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Yang C, Dong X, Wang Q, Hou X, Yuan H, Li X. Mitochondrial genome characteristics of six Phylloscopus species and their phylogenetic implication. PeerJ 2023; 11:e16233. [PMID: 37842035 PMCID: PMC10576491 DOI: 10.7717/peerj.16233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
The mitochondrial genomes of six Phylloscopus species-small insectivores belonging to the Phylloscopidae family-were obtained using the Illumina sequencing platform. The mitogenomes were closed circular molecules 16,922-17,007 bp in size, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions (CR1 and remnant CR2). The gene orders were conserved in 35 sampled Phylloscopus mitogenomes in the GenBank database, with a gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. The average base compositions of the six Phylloscopus mitogenomes were 29.43% A, 32.75% C, 14.68% G, and 23.10% T, with the A+T content slightly higher than that of G+C. ATG and TAA were the most frequent initiating and terminating codons, respectively. Several conserved boxes were identified in CR1, including C-string in domain I; F, E, D, and C boxes, as well as bird similarity and B boxes, in domain II; and CSB1 in domain III. Tandem repeats were observed in remnant CR2 of the Phylloscopus fuscatus and Phylloscopus proregulus mitogenomes. A phylogenetic analysis with maximum likelihood (ML) and Bayesian inference (BI) methods, based on 13 protein-coding genes and two rRNA genes, indicated that the Phylloscopus species was divided into two larger clades, with a splitting time approximately 11.06 million years ago (mya). The taxa of Phylloscopus coronatus/Phylloscopus burkii and Phylloscopus inornatus/P. proregulus were located at the basal position of the different clades. The phylogenetic result of the cox1 gene showed that Seicercus was nested within Phylloscopus. The complete set of mitogenomes of the Phylloscopus species provides potentially useful resources for the further exploration of the taxonomic status and phylogenetic history of Phylloscopidae.
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Affiliation(s)
- Chao Yang
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an, China
| | - Xiaomei Dong
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Qingxiong Wang
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an, China
| | - Xiang Hou
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an, China
| | - Hao Yuan
- School of Basic Medical Sciences, Xi’an Medical University, Xi’an, China
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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Vianna JA, Noll D, Mura-Jornet I, Valenzuela-Guerra P, González-Acuña D, Navarro C, Loyola DE, Dantas GPM. Comparative genome-wide polymorphic microsatellite markers in Antarctic penguins through next generation sequencing. Genet Mol Biol 2017; 40:676-687. [PMID: 28898354 PMCID: PMC5596379 DOI: 10.1590/1678-4685-gmb-2016-0224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 03/17/2017] [Indexed: 12/01/2022] Open
Abstract
Microsatellites are valuable molecular markers for evolutionary and ecological
studies. Next generation sequencing is responsible for the increasing number of
microsatellites for non-model species. Penguins of the Pygoscelis
genus are comprised of three species: Adélie (P. adeliae), Chinstrap
(P. antarcticus) and Gentoo penguin (P. papua),
all distributed around Antarctica and the sub-Antarctic. The species have been
affected differently by climate change, and the use of microsatellite markers will be
crucial to monitor population dynamics. We characterized a large set of genome-wide
microsatellites and evaluated polymorphisms in all three species. SOLiD reads were
generated from the libraries of each species, identifying a large amount of
microsatellite loci: 33,677, 35,265 and 42,057 for P. adeliae, P.
antarcticus and P. papua, respectively. A large number
of dinucleotide (66,139), trinucleotide (29,490) and tetranucleotide (11,849)
microsatellites are described. Microsatellite abundance, diversity and orthology were
characterized in penguin genomes. We evaluated polymorphisms in 170 tetranucleotide
loci, obtaining 34 polymorphic loci in at least one species and 15 polymorphic loci
in all three species, which allow to perform comparative studies. Polymorphic markers
presented here enable a number of ecological, population, individual identification,
parentage and evolutionary studies of Pygoscelis, with potential use
in other penguin species.
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Affiliation(s)
- Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Santiago, Chile.,Centro de Cambio Global UC, Santiago, Chile
| | - Daly Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isidora Mura-Jornet
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paulina Valenzuela-Guerra
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniel González-Acuña
- Departamento de Ciencias Pecuarias, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | | | - David E Loyola
- Centro Nacional de Genómica y Bioinformática, Santiago, Chile
| | - Gisele P M Dantas
- Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, MG, Brazil
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Xu Q, Xia Y, Dang X, Chen X. The complete mitochondrial genome sequence of Emperor Penguins (Aptenodytes forsteri). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3646-7. [PMID: 26403091 DOI: 10.3109/19401736.2015.1079837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The emperor penguin (Aptenodytes forsteri) is the largest living species of penguin. Herein, we first reported the complete mitochondrial genome of emperor penguin. The mitochondrial genome is a circular molecule of 17 301 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA, and one control region. To verify the accuracy and the utility of new determined mitogenome sequences, we constructed the species phylogenetic tree of emperor penguin together with 10 other closely species. This is the second complete mitochondrial genome of penguin, and this is going to be an important data to study mitochondrial evolution of birds.
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Affiliation(s)
- Qiwu Xu
- a BGI Education Center, University of Chinese Academy of Sciences , Shenzhen , China and.,b BGI-Shenzhen , Shenzhen , China
| | - Yan Xia
- a BGI Education Center, University of Chinese Academy of Sciences , Shenzhen , China and.,b BGI-Shenzhen , Shenzhen , China
| | - Xiao Dang
- a BGI Education Center, University of Chinese Academy of Sciences , Shenzhen , China and.,b BGI-Shenzhen , Shenzhen , China
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Yoon KB, Cho CU, Park YC. The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes). Gene 2015; 572:227-36. [PMID: 26165451 DOI: 10.1016/j.gene.2015.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 06/20/2015] [Accepted: 07/07/2015] [Indexed: 01/22/2023]
Abstract
The complete mitogenome of Chroicocephalus saundersi was characterized and compared with the 6 published Charadriiformes mitogenomes. The mitogenome of C. saundersi is a closed circular molecule 16,739 bp in size, and contains 37 genes and a control region. The AT and GC skews are positive and negative, respectively, and in agreement with those of the other Charadriiformes mitogenomes. The mitogenome of C. saundersi contains 3 start codons (ATG, GTG, and ATT), 4 stop codons (TAA, TAG, AGG, and AGA), and an incomplete stop codon (T-) in 13 PCGs. A codon usage analysis of all available Charadriiformes mitogenomes showed that the ATG (78%) and TAA (50.5%) were the most common start codon and stop codon, respectively. An unusual start codon, ATT, is commonly found in the ND3s of Charadriiformes mitogenomes, whereas the more common start codons, ATC and ATA, are rarely found. In all the Laridae species, one extra cytosine was inserted at position 174 in ND3. The control region of C. saundersi is 1180-bp long, with a nucleotide composition of 30.2% A, 28.6% T, 27.3% C, and 14.0% G. Variable numbers of tandem repeats (VNTRs) with nine copies of the 10 bp repeat sequence (AACAACAAAC) are found within the CSB domain of the control region. The ML/BI analyses, based on the amino acids of the 13 mitochondrial PCGs, strongly support the monophyly of the order Charadriiformes, with the suborder Lari considered sister to the Scolopaci, which is in turn a sister group to the suborder Charadrii.
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Affiliation(s)
- Kwang Bae Yoon
- Division of Forest Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chea Un Cho
- Species Restoration Technology Institute, Korea National Park Service, Inje 252-829, Republic of Korea
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
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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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Han YD, Baek YS, Kim JH, Choi HG, Kim S. Complete mitochondrial genome of the South Polar Skua Stercorarius maccormicki (Charadriiformes, Stercorariidae) in Antarctica. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1783-4. [PMID: 25268998 DOI: 10.3109/19401736.2014.963811] [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] [Indexed: 11/13/2022]
Abstract
The South Polar Skua, gull-like seabirds is the most fascinating Antarctic seabirds that lay two eggs at sites free of snow and ice and predominantly hunt pelagic fish and penguins. Blood samples of the South Polar Skua Stercorarius maccormicki was collected during the summer activity near King Sejong station in Antarctica. The complete mitochondrial DNA sequence of S. maccormicki was 16,669 bp, showing conserved genome structure and orientation found in other avian species. The control region of S. maccormicki was 93- and 80 bp shorter compared to those of Chroicocephalus saundersi and Synthliboramphus antiquus respectively. Interestingly, there is a (CAACAAACAA)6 repeat sequence in the control region. Our results of S. maccormicki mt genome including the repeat sequence, may provide useful genetic information for phylogenetic and phylogeographic histories of the southern skua complex.
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Affiliation(s)
- Yeong-Deok Han
- a Department of Biological Sciences , Kongju National University , Gongju-si , Chungcheongnam-do , South Korea and
| | - Ye-Seul Baek
- b Division of Life Sciences , Korea Polar Research Institute, KIOST , 26 Songdomirae-ro , Yeonsu-gu , Incheon , South Korea
| | - Jeong-Hoon Kim
- b Division of Life Sciences , Korea Polar Research Institute, KIOST , 26 Songdomirae-ro , Yeonsu-gu , Incheon , South Korea
| | - Han-Gu Choi
- b Division of Life Sciences , Korea Polar Research Institute, KIOST , 26 Songdomirae-ro , Yeonsu-gu , Incheon , South Korea
| | - Sanghee Kim
- b Division of Life Sciences , Korea Polar Research Institute, KIOST , 26 Songdomirae-ro , Yeonsu-gu , Incheon , South Korea
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Zhou X, Lin Q, Fang W, Chen X. The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements. BMC Genomics 2014; 15:573. [PMID: 25001581 PMCID: PMC4111848 DOI: 10.1186/1471-2164-15-573] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 07/03/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds. RESULTS The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea. CONCLUSIONS The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.
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Affiliation(s)
- Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
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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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Sammler S, Bleidorn C, Tiedemann R. Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination. BMC Genomics 2011; 12:35. [PMID: 21235758 PMCID: PMC3025957 DOI: 10.1186/1471-2164-12-35] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 01/14/2011] [Indexed: 01/07/2023] Open
Abstract
Background Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i.e., in every generation. Conclusions The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.
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Affiliation(s)
- Svenja Sammler
- University of Potsdam, Institute for Biology and Biochemistry, Unit of Evolutionary Biology/Systematic Zoology, Karl-Liebknecht-Str. 24-25, Haus 26, D-14476 Potsdam, Germany
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Lee JCI, Tsai LC, Liao SP, Linacre A, Hsieh HM. Evaluation of the polymorphic D-loop of Columba livia in forensic applications. Electrophoresis 2010; 31:3889-94. [DOI: 10.1002/elps.201000414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Cho HJ, Eda M, Nishida S, Yasukochi Y, Chong JR, Koike H. Tandem duplication of mitochondrial DNA in the black-faced spoonbill, Platalea minor. Genes Genet Syst 2010; 84:297-305. [PMID: 20057167 DOI: 10.1266/ggs.84.297] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial (mt) heteroplasmy in the control region (CR) of the black-faced spoonbill was investigated using LA-PCR. To avoid amplification of transpositioned nuclear genome fragment from mtDNA (numt), PCR product of the almost-complete mitochondrial genome was amplified using primers designed to anneal on the COIII gene. Then nested LA-PCR product was amplified between the cyt b and 12S rRNA genes using the almost-complete mitochondrial genome PCR product as a template. Nucleotide sequencing revealed tandem duplication composed of two units. The first contains cyt b-1, tRNA(Thr)-1, tRNA(Pro)-1, ND6-1, tRNA(Glu)-1 and CR1, and the second consists of cyt b-2, tRNA(Thr)-2, tRNA(Pro)-2, ND6-2, tRNA(Glu)-2 and CR2, followed by tRNA(Phe) and 12S rRNA. The duplicated cyt b-2 sequence coincided with 499 bp at the 3' end of cyt b-1. With the exception of the CR, the other genes in the duplicated sequence were identical to the original corresponding gene. Even though both CR1 and CR2 contain functional blocks, such as a poly-C site, a goose hairpin and a TAS structure in Domain I, the 3' end of CR1 was followed by a 112 bp sequence (non-coding region) that was not found in CR2 or in sequence homology analysis of similar genes. Meanwhile, CR2 ended in a complicated repeat sequence. The 5' franking region in the Domain I (Region A) and the 3' franking region in the Domain I (Region B) of the two CRs evolve in quite different manners: Region A was highly variable between CR1 and CR2 in the same individuals, while Region B was almost identical between them, which indicates concerted evolution.
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Affiliation(s)
- Hyong-Ju Cho
- Laboratory of Biodiversity, Department Environmental Changes, SCS, Kyushu University, Fukuoka City 819-0395, Japan
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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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Xiao B, Ma F, Sun Y, Li QW. Comparative analysis of complete mitochondrial DNA control region of four species of Strigiformes. ACTA ACUST UNITED AC 2009; 33:965-74. [PMID: 17112967 DOI: 10.1016/s0379-4172(06)60131-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 07/17/2006] [Indexed: 11/30/2022]
Abstract
The sequence of the whole mitochondrial (mt) DNA control region (CR) of four species of Strigiformes was obtained. Length of the CR was 3,290 bp, 2,848 bp, 2,444 bp, and 1,771 bp for Asio flammeus, Asio otus, Athene noctua, and Strix aluco, respectively. Interestingly, the length of the control region was maximum in Asio flammeus among all the avian mtDNA control regions sequenced thus far. In addition, the base composition and organization of mtDNA CR of Asio flammeus were identical to those reported for other birds. On the basis of the differential frequencies of base substitutions, the CR may be divided two variable domains, I and III, and a central conserved domain, II. The 3' end of the CR contained many tandem repeats of varying lengths and repeat numbers. In Asio flammeus, the repeated sequences consisted of a 126 bp sequence that was repeated seven times and a 78 bp sequence that was repeated 14 times. In Asio otus, there were also two repeated sequences, namely a 127 bp sequence that was repeated eight times and a 78 bp sequence that was repeated six times. The control region of Athene noctua contained three sets of repeats: a 89 bp sequence that was repeated three times, a 77 bp sequence that was repeated four times, and a 71 bp sequence that was repeated six times. Strix aluco, however, had only one repeated sequence, a 78 bp sequence that was repeated five times. The results of this study seem to indicate that these tandem repeats may have resulted from slipped-strand mispairing during mtDNA replication. Moreover, there are many conserved motifs within the repeated units. These sequences could form stable stem-loop secondary structures, which suggests that these repeated sequences play an important role in regulating transcription and replication of the mitochondrial genome.
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Affiliation(s)
- Bing Xiao
- College of Life Sciences, Liaoning Normal University, Dalian 116029, China
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14
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Jouventin P, Cuthbert RJ, Ottvall R. Genetic isolation and divergence in sexual traits: evidence for the northern rockhopper penguin Eudyptes moseleyi being a sibling species. Mol Ecol 2006; 15:3413-23. [PMID: 16968279 DOI: 10.1111/j.1365-294x.2006.03028.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The taxonomic status of populations of rockhopper penguins (Eudyptes chrysocome) is still enigmatic. Northern populations differ from southern ones in breeding phenology, song characteristics and head ornaments used as mating signals. We conducted a molecular analysis using mitochondrial DNA sequencing to test if there is a gene flow barrier between northern (subtropical) populations and southern (subantarctic) populations in relation to the Subtropical Convergence, a major ecological boundary for marine organisms. Sequences of the control region and the ND2 gene were analysed in rockhopper penguins and in the macaroni penguin (Eudyptes chrysolophus), a closely related species. Genetic distances and phylogenetic analyses showed a clear split into three clades, two rockhopper clades and the macaroni penguin. Moreover, Theta(ST) and gene flow estimates also suggested genetic structuring within the northern rockhoppers. Our results add further support to the notion that the two rockhopper penguin taxa, often considered as two subspecies, can be recognized as two species E. chrysocome and E. moseleyi. The divergence in mating signals found between these two taxa seems to have occurred recently and relatively rapidly. Thus, the behavioural changes may have been enough to isolate these taxa without the need for morphological differentiation. The findings have important conservational implications, since E. moseleyi is far less abundant than E. chrysocome, but more populations may warrant an uplisting to endangered status if full species status should be recognized for more subpopulations.
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Affiliation(s)
- P Jouventin
- Centre d'Ecologie Fonctionnelle et Evolutive, 1919 Route de Mende, 342 93 Montpellier cedex 5, France
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15
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Hauth AM, Maier UG, Lang BF, Burger G. The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region. Nucleic Acids Res 2005; 33:4433-42. [PMID: 16085754 PMCID: PMC1183108 DOI: 10.1093/nar/gki757] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas salina. The 48 063 bp circular-mapping molecule codes for 2 rRNAs, 27 tRNAs and 40 proteins including 23 components of oxidative phosphorylation, 15 ribosomal proteins and two subunits of tat translocase. One potential protein (ORF161) is without assigned function. Only two introns occur in the genome; both are present within cox1 belong to group II and contain RT open reading frames. Primitive genome features include bacteria-like rRNAs and tRNAs, ribosomal protein genes organized in large clusters resembling bacterial operons and the presence of the otherwise rare genes such as rps1 and tatA. The highly compact gene organization contrasts with the presence of a 4.7 kb long, repeat-containing intergenic region. Repeat motifs ∼40–700 bp long occur up to 31 times, forming a complex repeat structure. Tandem repeats are the major arrangement but the region also includes a large, ∼3 kb, inverted repeat and several potentially stable ∼40–80 bp long hairpin structures. We provide evidence that the large repeat region is involved in replication and transcription initiation, predict a promoter motif that occurs in three locations and discuss two likely scenarios of how this highly structured repeat region might have evolved.
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Affiliation(s)
- Amy M Hauth
- Département de Biochimie, Robert Cedergren Research Center for Bioinformatics and Genomics, Canadian Institute for Advanced Research, Université de Montréal 2900 Boulevard Edouard-Montpetit, Montréal, Québec, Canada H3T 1J4.
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16
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Mundy NI, Helbig AJ. Origin and evolution of tandem repeats in the mitochondrial DNA control region of shrikes (Lanius spp.). J Mol Evol 2005; 59:250-7. [PMID: 15486698 DOI: 10.1007/s00239-004-2619-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2003] [Accepted: 02/12/2004] [Indexed: 10/26/2022]
Abstract
The origin and evolution of a 128-bp tandem repeat in the mtDNA control region of shrikes (Lanius: Aves) were investigated. The tandem repeat is present in only two species, L. excubitor and L. ludovicianus. In contrast to the variation in repeat number in L. ludovicianus, all individuals of three subspecies of L. excubitor had three repeats. Comparative analysis suggests that a short direct repeat, and a secondary structure including the tandem repeat and a downstream inverted repeat, may be important in the origin of the tandem repeat by slipped-strand mispairing and its subsequent turnover. Homogenization of repeat sequences is most simply explained by expansion and contraction of the repeat array. Surprisingly, mtDNA sequences from L. excubitor were found to be paraphyletic with respect to L. ludovicianus. These results show the utility of a comparative analysis for insights into the evolutionary dynamics of mtDNA tandem repeats.
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Affiliation(s)
- Nicholas I Mundy
- Department of Zoology, University of Cambridge, Downing Street, CB2 3EJ Cambridge, UK.
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17
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Kikkawa EF, Tsuda TT, Naruse TK, Sumiyama D, Fukuda M, Kurita M, Murata K, Wilson RP, LeMaho Y, Tsuda M, Kulski JK, Inoko H. Analysis of the sequence variations in the Mhc DRB1-like gene of the endangered Humboldt penguin (Spheniscus humboldti). Immunogenetics 2005; 57:99-107. [PMID: 15714307 DOI: 10.1007/s00251-005-0774-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Revised: 12/21/2004] [Indexed: 10/25/2022]
Abstract
The Major Histocompatibility Complex (Mhc) genomic region of many vertebrates is known to contain at least one highly polymorphic class II gene that is homologous in sequence to one or other of the human Mhc DRB1 class II genes. The diversity of the avian Mhc class II gene sequences have been extensively studied in chickens, quails, and some songbirds, but have been largely ignored in the oceanic birds, including the flightless penguins. We have previously reported that several penguin species have a high degree of polymorphism on exon 2 of the Mhc class II DRB1-like gene. In this study, we present for the first time the complete nucleotide sequences of exon 2, intron 2, and exon 3 of the DRB1-like gene of 20 Humboldt penguins, a species that is presently vulnerable to the dangers of extinction. The Humboldt DRB1-like nucleotide and amino acid sequences reveal at least eight unique alleles. Phylogenetic analysis of all the available avian DRB-like sequences showed that, of five penguin species and nine other bird species, the sequences of the Humboldt penguins grouped most closely to the Little penguin and the mallard, respectively. The present analysis confirms that the sequence variations of the Mhc class II gene, DRB1, are useful for discriminating among individuals within the same penguin population as well those within different penguin population groups and species.
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Affiliation(s)
- Eri F Kikkawa
- Department of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan
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18
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Pereira SL, Grau ET, Wajntal A. Molecular architecture and rates of DNA substitutions of the mitochondrial control region of cracid birds. Genome 2005; 47:535-45. [PMID: 15190371 DOI: 10.1139/g04-009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
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.
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Affiliation(s)
- Sergio L Pereira
- Departamento de Biologia, Instituto de Biociências, Universidade de São Paulo, Brazil.
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19
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Buehler DM, Baker AJ. Characterization of the red knot (Calidris canutus) mitochondrial control region. Genome 2003; 46:565-72. [PMID: 12897864 DOI: 10.1139/g03-034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We sequenced the complete mitochondrial control regions of 11 red knots (Calidris canutus). The control region is 1168 bp in length and is flanked by tRNA glutamate (glu) and the gene ND6 at its 5' end and tRNA phenylalanine (phe) and the gene 12S on its 3' end. The sequence possesses conserved sequence blocks F, E, D, C, CSB-1, and the bird similarity box (BSB), as expected for a mitochondrial copy. Flanking tRNA regions show correct secondary structure, and a relative rate test indicated no significant difference between substitution rates in the sequence we obtained versus the known mitochondrial sequence of turnstones (Charadriiformes: Scolopacidae). These characteristics indicate that the sequence is mitochondrial in origin. To confirm this, we sequenced the control region of a single individual using both purified mitochondrial DNA and genomic DNA. The sequences were identical using both methods. The sequence and methods presented in this paper may now serve as a reference for future studies using knot and other avian control regions. Furthermore, the discovery of five variable sites in 11 knots towards the 3' end of the control region, and the variability of this region in contrast to the more conserved central domain in the alignment between knots and other Charadriiformes, highlights the importance of this area as a source of variation for future studies in knots and other birds.
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Affiliation(s)
- Deborah M Buehler
- Center for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
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20
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Slack KE, Janke A, Penny D, Arnason U. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 2003; 302:43-52. [PMID: 12527195 DOI: 10.1016/s0378111902010533] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We report complete mitochondrial (mt) genomes for a penguin (little blue, Eudyptula minor) and a goose (greater white-fronted, Anser albifrons). A revised annotation of avian and reptile mt genomes has been carried out, which improves consistency of labeling gene start and stop positions. In conjunction with this, a summary of mt gene features is presented and a number of conserved patterns and interesting differences identified. The protein-coding genes from the two new genomes were analysed together with those from 17 other birds plus outgroup (reptile) taxa. The unrooted amino acid tree from 19 avian genomes was locally stable with many high bootstrap values using several maximum likelihood methods. In particular, Anseriformes (goose and duck) grouped strongly with Galliformes (chicken) to form Gallianseres, while the penguin paired firmly with the stork. The position where the outgroup joined the avian tree varied with the combination of outgroup taxa used. The three best supported positions of the root were passerine, but the traditional rooting position between paleognaths and neognaths could not be excluded.
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Affiliation(s)
- Kerryn E Slack
- Division of Evolutionary Molecular Systematics, Department of Cell and Organism Biology, University of Lund, Sölvegatan 29, S-223 62, Lund, Sweden.
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Ray DA, Densmore L. The crocodilian mitochondrial control region: general structure, conserved sequences, and evolutionary implications. THE JOURNAL OF EXPERIMENTAL ZOOLOGY 2002; 294:334-45. [PMID: 12461813 DOI: 10.1002/jez.10198] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We present the first comprehensive analysis of the crocodilian control region. We have analyzed sequences from all three families of Crocodylia (Crocodylidae, Gavialidae, Alligatoridae), incorporating all genera except Paleosuchus and Melanosuchus. Within the control region of other vertebrates, several sequence motifs and their order appear to be conserved. Herein, we compare aligned crocodilian D-loop sequences to homologous sequences from other vertebrates ranging from fish to birds. Among other findings, we have discovered that while domain I tends to be shorter than the same region in mammals and birds, it contains sequences similar in structure to both the goose-hairpin and termination associated sequences (TAS). Domain II is highly conservative with regard to size among the taxa examined and contains several of the conserved sequence boxes characterized in other vertebrates. Domain III contains several interesting sequence motifs including tandemly repeated sequences, a long poly-A region in the Crocodylidae, and possible bidirection promoter sequences.
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Affiliation(s)
- David Alfred Ray
- Texas Tech University, Department of Biological Sciences, Lubbock, Texas 79409, USA.
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