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Escobedo-Morales LA, Castañeda-Rico S, Mandujano S, León-Paniagua L, Maldonado JE. First description of the mitochondrial genomes of the Central American brocket deer Mazama temama (Kerr, 1792) and the Yucatán Peninsula brocket deer Odocoileus pandora Merriam, 1901. Mol Biol Rep 2023; 50:4851-4863. [PMID: 37039999 DOI: 10.1007/s11033-023-08407-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/24/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND The Central American (Mazama temama) and the Yucatán Peninsula brocket deer (Odocoileus pandora) are deer species with cryptic habits, and little is known about their biology. Odocoileus pandora is listed as Vulnerable on the 2015 IUCN Red List of Threatened Species, while M. temama is considered Data Deficient; however, it currently faces a decreasing population trend. METHODS AND RESULTS We assembled the complete mitochondrial genome for two M. temama specimens and one complete and one partial for O. pandora from Illumina 150 bp paired-end reads. The mitogenomes of M. temama and O. pandora have a length of 16,479-16,480 and 16,419 bp, respectively, AT-biased; they consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region, most of them follow a transcription direction in the heavy strand of the molecule. The mitochondrial genome of O. pandora shows some particularities compared to other deer species, like a shorter control region of 987-990 bp and a cytochrome b gene with a length of 1,143 bp. Our phylogenetic analyses confirm the close affinity of M. temama to South American M. americana and the nested position of the genus Odocoileus, including O. pandora, into the genus Mazama. CONCLUSIONS Here, we described for the first time the complete mitochondrial genome for these two species. While our study provides additional information about the taxonomic status of the northern neotropical brocket deer, further research is needed to solve the complicated taxonomy of neotropical deer.
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Affiliation(s)
- Luis A Escobedo-Morales
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D, Primer piso, Circuito de Posgrados, AP 70-153, Ciudad Universitaria, Mexico City, 04510, Mexico.
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA.
| | - Susette Castañeda-Rico
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA
- Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA
- Department of Biology, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA
| | - Salvador Mandujano
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Xalapa, Veracruz, 91070, Mexico
| | - Livia León-Paniagua
- Museo de Zoología Alfonso L. Herrera, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA
- Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA
- Department of Biology, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA
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2
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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3
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Westerman M, Loke S, Tan MH. Molecular relationships of the red-bellied dasyure (Phascolosorex doriae) – a rare marsupial from western New Guinea. AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am21011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The mitochondrial genome of the rare endemic New Guinean dasyurid Phascolosorex doriae (Thomas 1886) has been used to clarify relationships within ‘phascolosoricinae’. The mitochondrial genome has the typical gene arrangement seen in other marsupials. Molecular analyses using complete mitogenomes of other dasyurids resolve the red-bellied dasyure as sister to the narrow-striped dasyure Phascolosorex dorsalis and show that these two species diverged in the early Pliocene. The invasion of emergent New Guinean rainforest habitats (in the late Miocene) by the common ancestor of Ph. doriae, Ph. dorsalis and Neophascogale lorentzii represents one of three separate such invasions by dasyurid lineages.
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4
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Comparative mitogenomes of three species in Moenkhausia: Rare irregular gene rearrangement within Characidae. Int J Biol Macromol 2021; 183:1079-1086. [PMID: 33984380 DOI: 10.1016/j.ijbiomac.2021.05.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022]
Abstract
Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangements. However, a new type of gene arrangement has been identified in the mitochondrial genomes (mitogenomes) of Moenkhausia. Here, three newly sequenced complete mitogenomes of tetras (Characidae: Moenkhausia) are presented (M. costae, M. pittieri, and M. sanctaefilomenae). The three mitogenomes had a classical circular structure, with total lengths ranging from 15,811 to 18,435 bp. Base composition analysis indicated that the sequences were biased toward adenine (A) and thymine (T), with A + T content of 54.63% in M. costae, 58.47% in M. pittieri, and 59.98% in M. sanctaefilomenae. The gene order and organization of M. sanctaefilomenae differed from those of typical teleostean mitogenomes. The genes tRNA-Ile, tRNA-Gln, and tRNA-Pro were translocated between tRNA-Trp and tRNA-Asn. One extra tRNA-Met and an extra CR were also discovered in the mitogenome. BI and ML analyses based on sequences of 38 different mitogenomes showed that M. costae and M. pittieri were classified together, and M. sanctaefilomenae was slightly further from other fish of the same genus. These results provide insight into the gene arrangement features of Characidae mitogenomes and lay the foundation for further phylogenetic studies on Characidae.
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5
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Dias CAR, Santos Júnior JE, Pinto CM, Santos FR, Perini FA. Mitogenomics of
Didelphis
(Mammalia; Didelphimorphia; Didelphidae) and insights into character evolution in the genus. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Cayo Augusto Rocha Dias
- Laboratório de Evolução de Mamíferos Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - José Eustáquio Santos Júnior
- Laboratório de Biodiversidade e Evolução Molecular Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Christian Miguel Pinto
- Departamento de Biologia Facultad de Ciencias Escuela Politécnica Nacional Quito Ecuador
| | - Fabrício Rodrigues Santos
- Laboratório de Biodiversidade e Evolução Molecular Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Fernando Araújo Perini
- Laboratório de Evolução de Mamíferos Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
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6
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Geng Y, Yang C, Guo H, Thomas PB, Jeffery PL, Chopin LK, Baker AM, Tian R, Seim I. The mitochondrial genome of the black-tailed dusky antechinus ( Antechinus arktos). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3835-3837. [PMID: 33426294 PMCID: PMC7759261 DOI: 10.1080/23802359.2020.1840940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this study, we report the mitochondrial genome of the black-tailed antechinus (Antechinus arktos), a recently-discovered, endangered carnivorous marsupial inhabiting a caldera that straddles the border of Australia’s mid-east coast. The circular A. arktos genome is 17,334 bp in length and has an AT content of 63.3%. Its gene content and arrangement are consistent with reported marsupial mitogenome assemblies.
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Affiliation(s)
- Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Chen Yang
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Han Guo
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Patrick B Thomas
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Penny L Jeffery
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Lisa K Chopin
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.,Ghrelin Research Group, Translational Research Institute -Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Andrew M Baker
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Australia.,Natural Environments Program, Queensland Museum, Queensland, Australia
| | - Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.,Ghrelin Research Group, Translational Research Institute -Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.,School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Australia
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7
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Novel gene rearrangement pattern in Cynoglossus melampetalus mitochondrial genome: New gene order in genus Cynoglossus (Pleuronectiformes: Cynoglossidae). Int J Biol Macromol 2020; 149:1232-1240. [DOI: 10.1016/j.ijbiomac.2020.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 11/24/2022]
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8
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Tian R, Geng Y, Thomas PB, Jeffery PL, Mutton TY, Chopin LK, Baker AM, Seim I. The mitochondrial genome of the black-tailed dasyure ( Murexia melanurus). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3598-3600. [PMID: 33366102 PMCID: PMC7707616 DOI: 10.1080/23802359.2019.1677526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this study, we report the mitochondrial genome of the black-tailed dasyure (Murexia melanurus) of New Guinea. The circular genome is 17,736 bp in length and has an AT content of 60.5%. Its gene content – 13 protein-coding genes (PCGs), 2 ribosomal (rRNA) genes, 21 transfer RNA (tRNA) genes, a tRNA pseudogene (tRNALys), and a non-coding control region (CR) – and gene arrangement are consistent with previous marsupial mitogenome assemblies.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Patrick B Thomas
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.,Queensland Bladder Cancer Initiative, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Penny L Jeffery
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Thomas Y Mutton
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Lisa K Chopin
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Andrew M Baker
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Natural Environments Program, Queensland Museum, South Brisbane, Queensland, Australia
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.,Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.,Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, Queensland, Australia
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9
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Prada CF, Boore JL. Gene annotation errors are common in the mammalian mitochondrial genomes database. BMC Genomics 2019; 20:73. [PMID: 30669991 PMCID: PMC6341679 DOI: 10.1186/s12864-019-5447-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/10/2019] [Indexed: 11/13/2022] Open
Abstract
Background Although animal mitochondrial DNA sequences are known to evolve rapidly, their gene arrangements often remain unchanged over long periods of evolutionary time. Therefore, comparisons of mitochondrial genomes may result in significant insights into the evolution both of organisms and of genomes. Mammalian mitochondrial genomes recently published in the GenBank database of NCBI show numerous rearrangements in various regions of the genome, from which it may be inferred that the mammalian mitochondrial genome is more dynamic than expected. However, it is alternatively possible that these are errors of annotation and, if so, are misleading our interpretations. In order to verify these possible errors of annotation, we performed a comparative genomic analysis of mammalian mitochondrial genomes available in the NCBI database. Results Using a combination of bioinformatics methods to carefully examine the mitochondrial gene arrangements in 304 mammalian species, we determined that there are only two sets of gene arrangements, one that is shared by all of the marsupials and another that is shared by all of the monotremes and eutherians, with these two arrangements differing only by the positions of tRNA genes in the region commonly designated as “WANCY” for the genes it comprises. All of the 68 other cases of reported gene rearrangements are errors. We note that there are also numerous errors of impossibly short, incorrect gene annotations, cases where genomes that are reported as complete are actually missing portions of the sequence, and genes that are clearly present but were not annotated in these records. Conclusions We judge that the application of simple bioinformatic tools in the verification of gene annotation, particularly for organelle genomes, would be a very useful enhancement for the curation of genome sequences submitted to GenBank. Electronic supplementary material The online version of this article (10.1186/s12864-019-5447-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carlos F Prada
- Departamento de Biología, Facultad de ciencias, Universidad del Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA
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10
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Molecular resolution to a morphological controversy: The case of North American fossil muskoxen Bootherium and Symbos. Mol Phylogenet Evol 2018; 129:70-76. [DOI: 10.1016/j.ympev.2018.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/29/2023]
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11
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The complete mitochondrial genomes of Tarsiger cyanurus and Phoenicurus auroreus: a phylogenetic analysis of Passeriformes. Genes Genomics 2018; 40:151-165. [PMID: 29892923 DOI: 10.1007/s13258-017-0617-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
Passeriformes is the largest group within aves and the phylogenetic relationships between Passeriformes have caused major disagreement in ornithology. Particularly, the phylogenetic relationships between muscicapoidea and sylvioidea are complex, and their taxonomic boundaries have not been clearly defined. Our aim was to study the status of two bird species: Tarsiger cyanurus and Phoenicurus auroreus. Furthermore, we analyzed the phylogenetic relationships of Passeriformes. Complete mitochondrial DNA (mtDNA) sequences of both species were determined and the lengths were 16,803 (T. cyanurus) and 16,772 bp (P. auroreus), respectively. Thirteen protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region were identified in these mtDNAs. The contents of A and T at the base compositions was significantly higher than the content of G and C, and this AT skew was positive, while the GC skew was negative. The monophyly of Passeriformes is divided into four major clades: Corvoidea, Sylvioidea, Passeroidea, and Musicicapoidea. Paridae should be separated from the superfamily Sylvioidea and placed within the superfamily Muscicapoidea. The family Muscicapidae and Corvida were paraphyly, while Carduelis and Emberiza were grouped as a sister taxon. The relationships between some species of the order passeriformes may remain difficult to resolve despite an effort to collect additional characters for phylogenetic analysis. Current research of avian phylogeny should focus on adding characters and taxa and use both effectively to obtain a better resolution for deeper and shallow nodes.
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12
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Qian L, Wang H, Yan J, Pan T, Jiang S, Rao D, Zhang B. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes. BMC Genomics 2018; 19:354. [PMID: 29747572 PMCID: PMC5946542 DOI: 10.1186/s12864-018-4717-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. RESULTS In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. CONCLUSIONS The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.
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Affiliation(s)
- Lifu Qian
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Shanqun Jiang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.
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13
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Sarver BAJ, Demboski JR, Good JM, Forshee N, Hunter SS, Sullivan J. Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias). Genome Biol Evol 2018; 9:7-19. [PMID: 28172670 PMCID: PMC5381575 DOI: 10.1093/gbe/evw254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2016] [Indexed: 11/16/2022] Open
Abstract
Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here, we investigate extensive mtDNA introgression in western chipmunks, focusing on species in the Tamias quadrivittatus group from the central and southern Rocky Mountains. Specifically, we investigate the role of selection in driving patterns of introgression. We sequenced 51 mtDNA genomes from six species and combine these sequences with other published genomic data to yield annotated mitochondrial reference genomes for nine species of chipmunks. Genomic characterization was performed using a series of molecular evolutionary and phylogenetic analyses to test protein-coding genes for positive selection. We fit a series of maximum likelihood models using a model-averaging approach, assessed deviations from neutral expectations, and performed additional tests to search for codons under the influence of selection. We found no evidence for positive selection among these genomes, suggesting that selection has not been the driving force of introgression in these species. Thus, extensive mtDNA introgression among several species of chipmunks likely reflects genetic drift of introgressed alleles in historically fluctuating populations.
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Affiliation(s)
- Brice A J Sarver
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO.,Department of Biological Sciences, University of Idaho, Moscow, ID.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Nicholas Forshee
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
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14
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Mol Phylogenet Evol 2016; 94:447-62. [DOI: 10.1016/j.ympev.2015.10.027] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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15
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Bidon T, Schreck N, Hailer F, Nilsson MA, Janke A. Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses. Genome Biol Evol 2015; 7:2010-22. [PMID: 26019166 PMCID: PMC4524476 DOI: 10.1093/gbe/evv103] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears.
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Affiliation(s)
- Tobias Bidon
- Senckenberg Biodiversity and Climate Research Centre Frankfurt, Frankfurt am Main, Germany International Graduate School of Science and Engineering (IGSSE), Technische Universität München, Garching, Germany
| | - Nancy Schreck
- Senckenberg Biodiversity and Climate Research Centre Frankfurt, Frankfurt am Main, Germany
| | - Frank Hailer
- Senckenberg Biodiversity and Climate Research Centre Frankfurt, Frankfurt am Main, Germany School of Biosciences, Cardiff University, Wales, United Kingdom
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre Frankfurt, Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre Frankfurt, Frankfurt am Main, Germany Institute for Ecology, Evolution & Diversity, Goethe University Frankfurt, Germany
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Kumazawa Y, Miura S, Yamada C, Hashiguchi Y. Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes. BMC Genomics 2014; 15:930. [PMID: 25344428 PMCID: PMC4223735 DOI: 10.1186/1471-2164-15-930] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 10/13/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Vertebrate mitochondrial genomes (mitogenomes) are 16-18 kbp double-stranded circular DNAs that encode a set of 37 genes. The arrangement of these genes and the major noncoding region is relatively conserved through evolution although gene rearrangements have been described for diverse lineages. The tandem duplication-random loss model has been invoked to explain the mechanisms of most mitochondrial gene rearrangements. Previously reported mitogenomic sequences for geckos rarely included gene rearrangements, which we explore in the present study. RESULTS We determined seven new mitogenomic sequences from Gekkonidae using a high-throughput sequencing method. The Tropiocolotes tripolitanus mitogenome involves a tandem duplication of the gene block: tRNAArg, NADH dehydrogenase subunit 4L, and NADH dehydrogenase subunit 4. One of the duplicate copies for each protein-coding gene may be pseudogenized. A duplicate copy of the tRNAArg gene appears to have been converted to a tRNAGln gene by a C to T base substitution at the second anticodon position, although this gene may not be fully functional in protein synthesis. The Stenodactylus petrii mitogenome includes several tandem duplications of tRNALeu genes, as well as a translocation of the tRNAAla gene and a putative origin of light-strand replication within a tRNA gene cluster. Finally, the Uroplatus fimbriatus and U. ebenaui mitogenomes feature the apparent loss of the tRNAGlu gene from its original position. Uroplatus fimbriatus appears to retain a translocated tRNAGlu gene adjacent to the 5' end of the major noncoding region. CONCLUSIONS The present study describes several new mitochondrial gene rearrangements from Gekkonidae. The loss and reassignment of tRNA genes is not very common in vertebrate mitogenomes and our findings raise new questions as to how missing tRNAs are supplied and if the reassigned tRNA gene is fully functional. These new examples of mitochondrial gene rearrangements in geckos should broaden our understanding of the evolution of mitochondrial gene arrangements.
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Affiliation(s)
- Yoshinori Kumazawa
- Department of Information and Biological Sciences and Research Center for Biological Diversity, Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya 467-8501, Japan.
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17
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Idiosyncrasies in decoding mitochondrial genomes. Biochimie 2014; 100:95-106. [PMID: 24440477 DOI: 10.1016/j.biochi.2014.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022]
Abstract
Mitochondria originate from the α-proteobacterial domain of life. Since this unique event occurred, mitochondrial genomes of protozoans, fungi, plants and metazoans have highly derived and diverged away from the common ancestral DNA. These resulting genomes highly differ from one another, but all present-day mitochondrial DNAs have a very reduced coding capacity. Strikingly however, ATP production coupled to electron transport and translation of mitochondrial proteins are the two common functions retained in all mitochondrial DNAs. Paradoxically, most components essential for these two functions are now expressed from nuclear genes. Understanding how mitochondrial translation evolved in various eukaryotic models is essential to acquire new knowledge of mitochondrial genome expression. In this review, we provide a thorough analysis of the idiosyncrasies of mitochondrial translation as they occur between organisms. We address this by looking at mitochondrial codon usage and tRNA content. Then, we look at the aminoacyl-tRNA-forming enzymes in terms of peculiarities, dual origin, and alternate function(s). Finally we give examples of the atypical structural properties of mitochondrial tRNAs found in some organisms and the resulting adaptive tRNA-protein partnership.
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Stöger I, Schrödl M. Mitogenomics does not resolve deep molluscan relationships (yet?). Mol Phylogenet Evol 2012; 69:376-92. [PMID: 23228545 DOI: 10.1016/j.ympev.2012.11.017] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 11/08/2012] [Accepted: 11/22/2012] [Indexed: 10/27/2022]
Abstract
The origin of molluscs among lophotrochozoan metazoans is unresolved and interclass relationships are contradictory between morphology-based, multi-locus, and recent phylogenomic analyses. Within the "Deep Metazoan Phylogeny" framework, all available molluscan mitochondrial genomes were compiled, covering 6 of 8 classes. Genomes were reannotated, and 13 protein coding genes (PCGs) were analyzed in various taxon settings, under multiple masking and coding regimes. Maximum Likelihood based methods were used for phylogenetic reconstructions. In all cases, molluscs result mixed up with lophotrochozoan outgroups, and most molluscan classes with more than single representatives available are non-monophyletic. We discuss systematic errors such as long branch attraction to cause aberrant, basal positions of fast evolving ingroups such as scaphopods, patellogastropods and, in particular, the gastropod subgroup Heterobranchia. Mitochondrial sequences analyzed either as amino acids or nucleotides may perform well in some (Cephalopoda) but not in other palaeozoic molluscan groups; they are not suitable to reconstruct deep (Cambrian) molluscan evolution. Supposedly "rare" mitochondrial genome level features have long been promoted as phylogenetically informative. In our newly annotated data set, features such as genome size, transcription on one or both strands, and certain coupled pairs of PCGs show a homoplastic, but obviously non-random distribution. Apparently congruent (but not unambiguous) signal for non-trivial subclades, e.g. for a clade composed of pteriomorph and heterodont bivalves, needs confirmation from a more comprehensive bivalve sampling. We found that larger clusters not only of PCGs but also of rRNAs and even tRNAs can bear local phylogenetic signal; adding trnG-trnE to the end of the ancestral cluster trnM-trnC-trnY-trnW-trnQ might be synapomorphic for Mollusca. Mitochondrial gene arrangement and other genome level features explored and reviewed herein thus failed as golden bullets, but are promising as additional characters or evidence supporting deep molluscan clades revealed by other data sets. A representative and dense sampling of molluscan subgroups may contribute to resolve contentious interclass relationships in the future, and is vital for exploring the evolution of especially diverse mitochondrial genomes in molluscs.
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Affiliation(s)
- I Stöger
- Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany.
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19
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Luo H, Arndt W, Zhang Y, Shi G, Alekseyev M, Tang J, Hughes AL, Friedman R. Phylogenetic analysis of genome rearrangements among five mammalian orders. Mol Phylogenet Evol 2012; 65:871-82. [PMID: 22929217 PMCID: PMC4425404 DOI: 10.1016/j.ympev.2012.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 08/11/2012] [Accepted: 08/13/2012] [Indexed: 01/16/2023]
Abstract
Evolutionary relationships among placental mammalian orders have been controversial. Whole genome sequencing and new computational methods offer opportunities to resolve the relationships among 10 genomes belonging to the mammalian orders Primates, Rodentia, Carnivora, Perissodactyla and Artiodactyla. By application of the double cut and join distance metric, where gene order is the phylogenetic character, we computed genomic distances among the sampled mammalian genomes. With a marsupial outgroup, the gene order tree supported a topology in which Rodentia fell outside the cluster of Primates, Carnivora, Perissodactyla, and Artiodactyla. Results of breakpoint reuse rate and synteny block length analyses were consistent with the prediction of random breakage model, which provided a diagnostic test to support use of gene order as an appropriate phylogenetic character in this study. We discussed the influence of rate differences among lineages and other factors that may contribute to different resolutions of mammalian ordinal relationships by different methods of phylogenetic reconstruction.
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Affiliation(s)
- Haiwei Luo
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
| | - William Arndt
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Yiwei Zhang
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Guanqun Shi
- Department of Computer Science, University of California, Riverside, 92521, USA
| | - Max Alekseyev
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Jijun Tang
- Department of Computer Science and Engineering, University of South Carolina, Columbia 29208, USA
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
| | - Robert Friedman
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
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20
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Affiliation(s)
- A Meyer
- Dept of Ecology and Evolution, and Program in Genetics, State University of New York, Stony Brook, NY 11790-5245, USA
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21
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Williams EP, Peer AC, Miller TJ, Secor DH, Place AR. A phylogeny of the temperate seabasses (Moronidae) characterized by a translocation of the mt-nd6 gene. JOURNAL OF FISH BIOLOGY 2012; 80:110-130. [PMID: 22220893 DOI: 10.1111/j.1095-8649.2011.03158.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The entire mitochondrial genome of the striped bass Morone saxatilis was sequenced together with the mitochondrial (mt) control regions of the white bass Morone chrysops, white perch Morone americana, yellow bass Morone mississippiensis, spotted seabass Dicentrarchus punctatus, European seabass Dicentrarchus labrax and the Japanese seabass Lateolabrax japonicus. The resultant 17 580 base pair circular genome of M. saxatilis contains 38 genes (13 proteins, 23 transfer RNAs and two ribosomal RNAs) and a control region bordered by the proline and phenylalanine mitochondrial tRNAs. Gene arrangement was similar to other vertebrates, except that the mt-nd6 gene was found within the control region rather than the canonical position between the mt-nd5 and mt-cyb genes. This translocation was found in all the Morone and Dicentrarchus species studied without functional copies or pseudogenes in the ancestral position. In L. japonicus, the mt-nd6 gene was found in the canonical position without evidence of an mt-nd6 gene in the control region. A Bayesian analysis of these and published mt-nd6 sequences from 45 other Perciformes grouped the Morone and Dicentrarchus species monophyletically with a probability of 1·00 with respect to L. japonicus and all other perciforms, and placed the Dicentrarchus species in the basal position. These data reinforce current placement of L. japonicus outside the Moronidae and provide a clear evolutionary character to define this family. The phylogeny of the Moronidae presented here also supports the hypothesis of an anadromous common ancestor to this family that gave rise to the North American estuarine and freshwater species. A series of tandem repeats previously reported in M. saxatilis was found in the control region of all Morone species between the mt-nd6 and mt-rnr1 genes, but not in either Dicentrarchus species, which reinforces the continued use of these two separate genera.
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Affiliation(s)
- E P Williams
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
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22
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Wei L, Wu X, Zhu L, Jiang Z. Mitogenomic analysis of the genus Panthera. SCIENCE CHINA-LIFE SCIENCES 2011; 54:917-30. [PMID: 22038004 DOI: 10.1007/s11427-011-4219-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 06/10/2011] [Indexed: 11/25/2022]
Abstract
The complete sequences of the mitochondrial DNA genomes of Panthera tigris, Panthera pardus, and Panthera uncia were determined using the polymerase chain reaction method. The lengths of the complete mitochondrial DNA sequences of the three species were 16990, 16964, and 16773 bp, respectively. Each of the three mitochondrial DNA genomes included 13 protein-coding genes, 22 tRNA, two rRNA, one O(L)R, and one control region. The structures of the genomes were highly similar to those of Felis catus, Acinonyx jubatus, and Neofelis nebulosa. The phylogenies of the genus Panthera were inferred from two combined mitochondrial sequence data sets and the complete mitochondrial genome sequences, by MP (maximum parsimony), ML (maximum likelihood), and Bayesian analysis. The results showed that Panthera was composed of Panthera leo, P. uncia, P. pardus, Panthera onca, P. tigris, and N. nebulosa, which was included as the most basal member. The phylogeny within Panthera genus was N. nebulosa (P. tigris (P. onca (P. pardus, (P. leo, P. uncia)))). The divergence times for Panthera genus were estimated based on the ML branch lengths and four well-established calibration points. The results showed that at about 11.3 MYA, the Panthera genus separated from other felid species and then evolved into the several species of the genus. In detail, N. nebulosa was estimated to be founded about 8.66 MYA, P. tigris about 6.55 MYA, P. uncia about 4.63 MYA, and P. pardus about 4.35 MYA. All these estimated times were older than those estimated from the fossil records. The divergence event, evolutionary process, speciation, and distribution pattern of P. uncia, a species endemic to the central Asia with core habitats on the Qinghai-Tibetan Plateau and surrounding highlands, mostly correlated with the geological tectonic events and intensive climate shifts that happened at 8, 3.6, 2.5, and 1.7 MYA on the plateau during the late Cenozoic period.
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Affiliation(s)
- Lei Wei
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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23
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CARAMASCHI FABIANAP, NASCIMENTO FABRÍCIAF, CERQUEIRA RUI, BONVICINO CIBELER. Genetic diversity of wild populations of the grey short-tailed opossum,Monodelphis domestica(Didelphimorphia: Didelphidae), in Brazilian landscapes. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01724.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ong PS, Luczon AU, Quilang JP, Sumaya AMT, Ibañez JC, Salvador DJ, Fontanilla IKC. DNA barcodes of Philippine accipitrids. Mol Ecol Resour 2011; 11:245-54. [PMID: 21429130 DOI: 10.1111/j.1755-0998.2010.02928.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
DNA barcoding is a molecular method that rapidly identifies an individual to a known taxon or its closest relative based on a 650-bp fragment of the cytochrome c oxidase subunit I (COI). In this study, DNA barcodes of members of the family Accipitridae, including Haliastur indus (brahminy kite), Haliaeetus leucogaster (white-bellied sea eagle), Ichthyophaga ichthyaetus (grey-headed fish eagle), Spilornis holospilus (crested serpent-eagle), Spizaetus philippensis (Philippine hawk-eagle), and Pithecophaga jefferyi (Philippine eagle), are reported for the first time. All individuals sampled are kept at the Philippine Eagle Center in Davao City, Philippines. Basic local alignment search tool results demonstrated that the COI sequences for these species were unique. The COI gene trees constructed using the maximum-likelihood and neighbour-joining (NJ) methods supported the monophyly of the booted eagles of the Aquilinae and the sea eagles of the Haliaeetinae but not the kites of the Milvinae.
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Affiliation(s)
- Perry S Ong
- DNA Barcoding Laboratory, Institute of Biology, University of the Philippines, Diliman 1101, Quezon City, Philippines
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25
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Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV. Genome evolution in Reptilia, the sister group of mammals. Annu Rev Genomics Hum Genet 2010; 11:239-64. [PMID: 20590429 DOI: 10.1146/annurev-genom-082509-141646] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.
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Affiliation(s)
- Daniel E Janes
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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26
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Yan J, Liu L, Liu S, Guo X, Liu Y. Comparative analysis of mitochondrial control region in polyploid hybrids of red crucian carp (Carassius auratus) x blunt snout bream (Megalobrama amblycephala). FISH PHYSIOLOGY AND BIOCHEMISTRY 2010; 36:263-272. [PMID: 18815893 DOI: 10.1007/s10695-008-9251-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 07/21/2008] [Indexed: 05/26/2023]
Abstract
The entire sequences of the mitochondrial (mt)DNA control region (CR) and portions of its flanking genes in the red crucian carp (RC) and blunt snout bream (BSB) as well as their polyploid hybrids (3nRB, 4nRB and 5nRB) were determined and subjected to a comparative analysis. The mtDNA-CRs of these five fish species ranged from 923 to 937 bp in length, they had the same flanking gene arrangement as other vertebrates and the pattern of nucleotide substitution bias was also similar to that in other vertebrates. Our data are consistent with the viewpoint of three domains [extended terminal associated sequence (ETAS domain), central conserved sequence block domain and conserved sequence block (CSB) domain] within the mtDNA-CR of mammals. On the basis our comparative analysis of the mtDNA-CRs of these five fish species, we were able to identify the consensus sequences of functional conserved units, including the ETAS, CSB-F, CSB-D, CSB-E, CSB1, CSB2 and CSB3 and putative promoter. The percentage of variable nucleotide positions (41.98%) in the central domain was lower than those in the ETAS and conserved domain (71.70 and 47.12%, respectively), suggesting that the central domain was the most conserved part of the mtDNA-CR. These results provide useful and important information for the further study of mtDNA-CR structure in fish. The sequence similarities of mtDNA-CR among the 3nRB, 4nRB, 5nRB hybrids and their respective female parents were higher than those among the 3nRB, 4nRB, 5nRB hybrids and their respective male parents, providing the direct evidence of stringent maternal inheritance of mtDNA-CR in the 3nRB, 4nRB and 5nRB hybrids.
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Affiliation(s)
- Jinpeng Yan
- College of Life Science, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
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27
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The impact of fossil calibrations, codon positions and relaxed clocks on the divergence time estimates of the native Australian rodents (Conilurini). Gene 2010; 455:22-31. [DOI: 10.1016/j.gene.2010.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 02/04/2010] [Accepted: 02/04/2010] [Indexed: 11/23/2022]
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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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Zhuang X, Cheng CHC. ND6 gene "lost" and found: evolution of mitochondrial gene rearrangement in Antarctic notothenioids. Mol Biol Evol 2010; 27:1391-403. [PMID: 20106908 DOI: 10.1093/molbev/msq026] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Evolution of Antarctic notothenioids in the frigid and oxygen-rich Southern Ocean had led to remarkable genomic changes, most notably the gain of novel antifreeze glycoproteins and the loss of oxygen-binding hemoproteins in the icefish family. Recently, the mitochondrial (mt) NADH dehydrogenase subunit 6 (ND6) gene and the adjacent transfer RNA(Glu) (tRNA(Glu)) were also reportedly lost. ND6 protein is crucial for the assembly and function of Complex I of the mt electron transport chain that produces adenosine triphosphate (ATP) essential for life; thus, ND6 absence would be irreconcilable with Antarctic notothenioids being thriving species. Here we report our discovery that the ND6 gene and tRNA(Glu) were not lost but had been translocated to the control region (CR) from their canonical location between ND5 and cytochrome b genes. We characterized the CR and adjacent sequences of 22 notothenioid species representing all eight families of Notothenioidei to elucidate the mechanism and evolutionary history of this mtDNA rearrangement. Species of the three basal non-Antarctic families have the canonical vertebrate mt gene order, whereas species of all five Antarctic families have a rearranged CR bearing the embedded ND6 (ND6(CR)) and tRNA(Glu), with additional copies of tRNA(Thr), tRNA(Pro), and noncoding region in various lineages. We hypothesized that an initial duplication of the canonical mt region from ND6 through CR occurred in the common ancestor to the Antarctic clade, and we deduced the succession of loss or modification of the duplicated region leading to the extant patterns of mt DNA reorganization that is consistent with notothenioid evolutionary history. We verified that the ND6(CR) gene in Antarctic notothenioids is transcribed and therefore functional. However, ND6(CR)-encoded protein sequences differ substantially from basal non-Antarctic notothenioid ND6, and we detected lineage-specific positive selection on the branch leading to the Antarctic clade of ND6(CR) under the branch-site model. Collectively, the novel mt ND6(CR) genotype of the Antarctic radiation represents another major molecular change in Antarctic notothenioid evolution and may reflect an adaptive change conducive to the functioning of the protein (Complex I) machinery of mt respiration in the polar environment, driven by the advent of freezing, oxygen-rich conditions in the Southern Ocean.
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Affiliation(s)
- Xuan Zhuang
- Department of Animal Biology, University of Illinois at Urbana-Champaign, IL, USA
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HANSEN BIRGITAD, HARLEY DANIELKP, LINDENMAYER DAVIDB, TAYLOR ANDREAC. Population genetic analysis reveals a long-term decline of a threatened endemic Australian marsupial. Mol Ecol 2009; 18:3346-62. [DOI: 10.1111/j.1365-294x.2009.04269.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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31
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Alekseyev MA, Pevzner PA. Breakpoint graphs and ancestral genome reconstructions. Genes Dev 2009; 19:943-57. [PMID: 19218533 PMCID: PMC2675983 DOI: 10.1101/gr.082784.108] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 01/22/2009] [Indexed: 11/24/2022]
Abstract
Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown.
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Affiliation(s)
- Max A. Alekseyev
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093-0404, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093-0404, USA
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Wägele JW. On the information content of characters in comparative morphology and molecular systematics. J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.1995.tb00205.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Wägele JW. On the information content of characters in comparative morphology and molecular systematics. J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.1995.tb00953.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ruedi M, Fumagalli L. Genetic structure of Gymnures (genus Hylomys; Erinaceidae) on continental islands of Southeast Asia: historical effects of fragmentation. J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.1996.tb00821.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zheng X, Dou Y, Wang J. Phylogenetic inference from binary sequences reduced by primary DNA sequences. JOURNAL OF MATHEMATICAL CHEMISTRY 2008; 46:1137-1148. [PMID: 32214589 PMCID: PMC7088321 DOI: 10.1007/s10910-008-9504-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2008] [Accepted: 10/31/2008] [Indexed: 06/10/2023]
Abstract
Given a bi-classification of nucleotides, we can obtain a reduced binary sequence of a primary DNA sequence. This binary sequence will undoubtedly retain some biological information and lose the rest. Here we want to know what kind of and how much biological information an individual binary sequence carries. Three classifications of nucleotides are explored in the present article. Phylogenetic trees are built from these binary sequences by the Neighbor-Joining (NJ) method, with evolutionary distance evaluated on the basis of a symbolic sequence complexity. We find that, for all data sets studied, binary sequences reduced by the purine/pyrimidine classification give reliable phylogeny (almost the same as that from the primary sequences), while the other two result in discrepancies at different levels. Some possible reasons and a simple model of sequence evolutionary are introduced to interpret this phenomenon.
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Affiliation(s)
- Xiaoqi Zheng
- Department of Applied Mathematics, Dalian University of Technology, Dalian, 116024 People’s Republic of China
- College of Advanced Science and Technology, Dalian University of Technology, Dalian, 116024 People’s Republic of China
| | - Yongchao Dou
- Department of Applied Mathematics, Dalian University of Technology, Dalian, 116024 People’s Republic of China
| | - Jun Wang
- Department of Mathematics, Shanghai Normal University, Shanghai, 200234 People’s Republic of China
- Scientific Computing Key Laboratory of Shanghai Universities, Shanghai, 200234 People’s Republic of China
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The marsupial CD8 gene locus: molecular cloning and expression analysis of the alpha and beta sequences in the gray short-tailed opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii). Vet Immunol Immunopathol 2008; 129:14-27. [PMID: 19135263 DOI: 10.1016/j.vetimm.2008.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 11/28/2008] [Accepted: 12/01/2008] [Indexed: 11/22/2022]
Abstract
In eutherian mammals, CD8 is a key receptor of cytotoxic T cells and plays a pivotal role in the recognition and elimination of infected host cells by cell-mediated cytotoxicity. Here, we report the molecular cloning and expression analysis of CD8alpha and CD8beta cDNAs in two marsupial species, the gray short-tailed opossum and the tammar wallaby. The opossum and tammar CD8 sequences share a high degree of amino acid identity of 63% (CD8alpha) and 57% (CD8beta) to each other as well as 36-45% (CD8alpha) and 38-41% (CD8beta) with their eutherian counterparts. In addition, many of the signature features of eutherian CD8alpha and CD8beta are preserved in both marsupials including the two invariant cysteines that form the intra-chain disulphide bond in the extracellular IgSfV domain and the two hinge region cysteines involved in dimerisation between the two subunits. The p56(lck) binding motif in the cytoplasmic tail of the CD8alpha subunit is also conserved. Interestingly, the opossum CD8alpha and the tammar CD8beta sequences have a truncated cytoplasmic tail. RT-PCR analysis of CD8alpha and CD8beta transcripts in the tissues of the adult opossum and tammar showed broad tissue expression with a high level of expression observed in the lymphoid tissues of both marsupials. Furthermore, RT-PCR analysis of CD8alpha and CD8beta transcripts in the immune tissues of tammar young over the first 120 days of pouch life revealed a pattern of expression analogous to the maturation of the lymphoid tissues. This is the first report confirming the presence of CD8 in the tissues of a marsupial and will provide the tools to further analyse T cell subsets in this unique group of mammals.
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Chen C, Chiou CY, Dai CF, Chen CA. Unique mitogenomic features in the scleractinian family pocilloporidae (scleractinia: astrocoeniina). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2008; 10:538-553. [PMID: 18478295 DOI: 10.1007/s10126-008-9093-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 02/28/2008] [Accepted: 03/02/2008] [Indexed: 05/26/2023]
Abstract
The complete DNA sequences of three mitochondrial (mt) genomes were obtained from the scleractinian corals, Stylophora pistillata, Pocillopora damicornis, and Madracis mirabilis, and were compared to the published mt genomes to elucidate phylogenetically unique features of the family Pocilloporidae. The entire mt genomes of pocilloporid corals ranged from 16,951 to 17,425 bp with the A+T contents of their sense strands ranging from 68.4% to 70.2%. The gene order of protein-coding genes was identical to those of other scleractinian corals. The novel atp8 gene, first described in confamilial Seriatopora corals, was also confirmed using reverse transcription-polymerase chain reaction (RT-PCR), Northern blot, and sequence analyses in other genera of the Pocilloporidae. The intergenic spacer between atp6 and nad4, containing distinct repeated elements, conserved sequence blocks and domains, and functional structures, possesses typical characteristics of a putative control region for the four coral genera. A duplicated trnW, detected in the region close to the cox1 gene and which shares the highly conserved primary and secondary structures of its original counterpart, was discovered in both Seriatopora and Stylophora. These molecular characteristics are unique and provide the phylogenetic information for future evaluation of the status of the family Pocilloporidae in the evolutionary history of scleractinian corals.
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Affiliation(s)
- Chienhsun Chen
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
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38
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GRAYBEAL ANNA. Phylogenetic relationships of bufonid frogs and tests of alternate macroevolutionary hypotheses characterizing their radiation. Zool J Linn Soc 2008. [DOI: 10.1111/j.1096-3642.1997.tb00139.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Popadin KY, Mamirova LA, Kondrashov FA. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics 2007; 8:441. [PMID: 17999775 PMCID: PMC2206058 DOI: 10.1186/1471-2105-8-441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 11/14/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. DESCRIPTION We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. CONCLUSION We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.
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Affiliation(s)
- Konstantin Yu Popadin
- Institute for Information Transmission Problems RAS, Bolshoi Karetny pereulok 19, Moscow.
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41
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Martin RD, Soligo C, Tavaré S. Primate Origins: Implications of a Cretaceous Ancestry. Folia Primatol (Basel) 2007; 78:277-96. [PMID: 17855783 DOI: 10.1159/000105145] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
It has long been accepted that the adaptive radiation of modern placental mammals, like that of modern birds, did not begin until after the Cretaceous/Tertiary (K/T) boundary 65 million years (Ma) ago, following the extinction of the dinosaurs. The first undoubted fossil relatives of modern primates appear in the record 55 Ma ago. However, in agreement with evidence from molecular phylogenies calibrated with dates from denser parts of the fossil record, a statistical analysis of the primate record allowing for major gaps now indicates a Cretaceous origin of euprimates 80-90 Ma ago. If this interpretation is correct, primates overlapped with dinosaurs by some 20 Ma prior to the K/T boundary, and the initial radiation of primates was probably truncated as part of the major extinction event that occurred at the end of the Cretaceous. Following a review of evidence for an early origin of primates, implications of this are discussed with respect to the likely ancestral condition for primates, including a southern continental area of origin and moderately large body size. The known early Tertiary primates are re-interpreted as northern continental offshoots of a 'second wave' of primate evolution.
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Affiliation(s)
- Robert D Martin
- Anthropology Department, Field Museum of Natural History, Chicago, Ill., USA
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42
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Kullberg M, Hallström B, Arnason U, Janke A. Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution. PLoS One 2007; 2:e775. [PMID: 17712423 PMCID: PMC1942079 DOI: 10.1371/journal.pone.0000775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 07/24/2007] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human), lagomorphs (rabbit), rodents (rat and mouse), artiodactyls (cow), carnivorans (dog) and proboscideans (elephant). METHODOLOGY/PRINCIPAL FINDINGS We have produced 2000 ESTs (1.2 mega bases) from a marsupial mouse and characterized the data for their use in phylogenetic analysis. The sequences were used to identify putative orthologous sequences from whole genome projects. Although most ESTs stem from single sequence reads, the frequency of potential sequencing errors was found to be lower than allelic variation. Most of the sequences represented slowly evolving housekeeping-type genes, with an average amino acid distance of 6.6% between human and mouse. Positive Darwinian selection was identified at only a few single sites. Phylogenetic analyses of the EST data yielded trees that were consistent with those established from whole genome projects. CONCLUSIONS The general quality of EST sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for phylogenetic analysis. The EST approach allows, at reasonable costs, a fast extension of data sampling from species outside the genome projects.
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Affiliation(s)
- Morgan Kullberg
- Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Lund, Sweden.
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Pütz J, Dupuis B, Sissler M, Florentz C. Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures. RNA (NEW YORK, N.Y.) 2007; 13:1184-90. [PMID: 17585048 PMCID: PMC1924894 DOI: 10.1261/rna.588407] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Mamit-tRNA (http://mamit-tRNA.u-strasbg.fr), a database for mammalian mitochondrial genomes, has been developed for deciphering structural features of mammalian mitochondrial tRNAs and as a helpful tool in the frame of human diseases linked to point mutations in mitochondrial tRNA genes. To accommodate the rapid growing availability of fully sequenced mammalian mitochondrial genomes, Mamit-tRNA has implemented a relational database, and all annotated tRNA genes have been curated and aligned manually. System administrative tools have been integrated to improve efficiency and to allow real-time update (from GenBank Database at NCBI) of available mammalian mitochondrial genomes. More than 3000 tRNA gene sequences from 150 organisms are classified into 22 families according to the amino acid specificity as defined by the anticodon triplets and organized according to phylogeny. Each sequence is displayed linearly with color codes indicating secondary structural domains and can be converted into a printable two-dimensional (2D) cloverleaf structure. Consensus and typical 2D structures can be extracted for any combination of primary sequences within a given tRNA specificity on the basis of phylogenetic relationships or on the basis of structural peculiarities. Mamit-tRNA further displays static individual 2D structures of human mitochondrial tRNA genes with location of polymorphisms and pathology-related point mutations. The site offers also a table allowing for an easy conversion of human mitochondrial genome nucleotide numbering into conventional tRNA numbering. The database is expected to facilitate exploration of structure/function relationships of mitochondrial tRNAs and to assist clinicians in the frame of pathology-related mutation assignments.
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Affiliation(s)
- Joern Pütz
- Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, Strasbourg, France
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Duncan LG, Nair SV, Deane EM. Molecular characterisation and expression of CD4 in two distantly related marsupials: the gray short-tailed opossum (Monodelphis domestica) and tammar wallaby (Macropus eugenii). Mol Immunol 2007; 44:3641-52. [PMID: 17521733 DOI: 10.1016/j.molimm.2007.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 04/16/2007] [Indexed: 11/21/2022]
Abstract
The gene and corresponding cDNA for CD4 in the gray short-tailed opossum, Monodelphis domestica, and the cDNA sequence for CD4 in the tammar wallaby, Macropus eugenii, have been characterised. The opossum CD4 homolog reveals conserved synteny, preserved genomic organisation and analogous structural arrangement to human and mouse CD4. Opossum and tammar CD4 exhibit typical eutherian CD4 features including the highly conserved p56(lck) binding motif in the cytoplasmic region and the invariant cysteine residues in extracellular domains 1 and 4. Interestingly, the marsupial CD4 sequences substitute a tryptophan for the first cysteine in domain 2 negating the formation of a disulphide bond as seen in other eutherian CD4 sequences except human and mouse. Overall the marsupial CD4 sequences share amino acid identity of 59% to each other and 37-41% with eutherian mammals. However, in contrast to eutherian homologs, the marsupial CD4 sequences were found to be truncated at the terminal end of the cytoplasmic tail. This is the first report confirming the presence of CD4 in a marsupial and describing its key features.
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Affiliation(s)
- Louise G Duncan
- Department of Biological Sciences, Division of Environmental and Life Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Arnason U, Gullberg A, Janke A, Kullberg M, Lehman N, Petrov EA, Väinölä R. Pinniped phylogeny and a new hypothesis for their origin and dispersal. Mol Phylogenet Evol 2006; 41:345-54. [PMID: 16815048 DOI: 10.1016/j.ympev.2006.05.022] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 05/11/2006] [Accepted: 05/19/2006] [Indexed: 11/16/2022]
Abstract
The relationships and the zoogeography of the three extant pinniped families, Otariidae (sea lions and fur seals), Odobenidae (one extant species, the walrus), and Phocidae (true seals), have been contentious. Here, we address these topics in a molecular study that includes all extant species of true seals and sea lions, four fur seals and the walrus. Contrary to prevailing morphological views the analyses conclusively showed monophyletic Pinnipedia with a basal split between Otarioidea (Otariidae+Odobenidae) and Phocidae. The northern fur seal was the sister to all remaining otariids and neither sea lions nor arctocephaline fur seals were recognized as monophyletic entities. The basal Phocidae split between Monachinae (monk seals and southern true seals) and Phocinae (northern true seals) was strongly supported. The phylogeny of the Phocinae suggests that the ancestors of Cystophora (hooded seal) and the Phocini (e.g. harp seal, ringed seal) adapted to Arctic conditions and ice-breeding before 12 MYA (million years ago) as supported by the white natal coat of these lineages. The origin of the endemic Caspian and Baikal seals was dated well before the onset of major Pleistocene glaciations. The current findings, together with recent advances in pinniped paleontology, allow the proposal of a new hypothesis for pinniped origin and early dispersal. The hypothesis posits that pinnipeds originated on the North American continent with early otarioid and otariid divergences taking place in the northeast Pacific and those of the phocids in coastal areas of southeast N America for later dispersal to colder environments in the N Atlantic and the Arctic Basin, and in Antarctic waters.
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Affiliation(s)
- Ulfur Arnason
- Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, S-223 62 Lund, Sweden.
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46
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Nilsson MA. Phylogenetic relationships of the Banded Hare wallaby (Lagostrophus fasciatus) and a map of the kangaroo mitochondrial control region. ZOOL SCR 2006. [DOI: 10.1111/j.1463-6409.2006.00237.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Satoh TP, Miya M, Endo H, Nishida M. Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: Evidence from the complete mitochondrial genome sequences. Mol Phylogenet Evol 2006; 40:129-38. [PMID: 16603389 DOI: 10.1016/j.ympev.2006.02.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2005] [Revised: 02/13/2006] [Accepted: 02/14/2006] [Indexed: 11/28/2022]
Abstract
The gene order of mitochondrial genomes (mitogenomes) has been employed as a useful phylogenetic marker in various metazoan animals, because it may represent uniquely derived characters shared by members of monophyletic groups. During the course of molecular phylogenetic studies of the order Gadiformes (cods and their relatives) based on whole mitogenome sequences, we found that two deep-sea grenadiers (Squalogadus modificatus and Trachyrincus murrayi: family Macrouridae) revealed a unusually identical gene order (translocation of the tRNA(Leu (UUR))). Both are members of the same family, although their external morphologies differed so greatly (e.g., round vs. pointed head) that they have been placed in different subfamilies Macrouroidinae and Trachyrincinae, respectively. Additionally, we determined the whole mitogenome sequences of two other species, Bathygadus antrodes and Ventrifossa garmani, representing a total of four subfamilies currently recognized within Macrouridae. The latter two species also exhibited gene rearrangements, resulting in a total of three different patterns of unique gene order being observed in the four subfamilies. Partitioned Bayesian analysis was conducted using available whole mitogenome sequences from five macrourids plus five outgroups. The resultant trees clearly indicated that S. modificatus and T. murrayi formed a monophyletic group, having a sister relationship to other macrourids. Thus, monophyly of the two species with disparate head morphologies was corroborated by two different lines of evidence (nucleotide sequences and gene order). The overall topology of the present tree differed from any of the previously proposed, morphology-based phylogenetic hypotheses.
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Affiliation(s)
- Takashi P Satoh
- Ocean Research Institute, The University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan
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Kullberg M, Nilsson MA, Arnason U, Harley EH, Janke A. Housekeeping Genes for Phylogenetic Analysis of Eutherian Relationships. Mol Biol Evol 2006; 23:1493-503. [PMID: 16751257 DOI: 10.1093/molbev/msl027] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The molecular relationship of placental mammals has attracted great interest in recent years. However, 2 crucial and conflicting hypotheses remain, one with respect to the position of the root of the eutherian tree and the other the relationship between the orders Rodentia, Lagomorpha (rabbits, hares), and Primates. Although most mitochondrial (mt) analyses have suggested that rodents have a basal position in the eutherian tree, some nuclear data in combination with mt-rRNA genes have placed the root on the so-called African clade or on a branch that includes this clade and the Xenarthra (e.g., anteater and armadillo). In order to generate a new and independent set of molecular data for phylogenetic analysis, we have established cDNA sequences from different tissues of various mammalian species. With this in mind, we have identified and sequenced 8 housekeeping genes with moderately fast rate of evolution from 22 placental mammals, representing 11 orders. In order to determine the root of the eutherian tree, the same genes were also sequenced for 3 marsupial species, which were used as outgroup. Inconsistent with the analyses of nuclear + mt-rRNA gene data, the current data set did not favor a basal position of the African clade or Xenarthra in the eutherian tree. Similarly, by joining rodents and lagomorphs on the same basal branch (Glires hypothesis), the data set is also inconsistent with the tree commonly favored in mtDNA analyses. The analyses of the currently established sequences have helped examination of problematic parts in the eutherian tree at the same time as they caution against suggestions that have claimed that basal eutherian relationships have been conclusively settled.
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Affiliation(s)
- Morgan Kullberg
- Division of Evolutionary Molecular Systematics, Department of Cell and Organism Biology, University of Lund, Lund, Sweden
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Jansa SA, Barker FK, Heaney LR. The pattern and timing of diversification of Philippine endemic rodents: evidence from mitochondrial and nuclear gene sequences. Syst Biol 2006; 55:73-88. [PMID: 16507525 DOI: 10.1080/10635150500431254] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The 22 genera and 64 species of rodents (Muridae: Murinae) distributed in the Philippine Islands provide a unique opportunity to study patterns and processes of diversification in island systems. Over 90% of these rodent species are endemic to the archipelago, but the relative importance of dispersal from the mainland, dispersal within the archipelago, and in situ differentiation as explanations of this diversity remains unclear, as no phylogenetic hypothesis for these species and relevant mainland forms is currently available. Here we report the results of phylogenetic analyses of the endemic Philippine murines and a wide sampling of murine diversity from outside the archipelago, based on the mitochondrial cytochrome b gene and the nuclear-encoded IRBP exon 1. Analysis of our combined gene data set consistently identified five clades comprising endemic Philippine genera, suggesting multiple invasions of the archipelago. Molecular dating analyses using parametric and semiparametric methods suggest that colonization occurred in at least two stages, one ca. 15 Mya, and another 8 to 12 million years later, consistent with the previous recognition of "Old" and "New" endemic rodent faunas. Ancestral area analysis suggests that the Old Endemics invaded landmasses that are now part of the island of Luzon, whereas the three New Endemic clades may have colonized through either Mindanao, Luzon, or both. Further, our results suggest that most of the diversification of Philippine murines took place within the archipelago. Despite heterogeneity between nuclear and mitochondrial genes in most model parameters, combined analysis of the two data sets using both parsimony and likelihood increased phylogenetic resolution; however, the effect of data combination on support for resolved nodes was method dependent. In contrast, our results suggest that combination of mitochondrial and nuclear data to estimate relatively ancient divergence times can severely compromise those estimates, even when specific methods that account for rate heterogeneity among genes are employed. [Biogeography; divergence date estimation; mitochondrial DNA; molecular systematics; Murinae; nuclear exon; Philippines; phylogeny.].
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Affiliation(s)
- Sharon A Jansa
- Bell Museum of Natural History, University of Minnesota, 1987 Upper Buford Circle, (S.A.J.), St. Paul, Minnesota 55108, USA.
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Rubio MAT, Ragone FL, Gaston KW, Ibba M, Alfonzo JD. C to U Editing Stimulates A to I Editing in the Anticodon Loop of a Cytoplasmic Threonyl tRNA in Trypanosoma brucei. J Biol Chem 2006; 281:115-20. [PMID: 16269406 DOI: 10.1074/jbc.m510136200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Editing of tRNAs is widespread in nature and either changes the decoding properties or restores the folding of a tRNA. Unlike the phylogenetically disperse adenosine (A) to inosine (I) editing, cytosine (C) to uridine (U) editing has only been previously described in organellar tRNAs. We have shown that cytoplasmic tRNA(Thr)(AGU) undergoes two distinct editing events in the anticodon loop: C to U and A to I. In vivo, every inosine-containing tRNA(Thr) is also C to U edited at position 32. In vitro, C to U editing stimulates conversion of A to I at the wobble base. Although the in vivo and in vitro requirements differ, in both cases, the C to U change plays a key role in A to I editing. Due to an unusual abundance of A34-containing tRNAs, our results also suggest that the unedited and edited tRNAs are functional, each dedicated to decoding a specific threonine codon. C to U editing of cytoplasmic tRNA expands the editing repertoire in eukaryotic cells, and when coupled to A to I changes, leads to an interrelation between editing sites.
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Affiliation(s)
- Mary Anne T Rubio
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
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