls were grouped into two main haplogroups, HgA and HgB. The wild population grouped into distinct mtDNA haplogroups. Two mtDNA haplotypes dominated across all populations of domesticated helmeted Guinea fowls: Hap2 and Hap4, while the dominant HSP70 haplotype found in all populations was CGC. Higher haplotype diversities were generally observed. The HSP70 haplotype diversities were low across all populations. The nucleotide diversity values for both mtDNA and HSP70 were generally low. Most mtDNA genetic variations occurred among populations for the three hierarchical categories considered while most variations in the HSP70 gene occurred among individuals within population. The lack of population structure among the domestic populations could suggest intensive genetic intermixing. The differentiation of the wild population may be due to a clearly distinct demographic history that shaped its genetic profile. Analysis of the Kenyan Guinea fowl population structure and history based on mtDNA D-loop variations and HSP70 gene functional polymorphisms complimented by archaeological and linguistic insight supports the hypothesis that most domesticated helmeted Guinea fowls in Kenya are related to the West African domesticated helmeted Guinea fowls. We recommend more molecular studies on this emerging poultry species with potential for poverty alleviation and food security against a backdrop of climate change in Africa.
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Evolutionary progression of mitochondrial gene rearrangements and phylogenetic relationships in Strigidae (Strigiformes). Gene 2018; 674:8-14. [PMID: 29940272 DOI: 10.1016/j.gene.2018.06.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 01/09/2023]
Abstract
The bird mitogenome is generally considered to have a conservative genome size, consistent gene content, and similar gene order. As more mitogenomes are sequenced, mitochondrial (mt) gene rearrangements have been frequently identified among diverse birds. Within two genera (Bubo and Strix) of typical owls (Strigidae, Strigiformes), the rearrangement of the mt gene has been a subject of debate. In the current study, we first sequenced the whole mitogenomes of S. uralensis and B. scandiaca and resequenced the entire mitogenome of B. bubo. By combining our data with previously sequenced mitogenomes in Strigidae, we examined the mt gene rearrangements in the family and attempted to reconstruct the evolutionary progression of these rearrangements. The mitogenomes were then used to review the phylogenies of Strigidae. Most mitogenomes exhibited the ancestral gene order (A) in Strigidae. The ancestral gene order in the previously published mitogenome of B. bubo was found to be incorrect. We determined the mt gene order (the duplicate tRNAThr-CR, B) and discovered two additional mt gene orders (the duplicate tRNAGlu-L-CR and CR, C and D) in the Bubo and Strix genera. Gene order B was likely derived from A by a tandem duplication of the region spanning from tRNAThr to CR. The other two modified gene orders, C and D, were likely derived from B by further degenerations or deletions of one copy of specific duplicated genes. We also preliminarily reconstructed the evolutionary progression of mt gene rearrangements and discussed maintenance of the duplicated CR in the genera. Additionally, the phylogenetic trees based on the mitogenomes supported the division of Strigidae into three subfamilies: Ninoxinae + (Surniinae + Striginae). Within the Striginae clade, the four genera formed a phylogenetic relationship: Otus + (Asio + (Bubo + Strix)). This suggests that Otus firstly diverges in their evolutionary history, and Bubo and Strix show a close relationship. B. bubo, B. blakistoni and B. scandiaca form a clade should be considered members of the same genus. The well-supported topology obtained in our Bayesian inference (BI) and maximum likelihood (ML) analyses of Strigid mitogenomes suggests that these genomes are informative for constructing phylogenetic relationships.
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Complete mitochondrial genome of Porzana fusca and Porzana pusilla and phylogenetic relationship of 16 Rallidae species. Genetica 2017; 145:559-573. [DOI: 10.1007/s10709-017-9982-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/31/2017] [Indexed: 12/25/2022]
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Two mitochondrial genomes in Alcedinidae (Ceryle rudis/Halcyon pileata) and the phylogenetic placement of Coraciiformes. Genetica 2017; 145:431-440. [PMID: 28791584 DOI: 10.1007/s10709-017-9978-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
Abstract
Coraciiformes comprises 209 species belonging to ten families with significant divergence on external morphologies and life styles. The phylogenetic placement of Coraciiformes was still in debate. Here, we determined the complete mitochondrial genomes (mitogenomes) of Crested Kingfisher (Ceryle rudis) and Black-capped Kingfisher (Halcyon pileata). The mitogenomes were 17,355 bp (C. rudis) and 17,612 bp (H. pileata) in length, and both of them contained 37 genes (two rRNA genes, 22 tRNA genes and 13 protein-coding genes) and one control region. The gene organizations and characters of two mitogenomes were similar with those of other mitogenomes in Coraciiformes, however the sizes and nucleotide composition of control regions in different mitogenomes were significantly different. Phylogenetic trees were constructed with both Bayesian and Maximum Likelihood methods based on mitogenome sequences from 11 families of six orders. The trees based on two different data sets supported the basal position of Psittacidae (Psittaciformes), the closest relationship between Cuculiformes (Cuculidae) and Trogoniformes (Trogonidae), and the close relationship between Coraciiformes and Piciformes. The phylogenetic placement of the clade including Cuculiformes and Trogoniformes has not been resolved in present study, which need further investigations with more molecular markers and species. The mitogenome sequences presented here provided valuable data for further taxonomic studies on Coraciiformes and other related groups.
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Vella N, Vella A. Population genetics of the deep-sea bluntnose sixgill shark, Hexanchus griseus, revealing spatial genetic heterogeneity. Mar Genomics 2017; 36:25-32. [PMID: 28602510 DOI: 10.1016/j.margen.2017.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/23/2017] [Accepted: 05/29/2017] [Indexed: 01/30/2023]
Abstract
Hexanchus griseus is a globally distributed deep-water shark species. It inhabits tropical and temperate waters throughout the world, including the Mediterranean Sea where it is by-caught by small-scale fisheries in the region. In this study, we analysed the genetic variation of H. griseus specimens collected from different areas within and outside the Mediterranean region, to assess its genetic connectivity. The mitochondrial DNA (mtDNA) sequence analysed in this study ranged from cytochrome b to 16S rRNA genes including the control region, the 12S rRNA gene and the interspersed tRNA genes in the region, covering a total of 3731 to 3914 nucleotides. Results have shown that this species exhibits geographically distinct maternal lineages, indicating population structure along geographical ranges. These findings reveal population subdivisions not only between the Pacific Ocean and the Atlantic Ocean, but also within the oceans and on a smaller scale within the Mediterranean Sea. This highlights the need to consider each population subdivision separately when designing management plans for the conservation of this species.
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Affiliation(s)
- Noel Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida MSD2080, Malta.
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida MSD2080, Malta.
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Two mitogenomes in Gruiformes (Amaurornis akool/A. phoenicurus) and the phylogenetic placement of Rallidae. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0562-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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13
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Wang YC, Zou Y, Sun XM, Gong J, Huang L, Jing MD. The complete mitochondrial genome sequence of the little grebe (Tachybaptus ruficollis). Genes Genomics 2017. [DOI: 10.1007/s13258-016-0480-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Satoh TP, Miya M, Mabuchi K, Nishida M. Structure and variation of the mitochondrial genome of fishes. BMC Genomics 2016; 17:719. [PMID: 27604148 PMCID: PMC5015259 DOI: 10.1186/s12864-016-3054-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/27/2016] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets. Results An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species. Conclusions Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3054-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takashi P Satoh
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8654, Japan. .,Collection Center, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba City, Ibaraki, 305-0005, Japan. .,Present address: Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama, 649-2211, Japan.
| | - Masaki Miya
- Natural History Museum and Institute, 955-2 Aoba-cho, Chuo-ku, Chiba City, Chiba, 260-8682, Japan
| | - Kohji Mabuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8654, Japan
| | - Mutsumi Nishida
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8654, Japan. .,Present address: University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa, 908-0213, Japan.
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15
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The mitochondrial genome of Atrijuglans hetaohei Yang (Lepidoptera: Gelechioidea) and related phylogenetic analyses. Gene 2016; 581:66-74. [PMID: 26800782 DOI: 10.1016/j.gene.2016.01.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/11/2016] [Accepted: 01/16/2016] [Indexed: 01/28/2023]
Abstract
Complete mitochondrial genome sequences are of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In this study, the complete mitochondrial genome of Atrijuglans hetaohei Yang is sequenced and analyzed, which is 15,379bp in length (GenBank: KT581634) and contains a typical set of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding region (control region). Except for cox1 gene that is initiated by CGA codon, all protein-coding genes start with ATN codons and end with the stop codon T, TA or TAA. All tRNAs have a typical clover-leaf secondary structure, except for trnS1, of which the DHU arm could not form a stable stem-loop structure. The secondary structure of rrnL and rrnS consists of 49 helices and 33 helices, respectively. Phylogenetic analyses of the complete mitochondrial genome sequences and of the amino acid sequences for 13 mitochondrial protein-coding genes among related species support the view that A. hetaohei is more closely related to the Gelechioidea than Yponomeutoidea. This result is consistent with a previous classification based on morphology.
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16
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Liu G, Zhou L, Gu C. The complete mitochondrial genome of Brown wood owl Strix leptogrammica (Strigiformes: Strigidae). ACTA ACUST UNITED AC 2015; 25:370-1. [PMID: 25204537 DOI: 10.3109/19401736.2013.803540] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial genome of Brown wood owl is a 16,308-bp circular molecule, which contains 37 typical mitochondrial genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and a 741-bp A+T-rich region. Its gene arrangement pattern is identical with typical bird species. All protein-coding genes start with an ATG codon. TAA is the most frequent stop codon, and TAG and T- are also occurred very common. The mtDNA sequence contains 12S rRNA and 16S rRNA of rRNA. Except for tRNA(Ser) ((AGY)) and tRNA(Leu) ((CUN)) without the dihydrouridine (DHU) arm, all tRNAs could be folded into canonical cloverleaf secondary structures.
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Affiliation(s)
- Gang Liu
- School of Resources and Environmental Engineering, Anhui University , Hefei 230601 , P.R. China
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17
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Eberhard JR, Wright TF. Rearrangement and evolution of mitochondrial genomes in parrots. Mol Phylogenet Evol 2015; 94:34-46. [PMID: 26291569 DOI: 10.1016/j.ympev.2015.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 07/15/2015] [Accepted: 08/11/2015] [Indexed: 12/27/2022]
Abstract
Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One potential cause for this compositional asymmetry is that parrots have unusually slow mtDNA replication. If this is the case, then any replicative advantage provided by having a second control region could result in selection for maintenance of both control regions once duplicated.
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Affiliation(s)
- Jessica R Eberhard
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Timothy F Wright
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
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18
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Zou Y, Jing MD, Bi XX, Zhang T, Huang L. The complete mitochondrial genome sequence of the little egret (Egretta garzetta). Genet Mol Biol 2015; 38:162-72. [PMID: 26273219 PMCID: PMC4530654 DOI: 10.1590/s1415-4757382220140203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 12/02/2014] [Indexed: 11/22/2022] Open
Abstract
Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3' end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.
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Affiliation(s)
- Yi Zou
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Mei-Dong Jing
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Xiao-Xin Bi
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Ting Zhang
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
| | - Ling Huang
- College of Life Sciences, Ludong University, Yantai, Shandong, P.R. China
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19
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The complete mitochondrial genome of Accipiter virgatus and evolutionary history of the pseudo-control regions in Falconiformes. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.10.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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The mitochondrial genome of Dastarcus helophoroides (Coleoptera: Bothrideridae) and related phylogenetic analyses. Gene 2014; 560:15-24. [PMID: 25523091 DOI: 10.1016/j.gene.2014.12.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/21/2014] [Accepted: 12/12/2014] [Indexed: 11/23/2022]
Abstract
The complete mitochondrial genome of Dastarcus helophoroides (Coleoptera: Bothrideridae) which consists of 13 PCGs, 22 tRNA genes, two rRNA genes and a non-coding region (D-loop), is sequenced for its nucleotide sequence of 15,878 bp (GenBank: KF811054.1). The genome has a typical gene order which is identical to other Coleoptera species. Except for COI gene generally starts with non-canonical initial codon, all protein-coding genes start with ATN codon and terminate with the stop codon TA(A) or TAG. The secondary structure of rrnL and rrnS consists of 48 helices (contains four newly proposed helices) and 35 helices (contains two newly proposed helices) respectively. All 22 tRNAs in D. helophoroides are predicted to fold into typical cloverleaf secondary structure, except trnS1 (AGN), in which the dihydrouracil arm (DHU arm) could not form stable stem-loop structure. Thirteen protein-coding genes (nucleotide dataset and nucleic acid dataset) of the available species (29 taxa) have been used to infer the phylogenetic relationships among these orders. Tenebrionoidea and Cucujoidea form a sister group, and D. helophoroides is classified into Cucujoidea (Bothrideridae). The study first research on the phylogenetic analyses involving to the D. helophoroides mitogenome, and the results strongly bolster the current morphology-based hypothesis.
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21
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He XL, Ding CQ, Han JL. Lack of Structural Variation but Extensive Length Polymorphisms and Heteroplasmic Length Variations in the Mitochondrial DNA Control Region of Highly Inbred Crested Ibis, Nipponia nippon. PLoS One 2013; 8:e66324. [PMID: 23805212 PMCID: PMC3689774 DOI: 10.1371/journal.pone.0066324] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/03/2013] [Indexed: 01/21/2023] Open
Abstract
The animal mitochondrial DNA (mtDNA) length polymorphism and heteroplasmy are accepted to be universal. Here we report the lack of structural variation but the presence of length polymorphism as well as heteroplasmy in mtDNA control region of an endangered avian species - the Crested Ibis (Nipponia nippon). The complete control region was directly sequenced while the distribution pattern and inheritance of the length variations were examined using both direct sequencing and genotyping of the PCR fragments from captive birds with pedigrees, wild birds and a historical specimen. Our results demonstrated that there was no structural variation in the control region, however, different numbers of short tandem repeats with an identical motif of CA3CA2CA3 at the 3'-end of the control region determined the length polymorphisms among and heteroplasmy within individual birds. There were one to three predominant fragments in every bird; nevertheless multiple minor fragments coexist in all birds. These extremely high polymorphisms were suggested to have derived from the 'replication slippage' of a perfect microsatellite evolution following the step-wise mutational model. The patterns of heteroplasmy were found to be shifted between generations and among siblings but rather stable between blood and feather samples. This study provides the first evidence of a very extensive mtDNA length polymorphism and heteroplasmy in the highly inbred Crested Ibis which carries an mtDNA genome lack of structural genetic diversity. The analysis of pedigreed samples also sheds light on the transmission of mtDNA length heteroplasmy in birds following the genetic bottleneck theory. Further research focusing on the generation and transmission of particular mtDNA heteroplasmy patterns in single germ line of Crested Ibis is encouraged by this study.
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Affiliation(s)
- Xue-Lian He
- College of Nature Conservation, Beijing Forestry University, Beijing, China
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chang-Qing Ding
- College of Nature Conservation, Beijing Forestry University, Beijing, China
- * E-mail: (CQD); (JLH)
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- * E-mail: (CQD); (JLH)
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22
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García CB, Gil JA, Alcántara M, González J, Cortés MR, Bonafonte JI, Arruga MV. The present Pyrenean population of bearded vulture (Gypaetus barbatus): its genetic characteristics. J Biosci 2013; 37:689-94. [PMID: 22922193 DOI: 10.1007/s12038-012-9229-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The Pyrenean population of the endangered bearded vulture (Gypaetus barbatus) is the largest natural population in Europe. In this study, its current genetic variability was assessed using 110 animals of the recent population in order to know what the present situation. Sex identification by DNA methodology in the 110 bearded vultures, mitochondrial DNA (mtDNA) and eight microsatellite markers in 87 bearded vultures have been analysed. Our results for sex identification present a number of 49 males and 61 females; no significant differences for number of males and females in this population have been observed. mtDNA studies indicate that nucleotide and haplotype diversities and number of variable sites were low. Tajima's D test and Fu and Li's D* and F* tests suggest that mutations are selectively neutral and the population is expanding. A mean number of alleles per locus and a mean observed heterozygosity have been obtained by microsatellite analysis. FIS is not high, and inbreeding depression could be discarded in the near future. The results suggest that the Pyrenean population of bearded vultures have to be controlled in order to avoid the loss of genetic variability. This data should be taken into account when considering conservation plans for the species.
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Affiliation(s)
- C B García
- Laboratory of Cytogenetics and Molecular Genetics, University of Zaragoza, Zaragoza, Spain
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23
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Liu G, Zhou LZ, Gu CM. Complete sequence and gene organization of the mitochondrial genome of scaly-sided merganser (Mergus squamatus) and phylogeny of some Anatidae species. Mol Biol Rep 2011; 39:2139-45. [PMID: 21655953 DOI: 10.1007/s11033-011-0961-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
The scaly-sided merganser (Mergus squamatus) is an endangered bird species on the IUCN Red List with the estimated global population of less than 2,500 individuals at present. In the present study, we studied the complete mitochondrial genome (mtDNA) and the phylogenetic of M. squamatus by PCR amplification and GenBank data. The genome was 16,595 bp in length and contained 37 genes (13 protein coding genes, two rRNAs, and 22 tRNAs) and a non-coding control region (D-loop). All protein-coding genes of M. squamatus mtDNA start with a typical ATG codon, except ND1, COI, and COII uses GTG as their initial codon. TAA, T- and TAG as the terminate codon occurred very commonly in the sequence. All tRNA genes can be folded into canonical cloverleaf secondary structure except for tRNA(Ser) (AGY) and tRNA(Leu) (CUN), which lose ''DHU'' arm. The genome sequences had been deposited in GenBank under accession number HQ833701. Based on the concatenated nucleotide sequences of mtDNA genes (Cyt b and D-loop), we reconstructed phylogenetic trees and discussed the phylogenetic relationships among ten Anatidae species. The results are different from the present classification, and we support Lophodytes cucullatus and Mergullus albellus to be members of the genus Mergus.
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Affiliation(s)
- Gang Liu
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601 Anhui, People's Republic of China
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24
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Agudo R, Alcaide M, Rico C, Lemus JA, Blanco G, Hiraldo F, Donázar JA. Major histocompatibility complex variation in insular populations of the Egyptian vulture: inferences about the roles of genetic drift and selection. Mol Ecol 2011; 20:2329-40. [PMID: 21535276 DOI: 10.1111/j.1365-294x.2011.05107.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Insular populations have attracted the attention of evolutionary biologists because of their morphological and ecological peculiarities with respect to their mainland counterparts. Founder effects and genetic drift are known to distribute neutral genetic variability in these demes. However, elucidating whether these evolutionary forces have also shaped adaptive variation is crucial to evaluate the real impact of reduced genetic variation in small populations. Genes of the major histocompatibility complex (MHC) are classical examples of evolutionarily relevant loci because of their well-known role in pathogen confrontation and clearance. In this study, we aim to disentangle the partial roles of genetic drift and natural selection in the spatial distribution of MHC variation in insular populations. To this end, we integrate the study of neutral (22 microsatellites and one mtDNA locus) and MHC class II variation in one mainland (Iberia) and two insular populations (Fuerteventura and Menorca) of the endangered Egyptian vulture (Neophron percnopterus). Overall, the distribution of the frequencies of individual MHC alleles (n=17 alleles from two class II B loci) does not significantly depart from neutral expectations, which indicates a prominent role for genetic drift over selection. However, our results point towards an interesting co-evolution of gene duplicates that maintains different pairs of divergent alleles in strong linkage disequilibrium on islands. We hypothesize that the co-evolution of genes may counteract the loss of genetic diversity in insular demes, maximize antigen recognition capabilities when gene diversity is reduced, and promote the co-segregation of the most efficient allele combinations to cope with local pathogen communities.
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Affiliation(s)
- Rosa Agudo
- Department of Conservation Biology, Doñana Biological Station-CSIC, Avenida Américo Vespucio s/n, E-41092 Sevilla, Spain.
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25
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Khaliq I, Tejedor MT, Monteagudo LV, Riaz M, Khan AA. Mitochondrial DNA diversity in Francolinus pondicerianus interpositus (grey francolin, Galliformes) from Pakistan. Hereditas 2011; 148:70-6. [DOI: 10.1111/j.1601-5223.2010.02206.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Kaur T, Ong AHK. Heteroplasmy, Length, and Sequence Characterization of the Mitochondrial Control Region in Tomistoma schlegelii. Biochem Genet 2011; 49:562-75. [DOI: 10.1007/s10528-011-9431-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 10/28/2010] [Indexed: 11/28/2022]
Affiliation(s)
- Taranjeet Kaur
- Universiti Tunku Abdul Rahman, Kuala Lumpur, Wilayah Persekutuan, Malaysia
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27
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Centeno-Cuadros A, Godoy JA. Structure, organization and nucleotide diversity of the mitochondrial control region and cytochromebof southern water vole (Arvicola sapidus). ACTA ACUST UNITED AC 2010; 21:48-53. [DOI: 10.3109/19401731003681103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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Nilsson MA. The structure of the Australian and South American marsupial mitochondrial control region. ACTA ACUST UNITED AC 2010; 20:126-38. [PMID: 19900062 DOI: 10.3109/19401730903180112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND AND AIMS The mitochondrial control region (CR) was studied across five marsupialian orders, in order to give a detailed overview of its features. RESULTS The CR is organised into three domains similar to the CR of placental mammals. However, the conservation of different features among the marsupial orders is in general more strict. In the first domain, two conserved blocks extended termination-associated sequences (ETAS 1 and ETAS 2) are present in all marsupial orders. In the third domain, the three conserved sequence blocks (CSB 1, CSB 2 and CSB 3) are present and complete, with CSB 1 being duplicated in four of five marsupial orders. CONCLUSIONS The nucleotide frequency and secondary structures of the repeats were typical for marsupial species. The repeats are generally AT-rich except in Dasyuridae and Paucituberculata, which show a significant increase in GC content.
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Affiliation(s)
- Maria A Nilsson
- Institute for Experimental Pathology/ZMBE, University of Münster, Münster, Germany.
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29
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Yang R, Wu X, Yan P, Su X, Yang B. Complete mitochondrial genome of Otis tarda (Gruiformes: Otididae) and phylogeny of Gruiformes inferred from mitochondrial DNA sequences. Mol Biol Rep 2009; 37:3057-66. [PMID: 19823949 DOI: 10.1007/s11033-009-9878-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Accepted: 09/30/2009] [Indexed: 01/19/2023]
Abstract
The complete nucleotide sequence of mitochondrial genome of the Great bustard (Otis tarda) was determined by using polymerase chain reaction (PCR) method. The genome is 16,849 bp in size, containing 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. Sequences of the tRNA genes can be folded into canonical cloverleaf secondary structure except for tRNA-Cys and tRNA-Ser (AGY), which lose "DHU" arm. Sequence analysis showed that the O. tarda mitochondrial control region (mtCR) contained many elements in common with other avian mtCRs. A microsatellite repeat was found in the 3'-peripheral domain of the O. tarda mtCR. Based on the mitochondrial DNA sequences of 12S rRNA, 16S rRNA and tRNA-Val, a phylogenetic study of Gruiformes was performed. The result showed that Otididae was a sister group to "core Gruiformes" and Charadriiformes with strong support (97% posterior probability values) in Bayesian analysis. The taxonomic status of Rhynochetidae, Mesitornithidae, Pedionomidae and Turnicidae that traditionally belonged to Gruiformes was also discussed in this paper.
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Affiliation(s)
- Rong Yang
- College of Life Sciences, Anhui Normal University, 241000, Wuhu, Anhui Province, People's Republic of China
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30
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Cadahía L, Pinsker W, Negro JJ, Pavlicev M, Urios V, Haring E. Repeated sequence homogenization between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2009; 312B:171-85. [PMID: 19205013 DOI: 10.1002/jez.b.21282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In birds, the noncoding control region (CR) and its flanking genes are the only parts of the mitochondrial (mt) genome that have been modified by intragenomic rearrangements. In raptors, two noncoding regions are present: the CR has shifted to a new position with respect to the "ancestral avian gene order," whereas the pseudo-control region (PsiCR) is located at the original genomic position of the CR. As possible mechanisms for this rearrangement, duplication and transposition have been considered. During characterization of the mt gene order in Bonelli's eagle Hieraaetus fasciatus, we detected intragenomic sequence similarity between the two regions supporting the duplication hypothesis. We performed intra- and intergenomic sequence comparisons in H. fasciatus and other falconiform species to trace the evolution of the noncoding mtDNA regions in Falconiformes. We identified sections displaying different levels of similarity between the CR and PsiCR. On the basis of phylogenetic analyses, we outline an evolutionary scenario of the underlying mutation events involving duplication and homogenization processes followed by sporadic deletions. Apparently, homogenization may easily occur if sufficient sequence similarity between the CR and PsiCR exists. Moreover, homogenization itself allows perpetuation of this continued equalization, unless this process is stopped by deletion. The Pandionidae and the Aquilinae seem to be the only two lineages of Falconiformes where homology between both regionsis still detectable, whereas in other raptors no similarity was found so far. In these two lineages, the process of sequence degeneration may have slowed down by homogenization events retaining high sequence similarity at least in some sections.
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Affiliation(s)
- Luis Cadahía
- Molecular Systematics, 1st Zoological Department, Museum of Natural History Vienna, Vienna, Austria.
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31
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Godoy JA, Negro JJ, Hiraldo F, Donázar JA. Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L) as revealed by mitochondrial DNA. Mol Ecol 2004; 13:371-90. [PMID: 14717893 DOI: 10.1046/j.1365-294x.2003.02075.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bearded vulture populations in the Western Palearctic have experienced a severe decline during the last two centuries that has led to the near extinction of the species in Europe. In this study we analyse the sequence variation at the mitochondrial control region throughout the species range to infer its recent evolutionary history and to evaluate the current genetic status of the species. This study became possible through the extensive use of museum specimens to study populations now extinct. Phylogenetic analysis revealed the existence of two divergent mitochondrial lineages, lineage A occurring mainly in Western European populations and lineage B in African, Eastern European and Central Asian populations. The relative frequencies of haplotypes belonging to each lineage in the different populations show a steep East-West clinal distribution with maximal mixture of the two lineages in the Alps and Greece populations. A genealogical signature for population growth was found for lineage B, but not for lineage A; futhermore the Clade B haplotypes in western populations and clade A haplo-types in eastern populations are recently derived, as revealed by their peripheral location in median-joining haplotype networks. This phylogeographical pattern suggests allopatric differentiation of the two lineages in separate Mediterranean and African or Asian glacial refugia, followed by range expansion from the latter leading to two secondary contact suture zones in Central Europe and North Africa. High levels of among-population differentiation were observed, although these were not correlated with geographical distance. Due to the marked genetic structure, extinction of Central European populations in the last century re-sulted in the loss of a major portion of the genetic diversity of the species. We also found direct evidence for the effect of drift altering the genetic composition of the remnant Pyrenean population after the demographic bottleneck of the last century. Our results argue for the management of the species as a single population, given the apparent ecological exchangeability of extant stocks, and support the ongoing reintroduction of mixed ancestry birds in the Alps and planned reintroductions in Southern Spain.
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Affiliation(s)
- José A Godoy
- Department of Applied Biology, Estación Biológica Doñana, CSIC, Pabellón del Perú, Avda María Luisa, s/n. 41013 Seville, Spain.
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