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Ghosh A, Tyagi K, Dubey AK, Sweet AD, Singha D, Goswami P, Kumar V. Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera). Funct Integr Genomics 2024; 24:121. [PMID: 38976062 DOI: 10.1007/s10142-024-01400-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/06/2024] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
Insect mitochondrial genomes (mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rates shape gene rearrangement in whiteflies is unclear due to the limited number of mitogenomes. Additionally, the mechanisms by which selection pressure drives adaptations in mitochondrial genes in the two subfamilies of whiteflies are not yet known. Here, we analyzed 18 whitefly mitogenomes, including one newly generated mitogenome, to compare nucleotide substitution rates, selection pressure, and gene arrangements. The newly generated mitogenome is reported along with reannotation of Pealius mori and comparisons to other whitefly mitogenomes. Comparative studies on nucleotide composition of 18 whiteflies revealed the positive GC skewness, confirming the reversal of strand asymmetry. We found 11 rearranged gene orders within two subfamilies of whiteflies with 8-18 breakpoints of gene rearrangements. Members of the subfamily Aleyrodinae exhibit more complex pathways in the evolution of gene order as compared to the subfamily Aleurodicinae. Our findings also revealed that the increase or reduction of nucleotide substitution rates does not have an impact on any of the gene rearrangement scenarios depicting neutral correlation. Selection pressure analysis revealed that the mitogenomes from members of both the subfamilies Aleurodicinae and Aleyrodinae are characterized by intense purifying selection pressure.
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Affiliation(s)
- Abhishek Ghosh
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Anil Kumar Dubey
- Hemiptera Section, Zoological Survey of India, West Bengal, Kolkata, India
| | | | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Prathana Goswami
- Lepidoptera Section, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, Gauhati University, Guwahati, Assam, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
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2
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Liu Q, Cai YD, Ma L, Liu H, Linghu T, Guo S, Wei S, Song F, Tian L, Cai W, Li H. Relaxed purifying selection pressure drives accelerated and dynamic gene rearrangements in thrips (Insecta: Thysanoptera) mitochondrial genomes. Int J Biol Macromol 2023; 253:126742. [PMID: 37689283 DOI: 10.1016/j.ijbiomac.2023.126742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/06/2023] [Accepted: 08/26/2023] [Indexed: 09/11/2023]
Abstract
Insect mitochondrial genomes (mitogenome) generally present a typical gene order, which is considered as the ancestral arrangement. All sequenced mitogenomes in the Thysanoptera display high levels of gene rearrangement. Due to limited number of thrips mitogenomes sequenced, how gene rearrangement may be shaped by evolution remain unclear. Here, we analyzed 33 thrips mitogenomes, including 14 newly sequenced. These mitogenomes were diverse in organization, nucleotides substitution and gene arrangements. We found 28 highly rearranged gene orders with the breakpoints of gene rearrangements from 25 to 33. Reconstruction of the ancestors mitochondrial gene arrangements states indicated that Tubulifera have more complex pathways than Terebrantia in the gene order evolution. Molecular calibration estimated that divergence of two suborders occurred in the middle Triassic while the radiation of thrips was associated with the arose and flourish of angiosperm. Our evolutionary hypothesis testing suggests that relaxation of selection pressure enabled the early phase of Thysanoptera evolution, followed by a stronger selective pressure fixed diversification. Our analyses found gene inversion increases the nonsynonymous substitution rates and provide an evolutionary hypothesis driving the diverse gene orders.
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Affiliation(s)
- Qiaoqiao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Tianye Linghu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shaokun Guo
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests of Ministry of Agriculture and Rural Affairs, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shujun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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Complete Mitogenome of Oreolalax Omeimontis Reveals Phylogenetic Status and Novel Gene Arrangement of Archaeobatrachia. Genes (Basel) 2022; 13:genes13112089. [DOI: 10.3390/genes13112089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/23/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Species of the genus Oreolalax displayed crucial morphological characteristics of vertebrates transitioning from aquatic to terrestrial habitats; thus, they can be regarded as a representative vertebrate genus for this landing phenomenon. But the present phylogenetic status of Oreolalax omeimontis has been controversial with morphological and molecular approaches, and specific gene rearrangements were discovered in all six published Oreolalax mitogenomes, which are rarely observed in Archaeobatrachia. Therefore, this study determined the complete mitogenome of O. omeimontis with the aim of identifying its precise phylogenetic position and novel gene arrangement in Archaeobatrachia. Phylogenetic analysis with Bayesian inference and maximum likelihood indicates O. omeimontis is a sister group to O. lichuanensis, which is consistent with previous phylogenetic analysis based on morphological characteristics, but contrasts with other studies using multiple gene fragments. Moreover, although the duplication of trnM occurred in all seven Oreolalax species, the translocation of trnQ and trnM occurred differently in O. omeimontis to the other six, and this unique rearrangement would happen after the speciation of O. omeimontis. In general, this study sheds new light on the phylogenetic relationships and gene rearrangements of Archaeobatrachia.
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Montaña-Lozano P, Moreno-Carmona M, Ochoa-Capera M, Medina NS, Boore JL, Prada CF. Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class. Sci Rep 2022; 12:5479. [PMID: 35361853 PMCID: PMC8971445 DOI: 10.1038/s41598-022-09512-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/21/2022] [Indexed: 11/09/2022] Open
Abstract
Vertebrate mitochondrial genomes have been extensively studied for genetic and evolutionary purposes, these are normally believed to be extremely conserved, however, different cases of gene rearrangements have been reported. To verify the level of rearrangement and the mitogenome evolution, we performed a comparative genomic analysis of the 2831 vertebrate mitochondrial genomes representing 12 classes available in the NCBI database. Using a combination of bioinformatics methods, we determined there is a high number of errors in the annotation of mitochondrial genes, especially in tRNAs. We determined there is a large variation in the proportion of rearrangements per gene and per taxonomic class, with higher values observed in Actinopteri, Amphibia and Reptilia. We highlight that these are results for currently available vertebrate sequences, so an increase in sequence representativeness in some groups may alter the rearrangement rates, so in a few years it would be interesting to see if these rates are maintained or altered with the new mitogenome sequences. In addition, within each vertebrate class, different patterns in rearrangement proportion with distinct hotspots in the mitochondrial genome were found. We also determined that there are eleven convergence events in gene rearrangement, nine of which are new reports to the scientific community.
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Affiliation(s)
- Paula Montaña-Lozano
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Manuela Moreno-Carmona
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Mauricio Ochoa-Capera
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Natalia S Medina
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia.
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Song MH, Yan C, Li JT. MEANGS: an efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data. Brief Bioinform 2021; 23:6481918. [PMID: 34941991 DOI: 10.1093/bib/bbab538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/23/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
Advances in next-generation sequencing (NGS) technologies have led to an exponential increase in the number of whole genome sequences (WGS) in databases. This wealth of WGS data has greatly facilitated the recovery of full mitochondrial genomes (mitogenomes), which are vital for phylogenetic, evolutionary and ecological studies. Unfortunately, most existing software cannot easily assemble mitogenome reference sequences conveniently or efficiently. Therefore, we developed a seed-free de novo assembly tool, MEANGS, which applies the trie-search method to extend contigs from self-discovery seeds and assemble a mitogenome from animal WGS data. We then used data from 16 species with different qualities to compare the performance of MEANGS with three other available programs. MEANGS exhibited the best overall performance since it was the only one that completed all tests, and it assembled full or partial mitogenomes for all of the tested samples while the others failed. Furthermore, MEANGS selects superior assembly sequences and annotates protein-coding genes. Thus, MEANGS can be one of the most efficient software for generating high-quality mitogenomes so far, the further use of it will benefit the study on mitogenome based on whole genome NGS data. MEANGS is available at https://github.com/YanCCscu/meangs.
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Affiliation(s)
- Meng-Huan Song
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
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Lyra ML, Monteiro JPC, Rancilhac L, Irisarri I, Künzel S, Sanchez E, Condez TH, Rojas-Padilla O, Solé M, Toledo LF, Haddad CFB, Vences M. Initial Phylotranscriptomic Confirmation of Homoplastic Evolution of the Conspicuous Coloration and Bufoniform Morphology of Pumpkin-Toadlets in the Genus Brachycephalus. Toxins (Basel) 2021; 13:816. [PMID: 34822600 PMCID: PMC8620806 DOI: 10.3390/toxins13110816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023] Open
Abstract
The genus Brachycephalus is a fascinating group of miniaturized anurans from the Brazilian Atlantic Forest, comprising the conspicuous, brightly colored pumpkin-toadlets and the cryptic flea-toads. Pumpkin-toadlets are known to contain tetrodotoxins and therefore, their bright colors may perform an aposematic function. Previous studies based on a limited number of mitochondrial and nuclear-encoded markers supported the existence of two clades containing species of pumpkin-toadlet phenotype, but deep nodes remained largely unresolved or conflicting between data sets. We use new RNAseq data of 17 individuals from nine Brachycephalus species to infer their evolutionary relationships from a phylogenomic perspective. Analyses of almost 5300 nuclear-encoded ortholog protein-coding genes and full mitochondrial genomes confirmed the existence of two separate pumpkin-toadlet clades, suggesting the convergent evolution (or multiple reversals) of the bufoniform morphology, conspicuous coloration, and probably toxicity. In addition, the study of the mitochondrial gene order revealed that three species (B. hermogenesi, B. pitanga, and B. rotenbergae) display translocations of different tRNAs (NCY and CYA) from the WANCY tRNA cluster to a position between the genes ATP6 and COIII, showing a new mitochondrial gene order arrangement for vertebrates. The newly clarified phylogeny suggests that Brachycephalus has the potential to become a promising model taxon to understand the evolution of coloration, body plan and toxicity. Given that toxicity information is available for only few species of Brachycephalus, without data for any flea-toad species, we also emphasize the need for a wider screening of toxicity across species, together with more in-depth functional and ecological study of their phenotypes.
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Affiliation(s)
- Mariana L. Lyra
- Instituto de Biociências, Departamento de Biodiversidade (Campus Rio Claro), Universidade Estadual Paulista (UNESP), Avenida 24A, N 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil; (M.L.L.); (J.P.C.M.); (C.F.B.H.)
| | - Juliane P. C. Monteiro
- Instituto de Biociências, Departamento de Biodiversidade (Campus Rio Claro), Universidade Estadual Paulista (UNESP), Avenida 24A, N 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil; (M.L.L.); (J.P.C.M.); (C.F.B.H.)
| | - Loïs Rancilhac
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (L.R.); (E.S.)
| | - Iker Irisarri
- Institute for Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goldschmidtstr, 1, 37077 Göttingen, Germany;
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
| | - Eugenia Sanchez
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (L.R.); (E.S.)
| | - Thais H. Condez
- Unidade Passos, Universidade do Estado de Minas Gerais (UEMG), Avenida Juca Stockler 1130, Passos 37900-106, MG, Brazil;
| | - Omar Rojas-Padilla
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, Porto Alegre 90619-900, RS, Brazil;
| | - Mirco Solé
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil;
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, SP, Brazil;
| | - Célio F. B. Haddad
- Instituto de Biociências, Departamento de Biodiversidade (Campus Rio Claro), Universidade Estadual Paulista (UNESP), Avenida 24A, N 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil; (M.L.L.); (J.P.C.M.); (C.F.B.H.)
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (L.R.); (E.S.)
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Mazumder GA, Uddin A, Chakraborty S. Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes. Mol Biochem Parasitol 2021; 245:111410. [PMID: 34487743 DOI: 10.1016/j.molbiopara.2021.111410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/19/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
The phenomenon of non-uniform usage of the synonymous codons, where some codons are given more preference to others, is known as codon usage bias (CUB). CUB is known to be determined by two major evolutionary forces i.e. mutation pressure and selection. We used various approaches to understand the codon usage pattern in mitochondrial CO (MT-CO) genes involved in complex IV of the respiratory chain (RC) as no work was reported yet. Our present study revealed that CUB was relatively high and the coding sequences were rich in A and T. Correspondence analysis further indicated that A/T compositional properties under mutational pressure might be affecting the codon usage pattern and was different in different classes for MT-CO gene. A highly significant correlation between A% and A3%, T% and T3%, G% and G3%, C% and C3%, GC% and GC3% in all the classes indicated that compositional constraints under mutational pressure and natural selection might affect the CUB. Neutrality plot indicated that both natural selection and mutational bias affected the CUB, where, natural selection played the major role as compared to mutational pressure.
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Affiliation(s)
- Gulshana A Mazumder
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India
| | - Arif Uddin
- Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
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Apine E, Rai P, Mani MK, Subramanian V, Karunasagar I, Godhe A, Turner LM. Comparative analysis of the intestinal bacterial communities in mud crab Scylla serrata in South India. Microbiologyopen 2021; 10:e1179. [PMID: 33970543 PMCID: PMC8088116 DOI: 10.1002/mbo3.1179] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Little is known about the functions of the crustacean gut microbiome, but environmental parameters and habitat are known to affect the composition of the intestinal microbiome, which may in turn affect the physiological status of the host. The mud crab Scylla serrata is an economically important species, and is wild‐caught, and farmed across the Indo‐Pacific region. In this study, we compared the composition of the gut microbiome (in terms of gut microbial species richness and abundance) of S. serrata collected from wild sites, and farms, from the east and west coast of India, and also tested the effects of the environment on the composition. The water temperature had a statistically significant effect on gut microbiome composition, with microbial biodiversity decreasing with increasing water temperature. This could have negative effects on both wild and farmed mud crabs under future climate change conditions, although further research into the effects of temperature on gut microbiomes is required. By comparison, salinity, crab mass and carapace width, geographical location as well as whether they were farmed or wild‐caught crabs did not have a significant impact on gut microbiome composition. The results indicate that farming does not significantly alter the composition of the gut microbiome when compared to wild‐caught crabs.
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Affiliation(s)
- Elina Apine
- Marine Biology and Ecology Research Centre, University of Plymouth, Plymouth, UK
| | - Praveen Rai
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangaluru, India
| | - Madhu K Mani
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangaluru, India
| | | | - Indrani Karunasagar
- Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Mangaluru, India
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Lucy M Turner
- Marine Biology and Ecology Research Centre, University of Plymouth, Plymouth, UK
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Papetti C, Babbucci M, Dettai A, Basso A, Lucassen M, Harms L, Bonillo C, Heindler FM, Patarnello T, Negrisolo E. Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish. Genome Biol Evol 2021; 13:6133229. [PMID: 33570582 PMCID: PMC7936035 DOI: 10.1093/gbe/evab017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.
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Affiliation(s)
- Chiara Papetti
- Department of Biology, University of Padova, Padova 35121,Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma 00196, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Agnes Dettai
- Institut de Systematique, Evolution, Biodiversité (ISYEB) Muséum national d'Histoire naturelle-CNRS-Sorbonne Université-EPHE, MNHN, Paris 75005, France
| | - Andrea Basso
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Magnus Lucassen
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany
| | - Lars Harms
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany.,Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg (HIFMB), Ammerlsity of Oldenburg (HIFMOldenburg 26129, Germany
| | - Celine Bonillo
- Service de Systématique Moléculaire, UMS2700 Acquisition et Analyse de Données (2AD), MNHN, Paris 75005, France
| | | | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy.,CRIBI Interdepartmental Research Centre for Innovative Biotechnologies, University of Padova, viale G. Colombo 3, Padova 35121, Italy
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Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes. Int J Mol Sci 2021; 22:ijms22041811. [PMID: 33670420 PMCID: PMC7918261 DOI: 10.3390/ijms22041811] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/08/2021] [Indexed: 01/06/2023] Open
Abstract
Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, Schistosoma haematobium, and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow.
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11
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Zhang J, Miao G, Hu S, Sun Q, Ding H, Ji Z, Guo P, Yan S, Wang C, Kan X, Nie L. Quantification and evolution of mitochondrial genome rearrangement in Amphibians. BMC Ecol Evol 2021; 21:19. [PMID: 33563214 PMCID: PMC7871395 DOI: 10.1186/s12862-021-01755-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution. RESULTS Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation. CONCLUSION It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.
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Affiliation(s)
- Jifeng Zhang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China.
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
- Anhui Key Laboratory of Low Temperature Co-Fired Materials, Huainan Normal University, Huainan, 232001, People's Republic of China.
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Health and Safety, Ministry of Education, Huainan, 232001, People's Republic of China.
- Anhui Shanhe Pharmaceutical Excipients Co., Ltd., Huainan, 232001, People's Republic of China.
| | - Guopen Miao
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Shunjie Hu
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Qi Sun
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Hengwu Ding
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China
| | - Zhicheng Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Pen Guo
- Life Science and Food Engineering College, Yibin University, Yibin, Sichuan, 644000, People's Republic of China
| | - Shoubao Yan
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Chengrun Wang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Xianzhao Kan
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
| | - Liuwang Nie
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
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12
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Barbhuiya PA, Uddin A, Chakraborty S. Understanding the codon usage patterns of mitochondrial CO genes among Amphibians. Gene 2021; 777:145462. [PMID: 33515725 DOI: 10.1016/j.gene.2021.145462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 11/17/2022]
Abstract
A universal phenomenon of using synonymous codons unequally in coding sequences known as codon usage bias (CUB) is observed in all forms of life. Mutation and natural selection drive CUB in many species but the relative role of evolutionary forces varies across species, genes and genomes. We studied the CUB in mitochondrial (mt) CO genes from three orders of Amphibia using bioinformatics approach as no work was reported yet. We observed that CUB of mt CO genes of Amphibians was weak across different orders. Order Caudata had higher CUB followed by Gymnophiona and Anura for all genes and CUB also varied across genes. Nucleotide composition analysis showed that CO genes were AT-rich. The AT content in Caudata was higher than that in Gymnophiona while Anura showed the least content. Multiple investigations namely nucleotide composition, correspondence analysis, parity plot analysis showed that the interplay of mutation pressure and natural selection caused CUB in these genes. Neutrality plot suggested the involvement of natural selection was more than the mutation pressure. The contribution of natural selection was higher in Anura than Gymnophiona and the lowest in Caudata. The codons CGA, TGA, AAA were found to be highly favoured by nature across all genes and orders.
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Affiliation(s)
- Parvin A Barbhuiya
- Department of Biotechnology, Assam University, Silchar 788150, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788150, Assam, India.
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13
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Jiang L, Zhang M, Deng L, Xu Z, Shi H, Jia X, Lai Z, Ruan Q, Chen W. Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships. Ecol Evol 2020; 10:12817-12837. [PMID: 33304496 PMCID: PMC7713938 DOI: 10.1002/ece3.6824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Lu Deng
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhongwen Xu
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Hongyan Shi
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Xiaodong Jia
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhenli Lai
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
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14
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Jiang LC, Lv GH, Jia XD, Ruan QP, Chen W. Mitogenome, Gene Rearrangement and Phylogeny of Dicroglossidae Revisited. ANN ZOOL FENN 2020. [DOI: 10.5735/086.057.0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Li-Chun Jiang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, CN-621000 Mianyang, Sichuan, P.R. China
| | - Gui-Hua Lv
- Dongyang Institute of Maize Research, Zhejiang Academy of Agricultural Sciences, CN-322100 Dongyang, Zhejiang, P.R. China
| | - Xiao-Dong Jia
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, CN-621000 Mianyang, Sichuan, P.R. China
| | - Qi-Ping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, CN-621000 Mianyang, Sichuan, P.R. China
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, CN-621000 Mianyang, Sichuan, P.R. China
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15
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Bernacki LE, Kilpatrick CW. Structural Variation of the Turtle Mitochondrial Control Region. J Mol Evol 2020; 88:618-640. [PMID: 32808073 DOI: 10.1007/s00239-020-09962-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/05/2020] [Indexed: 11/25/2022]
Abstract
The present study describes the most comprehensive comparison of turtle mtD-loop regions to date. The primary structure was compared from DNA sequences accessed from GenBank from 48 species in 13 families of extant turtles, and secondary structures of the mtD-loop region were inferred from thermal stabilities, using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order. The Cryptodira showed conservation in the primary structure at conserved sequence blocks (CSBs), but the Pleurodira displayed limited conservation of primary structural characters, other than the coreTAS, a binding site for the helicase TWINKLE, which was highly conserved in the Central and Right Domains across the order. No secondary structure was associated with a TAS, but an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop region was detected in all turtle superfamilies. Mapping of character states of structural features of the mtD-loop region revealed that most character states were autapomorphies and inferred a number of homoplasies. The Left Domain of turtles, containing no highly conserved structural elements, likely does not serve a functional role; therefore, the Central Domain in turtles is likely equivalent to the Left Domain of mammals. The AT-rich secondary structural element near the 3' terminus of the mtD-loop region may be conserved across turtles because of a functional role, perhaps containing the Light Strand Promotor, or perhaps interacting with the TWINKLE-coreTAS complex in the Central and Right Domains to regulate mtDNA replication and transcription.
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Affiliation(s)
- Lucas E Bernacki
- Department of Sciences, Saint Joseph's College, Mercy Hall, Rm 122, 278 Whites Bridge Road, Standish, ME, 04084, USA.
- Department of Biology, University of Vermont, Burlington, VT, USA.
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16
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Cabañas N, Becerra A, Romero D, Govezensky T, Espinosa-Aguirre JJ, Camacho-Carranza R. Repetitive DNA profile of the amphibian mitogenome. BMC Bioinformatics 2020; 21:197. [PMID: 32429835 PMCID: PMC7236288 DOI: 10.1186/s12859-020-3532-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/05/2020] [Indexed: 11/20/2022] Open
Abstract
Background Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not been extensively explored. We consider that the data of mitochondrial genomes in the NCBI database are a valuable alternative to generate a better understanding of the molecular dynamic of the repeat sequences in the amphibians. Results This work presents the development of a strategy to identify and quantify the total amount of repeat sequences with lengths from 5 to 30 base pairs in the amphibian mitogenomes. The results show differences in the abundance of repeat sequences among amphibians and bias to specific genomic regions that are not easily associated with the classical amphibian ancestry. Conclusions Derived from these analyses, we show that great variability of the repeat sequences exists among amphibians, demonstrating that the mitogenomes of these organisms are dynamic.
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Affiliation(s)
- Noel Cabañas
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - David Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Tzipe Govezensky
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Jesús Javier Espinosa-Aguirre
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Rafael Camacho-Carranza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico. .,Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico.
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17
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qMGR: A new approach for quantifying mitochondrial genome rearrangement. Mitochondrion 2020; 52:20-23. [DOI: 10.1016/j.mito.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/26/2019] [Accepted: 02/07/2020] [Indexed: 11/20/2022]
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18
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Cai YT, Li Q, Zhang JY, Storey KB, Yu DN. Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses. PeerJ 2020; 8:e8901. [PMID: 32328346 PMCID: PMC7164433 DOI: 10.7717/peerj.8901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/12/2020] [Indexed: 12/31/2022] Open
Abstract
Mitogenomes are useful in analyzing phylogenetic relationships and also appear to influence energy metabolism, thermoregulation and osmoregulation. Much evidence has accumulated for positive selection acting on mitochondrial genes associated with environmental adaptation. Hence, the mitogenome is a likely target for environmental selection. The family Bufonidae (true toads) has only nine complete and four partial mitogenomes published compared to the 610 known species of this family. More mitogenomes are needed in order to obtain a clearer understanding of the phylogenetic relationships within Bufonidae that are currently controversial. To date, no mitogenomes have been reported from the genera Anaxyrus and Bufotes. Anaxyrus americanus can live in low temperature environments and Bufotes pewzowi can live in high salinity environments. We sequenced the mitogenomes of these two species to discuss the phylogenetic relationships within Bufonidae and the selection pressures experienced by specimens living in low temperature or saline environments. Like other toads, the circular mitogenomes of both species contained the typical 37 genes. Anaxyrus americanus had the highest A+T content of the complete mitogenome among the Bufonidae. In addition, A. americanus showed a negative AT-skew in the control region, whereas Bufotes pewzowi showed a positive AT-skew. Additionally, both toad species had unique molecular features in common: an ND1 gene that uses TTG as the start codon, an extra unpaired adenine (A) in the anticodon arm of trnS (AGY), and the loss of the DHU loop in trnC. The monophyly of Bufonidae was corroborated by both BI and ML trees. An analysis of selective pressure based on the 13 protein coding genes was conducted using the EasyCodeML program. In the branch model analysis, we found two branches of A. americanus and Bufotes pewzowi that were under negative selection. Additionally, we found two positively selected sites (at positions 115 and 119, BEB value > 0.90) in the ND6 protein in the site model analysis. The residue D (119) was located only in A. americanus and may be related to adaptive evolution in low temperature environments. However, there was no evidence of a positively selected site in Bufotes pewzowi in this study.
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Affiliation(s)
- Yu-Ting Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Qin Li
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Jia-Yong Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | | | - Dan-Na Yu
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
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19
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Exceptional Enlargement of the Mitochondrial Genome Results from Distinct Causes in Different Rain Frogs (Anura: Brevicipitidae: Breviceps). Int J Genomics 2020; 2020:6540343. [PMID: 32064272 PMCID: PMC6998742 DOI: 10.1155/2020/6540343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/11/2019] [Indexed: 11/25/2022] Open
Abstract
The mitochondrial (mt) genome of the bushveld rain frog (Breviceps adspersus, Brevicipitidae, Afrobatrachia) is the largest (28.8 kbp) among the vertebrates investigated to date. The major cause of genome size enlargement in this species is the duplication of multiple genomic regions. To investigate the evolutionary lineage, timing, and process of mt genome enlargement, we sequenced the complete mtDNAs of two congeneric rain frogs, B. mossambicus and B. poweri. The mt genomic organization, gene content, and gene arrangements of these two rain frogs are very similar to each other but differ from those of B. adspersus. The B. mossambicus mt genome (22.5 kbp) does not differ significantly from that of most other afrobatrachians. In contrast, the B. poweri mtDNA (28.1 kbp) is considerably larger: currently the second largest among vertebrates, after B. adspersus. The main causes of genome enlargement differ among Breviceps species. Unusual elongation (12.5 kbp) of the control region (CR), a single major noncoding region of the vertebrate mt genome, is responsible for the extremely large mt genome in B. poweri. Based on the current Breviceps phylogeny and estimated divergence age, it can be concluded that the genome enlargements occurred independently in each species lineage within relatively short periods. Furthermore, a high nucleotide substitution rate and relaxation of selective pressures, which are considered to be involved in changes in genome size, were also detected in afrobatrachian lineages. Our results suggest that these factors were not direct causes but may have indirectly affected mt genome enlargements in Breviceps.
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20
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Wang Q, Tang D, Guo H, Wang J, Xu X, Wang Z. Comparative mitochondrial genomic analysis of Macrophthalmus pacificus and insights into the phylogeny of the Ocypodoidea & Grapsoidea. Genomics 2020; 112:82-91. [DOI: 10.1016/j.ygeno.2019.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 01/24/2023]
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21
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Cai YY, Shen SQ, Lu LX, Storey KB, Yu DN, Zhang JY. The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world's largest frogs. PeerJ 2019; 7:e7532. [PMID: 31497398 PMCID: PMC6709665 DOI: 10.7717/peerj.7532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/22/2019] [Indexed: 01/21/2023] Open
Abstract
The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr , tRNAPro , tRNAPhe , tRNAVal , tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).
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Affiliation(s)
- Yin-Yin Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Shi-Qi Shen
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Li-Xu Lu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | | | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
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22
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Huang A, Liu S, Li H, Luo H, Ni Q, Yao Y, Xu H, Zeng B, Li Y, Wei Z, Li S, Zhang M. The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis. PeerJ 2019; 7:e7415. [PMID: 31396450 PMCID: PMC6679912 DOI: 10.7717/peerj.7415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 07/04/2019] [Indexed: 11/30/2022] Open
Abstract
The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.
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Affiliation(s)
- An Huang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shuo Liu
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, China
| | - Haijun Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hongdi Luo
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Bo Zeng
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ying Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhimin Wei
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Song Li
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, China
| | - Mingwang Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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23
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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Zhang JY, Luu BE, Yu DN, Zhang LP, Al-attar R, Storey KB. The complete mitochondrial genome of Dryophytes versicolor: Phylogenetic relationship among Hylidae and mitochondrial protein-coding gene expression in response to freezing and anoxia. Int J Biol Macromol 2019; 132:461-469. [DOI: 10.1016/j.ijbiomac.2019.03.220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 11/17/2022]
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Liu J, Yu J, Zhou M, Yang J. Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species. Int J Biol Macromol 2019; 125:423-431. [DOI: 10.1016/j.ijbiomac.2018.12.068] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
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Eo SH, Lee BJ, Park CD, Jung JH, Hong N, Lee WS. Taxonomic identity of the Glandirana emeljanovi (Anura, Ranidae) in Korea revealed by the complete mitochondrial genome sequence analysis. MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1579074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Soo Hyung Eo
- Department of Forest Resources, Kongju National University, Chungnam, Republic of Korea
| | - Byeong-Ju Lee
- Department of Forest Resources, Kongju National University, Chungnam, Republic of Korea
| | - Chang-Deuk Park
- Department of Forest Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ji-Hwa Jung
- Department of Forest Sciences, Seoul National University, Seoul, Republic of Korea
| | - Nuri Hong
- Department of Forest Sciences, Seoul National University, Seoul, Republic of Korea
| | - Woo-Shin Lee
- Department of Forest Sciences, Seoul National University, Seoul, Republic of Korea
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Poulsen JY, Sado T, Miya M. Unique mitochondrial gene order in Xenodermichthys copei (Alepocephalidae: Otocephala) – a first observation of a large-scale rearranged 16S–WANCY region in vertebrates. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1551082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Jan Yde Poulsen
- Department of Fish and Shellfish, Pinngortitaleriffik (Greenland Institute of Natural Resources), Nuuk, Greenland
- Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
| | - Tetsuya Sado
- Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
| | - Masaki Miya
- Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
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Su T, He B, Li K, Liang A. Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa. BMC Genomics 2018; 19:961. [PMID: 30587118 PMCID: PMC6307326 DOI: 10.1186/s12864-018-5365-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 12/12/2018] [Indexed: 11/29/2022] Open
Abstract
Background Cosmoscartini (Hemiptera: Cercopoidea: Cercopidae) is a large and brightly colored Old World tropical tribe, currently containing over 310 phytophagous species (including some economically important pests of eucalyptus in China) in approximately 17 genera. However, very limited information of Cosmoscartini is available except for some scattered taxonomic studies. Even less is known about its phylogenetic relationship, especially among closely related genera or species. In this study, the detailed comparative genomic and phylogenetic analyses were performed on nine newly sequenced mitochondrial genomes (mitogenomes) of Cosmoscartini, with the purpose of exploring the taxonomic status of the previously defined genus Okiscarta and some closely related species within the genus Cosmoscarta. Results Mitogenomes of Cosmoscartini display similar genomic characters in terms of gene arrangement, nucleotide composition, codon usage and overlapping regions. However, there are also many differences in intergenic spacers, mismatches of tRNAs, and the control region. Additionally, the secondary structures of rRNAs within Cercopidae are inferred for the first time. Based on comparative genomic (especially for the substitution pattern of tRNA secondary structure) and phylogenetic analyses, the representative species of Okiscarta uchidae possesses similar structures with other Cosmoscarta species and is placed consistently in Cosmoscarta. Although Cosmoscarta bimacula is difficult to be distinguished from Cosmoscarta bispecularis by traditional morphological methods, evidence from mitogenomes highly support the relationships of (C. bimacula + Cosmoscarta rubroscutellata) + (C. bispecularis + Cosmoscarta sp.). Conclusions This study presents mitogenomes of nine Cosmoscartini species and represents the first detailed comparative genomic and phylogenetic analyses within Cercopidae. It is indicated that knowledge of mitogenomes can be effectively used to resolve phylogenetic relationships at low taxonomic levels. Sequencing more mitogenomes at various taxonomic levels will also improve our understanding of mitogenomic evolution and phylogeny in Cercopidae. Electronic supplementary material The online version of this article (10.1186/s12864-018-5365-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianjuan Su
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo He
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Kui Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aiping Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Phylogenetic relationships and cryptic species diversity in the Brazilian egg-brooding tree frog, genus Fritziana Mello-Leitão 1937 (Anura: Hemiphractidae). Mol Phylogenet Evol 2018; 123:59-72. [DOI: 10.1016/j.ympev.2018.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 02/11/2018] [Accepted: 02/11/2018] [Indexed: 11/23/2022]
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Jacob Machado D, Janies D, Brouwer C, Grant T. A new strategy to infer circularity applied to four new complete frog mitogenomes. Ecol Evol 2018; 8:4011-4018. [PMID: 29721275 PMCID: PMC5916287 DOI: 10.1002/ece3.3918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 11/10/2022] Open
Abstract
We applied a novel strategy to infer sequence circularity and complete assembly of four mitochondrial genomes (mitogenomes) of the frog families Bufonidae (Melanophryniscus moreirae), Dendrobatidae (Hyloxalus subpunctatus and Phyllobates terribilis), and Scaphiopodidae (Scaphiopus holbrookii). These are the first complete mitogenomes of these four genera and Scaphiopodidae. We assembled mitogenomes from short genomic sequence reads using a baiting and iterative mapping strategy followed by a new ad hoc mapping strategy developed to test for assembly circularization. To assess the quality of the inferred circularization, we used Bowtie2 alignment scores and a new per-position sequence coverage value (which we named "connectivity"). Permutation tests with 400 iterations per specimen and 1% or 5% chance of mutation at the ends of the putative circular sequences showed that the proposed method is highly sensitive, with a single nucleotide insertion or deletion being sufficient for circularity to be rejected. False positives comprised only 2% of all observations and possessed significantly lower alignment scores. The size, gene content, and gene arrangement of each mitogenome differed among the species but matched the expectations for their clades. We argue that basic studies on circular sequences can benefit from the results and bioinformatics procedures introduced here, especially when closely related references are lacking.
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Affiliation(s)
- Denis Jacob Machado
- Bioinformatics Interunits Graduate ProgramUniversity of São PauloSão PauloBrazil
| | - Daniel Janies
- Department of Bioinformatics and GenomicsUNC CharlotteCharlotteNCUSA
| | - Cory Brouwer
- Department of Bioinformatics and GenomicsUNC CharlotteCharlotteNCUSA
- UNC Charlotte Bioinformatics Service DivisionKannapolisNCUSA
| | - Taran Grant
- Department of ZoologyUniversity of São PauloSão PauloBrazil
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Barrow LN, Lemmon AR, Lemmon EM. Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data. Syst Biol 2018; 67:979-996. [DOI: 10.1093/sysbio/syy021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 03/15/2018] [Indexed: 01/09/2023] Open
Affiliation(s)
- Lisa N Barrow
- Department of Biology, Museum of Southwestern Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
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Zhang JY, Zhang LP, Yu DN, Storey KB, Zheng RQ. Complete mitochondrial genomes of Nanorana taihangnica and N. yunnanensis (Anura: Dicroglossidae) with novel gene arrangements and phylogenetic relationship of Dicroglossidae. BMC Evol Biol 2018; 18:26. [PMID: 29486721 PMCID: PMC6389187 DOI: 10.1186/s12862-018-1140-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 02/15/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. Large-scale mt genomic reorganizations have been observed among many fork-tongued frogs (family Dicroglossidae). The relationships among Dicroglossidae and validation of the genus Feirana are still problematic. Hence, we sequenced the complete mt genomes of Nanorana taihangnica (=F. taihangnica) and N. yunnanensis as well as partial mt genomes of six Quasipaa species (dicroglossid taxa), two Odorrana and two Amolops species (Ranidae), and one Rhacophorus species (Rhacophoridae) in order to identify unknown mt gene rearrangements, to investigate the validity of the genus Feirana, and to test the phylogenetic relationship of Dicroglossidae. RESULTS In the mt genome of N. taihangnica two trnM genes, two trnP genes and two control regions were found. In addition, the trnA, trnN, trnC, and trnQ genes were translocated from their typical positions. In the mt genome of N. yunnanensis, three control regions were found and eight genes (ND6, trnP, trnQ, trnA, trnN, trnC, trnY and trnS genes) in the L-stand were translocated from their typical position and grouped together. We also found intraspecific rearrangement of the mitochondrial genomes in N. taihangnica and Quasipaa boulengeri. In phylogenetic trees, the genus Feirana nested deeply within the clade of genus Nanorana, indicating that the genus Feirana may be a synonym to Nanorana. Ranidae as a sister clade to Dicroglossidae and the clade of (Ranidae + Dicroglossidae) as a sister clade to (Mantellidae + Rhacophoridae) were well supported in BI analysis but low bootstrap in ML analysis. CONCLUSIONS We found that the gene arrangements of N. taihangnica and N. yunnanensis differed from other published dicroglossid mt genomes. The gene arrangements in N. taihangnica and N. yunnanensis could be explained by the Tandem Duplication and Random Loss (TDRL) and the Dimer-Mitogenome and Non-Random Loss (DMNR) models, respectively. The invalidation of the genus Feirana is supported in this study.
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Affiliation(s)
- Jia-Yong Zhang
- Key lab of wildlife biotechnology, conservation and utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Le-Ping Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
| | - Dan-Na Yu
- Key lab of wildlife biotechnology, conservation and utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China.
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China.
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Rong-Quan Zheng
- Xingzhi College, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
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Chong RA, Mueller RL. Polymorphic duplicate genes and persistent non-coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders. BMC Genomics 2017; 18:992. [PMID: 29281973 PMCID: PMC5745709 DOI: 10.1186/s12864-017-4358-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 11/29/2017] [Indexed: 12/03/2022] Open
Abstract
Background Mitochondria are the site of the citric acid cycle and oxidative phosphorylation (OXPHOS). In metazoans, the mitochondrial genome is a small, circular molecule averaging 16.5 kb in length. Despite evolutionarily conserved gene content, metazoan mitochondrial genomes show a diversity of gene orders most commonly explained by the duplication-random loss (DRL) model. In the DRL model, (1) a sequence of genes is duplicated in tandem, (2) one paralog sustains a loss-of-function mutation, resulting in selection to retain the other copy, and (3) the non-functional paralog is eventually deleted from the genome. Despite its apparent role in generating mitochondrial gene order diversity, little is known about the tempo and mode of random gene loss after duplication events. Here, we determine mitochondrial gene order across the salamander genus Aneides, which was previously shown to include at least two DRL-mediated rearrangement events. We then analyze these gene orders in a phylogenetic context to reveal patterns of DNA loss after mitochondrial gene duplication. Results We identified two separate duplication events that resulted in mitochondrial gene rearrangements in Aneides; one occurred at the base of the clade tens of millions of years ago, while the other occurred much more recently (i.e. within a single species), resulting in gene order polymorphism and paralogs that are readily identifiable. We demonstrate that near-complete removal of duplicate rRNA genes has occurred since the recent duplication event, whereas duplicate protein-coding genes persist as pseudogenes and duplicate tRNAs persist as functionally intact paralogs. In addition, we show that non-coding DNA duplicated at the base of the clade has persisted across species for tens of millions of years. Conclusions The evolutionary history of the mitochondrial genome, from its inception as a bacterial endosymbiont, includes massive genomic reduction. Consistent with this overall trend, selection for efficiency of mitochondrial replication and transcription has been hypothesized to favor elimination of extra sequence. Our results, however, suggest that there may be no strong disadvantage to extraneous sequences in salamander mitochondrial genomes, although duplicate rRNA genes may be deleterious. Electronic supplementary material The online version of this article (10.1186/s12864-017-4358-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebecca A Chong
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA. .,Present address: Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
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Liu W, Tao J, Wang H, Zhao W, Liu P. Sequencing and analysis of the complete mitochondrial genome of Rugosa emeljanovi (Anura: Ranidae). Mitochondrial DNA B Resour 2017; 2:383-384. [PMID: 33490451 PMCID: PMC7801011 DOI: 10.1080/23802359.2017.1347841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Wanli Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, P.R. China
| | - Jiuchen Tao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, P.R. China
| | - Heng Wang
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, P.R. China
| | - Wenge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, P.R. China
| | - Peng Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, P.R. China
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Pie MR, Ströher PR, Belmonte-Lopes R, Bornschein MR, Ribeiro LF, Faircloth BC, McCormack JE. Phylogenetic relationships of diurnal, phytotelm-breeding Melanophryniscus (Anura: Bufonidae) based on mitogenomic data. Gene 2017; 628:194-199. [PMID: 28720533 DOI: 10.1016/j.gene.2017.07.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 06/20/2017] [Accepted: 07/14/2017] [Indexed: 11/19/2022]
Abstract
Melanophryniscus is a bufonid frog genus with a broad geographic distribution over southeastern South America. In recent years, several new species of Melanophryniscus have been discovered in southern Brazil showing a distinctive life-history strategy for the genus - breeding in phytotelmata - as well as a strong association with high-altitude regions. In this study, we use mitogenomic data to infer the phylogenetic relationships among diurnal, phytotelm-breeding Melanophryniscus and to determine the timing of their divergence. We obtained the mitochondrial genomes (not including the control region) for eight individuals of Melanophryniscus representing all three described species (M. alipioi, M. milanoi, and M. xanthostomus), as well as some recently-discovered and potentially new species. Gene order was conserved in all species and corresponded to the general order found in bufonids. Although the phylogenetic relationships among the studied species was poorly supported, dating confirmed that they diverged during the Pleistocene, suggesting that phytotelm breeding could have arisen during drier periods in the glacial/interglacial cycles due to a decrease in the availability of permanent streams or ephemeral/temporary streams or ponds in which Melanophryniscus species commonly breed.
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Affiliation(s)
- Marcio R Pie
- Departamento de Zoologia, Universidade Federal do Paraná, CEP 81531-980 Curitiba, Paraná, Brazil; Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil.
| | - Patrícia R Ströher
- Departamento de Zoologia, Universidade Federal do Paraná, CEP 81531-980 Curitiba, Paraná, Brazil
| | - Ricardo Belmonte-Lopes
- Departamento de Zoologia, Universidade Federal do Paraná, CEP 81531-980 Curitiba, Paraná, Brazil; Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil
| | - Marcos R Bornschein
- Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil; Instituto de Biociências, Universidade Estadual Paulista, Praça Infante Dom Henrique s/no, Parque Bitaru, CEP 11330-900 São Vicente, São Paulo, Brazil
| | - Luiz F Ribeiro
- Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil; Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Brant C Faircloth
- Dept. of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA
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Tavares WC, Seuánez HN. Disease-associated mitochondrial mutations and the evolution of primate mitogenomes. PLoS One 2017; 12:e0177403. [PMID: 28510580 PMCID: PMC5433710 DOI: 10.1371/journal.pone.0177403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/26/2017] [Indexed: 01/09/2023] Open
Abstract
Several human diseases have been associated with mutations in mitochondrial genes comprising a set of confirmed and reported mutations according to the MITOMAP database. An analysis of complete mitogenomes across 139 primate species showed that most confirmed disease-associated mutations occurred in aligned codon positions and gene regions under strong purifying selection resulting in a strong evolutionary conservation. Only two confirmed variants (7.1%), coding for the same amino acids accounting for severe human diseases, were identified without apparent pathogenicity in non-human primates, like the closely related Bornean orangutan. Conversely, reported disease-associated mutations were not especially concentrated in conserved codon positions, and a large fraction of them occurred in highly variable ones. Additionally, 88 (45.8%) of reported mutations showed similar variants in several non-human primates and some of them have been present in extinct species of the genus Homo. Considering that recurrent mutations leading to persistent variants throughout the evolutionary diversification of primates are less likely to be severely damaging to fitness, we suggest that these 88 mutations are less likely to be pathogenic. Conversely, 69 (35.9%) of reported disease-associated mutations occurred in extremely conserved aligned codon positions which makes them more likely to damage the primate mitochondrial physiology.
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Affiliation(s)
- William Corrêa Tavares
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N. Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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Dang NX, Wang JS, Liang J, Jiang DC, Liu J, Wang L, Li JT. The specialisation of the third metacarpal and hand in arboreal frogs: Adaptation for arboreal habitat? ACTA ZOOL-STOCKHOLM 2017. [DOI: 10.1111/azo.12196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ning-Xin Dang
- College of Life Sciences; Sichuan University; Chengdu China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu China
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Yezin Nay Pyi Taw Myanmar
| | - Ji-Shan Wang
- China Forest Exploration & Design Institute in Kunming; State Forestry Administration P.R.China; Yunnan China
| | - Jin Liang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu China
| | - De-Chun Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu China
| | - Jun Liu
- College of Life Sciences; Sichuan University; Chengdu China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu China
| | - Li Wang
- College of Life Sciences; Sichuan University; Chengdu China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu China
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Yezin Nay Pyi Taw Myanmar
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Pie MR, Ströher PR, Bornschein MR, Ribeiro LF, Faircloth BC, McCormack JE. The mitochondrial genome of Brachycephalus brunneus (Anura: Brachycephalidae), with comments on the phylogenetic position of Brachycephalidae. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Yuan S, Xia Y, Zheng Y, Zeng X. Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri. PeerJ 2016; 4:e2786. [PMID: 27994980 PMCID: PMC5162401 DOI: 10.7717/peerj.2786] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/11/2016] [Indexed: 01/01/2023] Open
Abstract
Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.
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Affiliation(s)
- Siqi Yuan
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yun Xia
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China
| | - Yuchi Zheng
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China
| | - Xiaomao Zeng
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China
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Xia Y, Zheng Y, Murphy RW, Zeng X. Intraspecific rearrangement of mitochondrial genome suggests the prevalence of the tandem duplication-random loss (TDLR) mechanism in Quasipaa boulengeri. BMC Genomics 2016; 17:965. [PMID: 27881087 PMCID: PMC5122201 DOI: 10.1186/s12864-016-3309-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tandem duplication followed by random loss (TDRL) is the most frequently invoked model to explain the diversity of gene rearrangements in metazoan mitogenomes. The initial stages of gene rearrangement are difficult to observe in nature, which limits our understanding of incipient duplication events and the subsequent process of random loss. Intraspecific gene reorganizations may represent intermediate states, and if so they potentially shed light on the evolutionary dynamics of TDRL. RESULTS Nucleotide sequences in a hotspot of gene-rearrangement in 28 populations of a single species of frog, Quasipaa boulengeri, provide such predicted intermediate states. Gene order and phylogenetic analyses support a single tandem duplication event and a step-by-step process of random loss. Intraspecific gene rearrangements are not commonly found through comparison of all mitochondrial DNA records of amphibians and squamate reptiles in GenBank. CONCLUSIONS The intraspecific variation in Q. boulengeri provides insights into the rate of partial duplications and deletions within a mitogenome, and reveals that fixation and gene-distribution in mitogenomic reorganization is likely non-adaptive.
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Affiliation(s)
- Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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41
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Ye F, Lan XE, Zhu WB, You P. Mitochondrial genomes of praying mantises (Dictyoptera, Mantodea): rearrangement, duplication, and reassignment of tRNA genes. Sci Rep 2016; 6:25634. [PMID: 27157299 PMCID: PMC4860592 DOI: 10.1038/srep25634] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/20/2016] [Indexed: 01/20/2023] Open
Abstract
Insect mitochondrial genomes (mitogenomes) contain a conserved set of 37 genes for an extensive diversity of lineages. Previously reported dictyopteran mitogenomes share this conserved mitochondrial gene arrangement, although surprisingly little is known about the mitogenome of Mantodea. We sequenced eight mantodean mitogenomes including the first representatives of two families: Hymenopodidae and Liturgusidae. Only two of these genomes retain the typical insect gene arrangement. In three Liturgusidae species, the trnM genes have translocated. Four species of mantis (Creobroter gemmata, Mantis religiosa, Statilia sp., and Theopompa sp.-HN) have multiple identical tandem duplication of trnR, and Statilia sp. additionally includes five extra duplicate trnW. These extra trnR and trnW in Statilia sp. are erratically arranged and form another novel gene order. Interestingly, the extra trnW is converted from trnR by the process of point mutation at anticodon, which is the first case of tRNA reassignment for an insect. Furthermore, no significant differences were observed amongst mantodean mitogenomes with variable copies of tRNA according to comparative analysis of codon usage. Combined with phylogenetic analysis, the characteristics of tRNA only possess limited phylogenetic information in this research. Nevertheless, these features of gene rearrangement, duplication, and reassignment provide valuable information toward understanding mitogenome evolution in insects.
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Affiliation(s)
- Fei Ye
- Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Science, Shaanxi Normal University, Xi’an, 710062, China
| | - Xu-e Lan
- Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Science, Shaanxi Normal University, Xi’an, 710062, China
| | - Wen-bo Zhu
- Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Science, Shaanxi Normal University, Xi’an, 710062, China
| | - Ping You
- Co-Innovation Center for Qinba Regions’ Sustainable Development, College of Life Science, Shaanxi Normal University, Xi’an, 710062, China
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42
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Peso-Fernández M, Ponti de la Iglesia R, Ponz Segrelles G, González Martínez R, Arcones Segovia A, Vieites DR. The complete mitochondrial genome of the Endangered European brown frog Rana pyrenaica through RNAseq. Mitochondrial DNA B Resour 2016; 1:394-396. [PMID: 33473495 PMCID: PMC7799604 DOI: 10.1080/23802359.2016.1174087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We sequenced the complete mitogenome of the Pyrenean frog Rana pyrenaica, which was determined from an Illumina Hi-seq RNAseq run (Illumina Inc., San Diego, CA). The genome is 17,213 bp in size, including 13 protein-coding genes, 21 transfer RNAs, two ribosomal RNAs and a control region. It shows the typical gene order of previously available frog mitogenomes, although it lacks the tRNAPhe. This is the first complete mitogenome described for a Western Palearctic brown frog species.
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Affiliation(s)
| | | | | | - Rubén González Martínez
- Museo Nacional De Ciencias Naturales – CSIC, Madrid, Spain
- BioCoRe, Calle Zurbarán 16, Collado Mediano, Madrid, Spain
| | | | - David R. Vieites
- Museo Nacional De Ciencias Naturales – CSIC, Madrid, Spain
- BioCoRe, Calle Zurbarán 16, Collado Mediano, Madrid, Spain
- CIBIO-InBIO, Universidade Do Porto, Campus Agrário De Vairão, Vairão, Portugal
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Machado DJ, Lyra ML, Grant T. Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs. Mol Ecol Resour 2015; 16:686-93. [PMID: 26607054 DOI: 10.1111/1755-0998.12492] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/09/2015] [Accepted: 11/17/2015] [Indexed: 11/27/2022]
Abstract
Next-generation sequencing continues to revolutionize biodiversity studies by generating unprecedented amounts of DNA sequence data for comparative genomic analysis. However, these data are produced as millions or billions of short reads of variable quality that cannot be directly applied in comparative analyses, creating a demand for methods to facilitate assembly. We optimized an in silico strategy to efficiently reconstruct high-quality mitochondrial genomes directly from genomic reads. We tested this strategy using sequences from five species of frogs: Hylodes meridionalis (Hylodidae), Hyloxalus yasuni (Dendrobatidae), Pristimantis fenestratus (Craugastoridae), and Melanophryniscus simplex and Rhinella sp. (Bufonidae). These are the first mitogenomes published for these species, the genera Hylodes, Hyloxalus, Pristimantis, Melanophryniscus and Rhinella, and the families Craugastoridae and Hylodidae. Sequences were generated using only half of one lane of a standard Illumina HiqSeq 2000 flow cell, resulting in fewer than eight million reads. We analysed the reads of Hylodes meridionalis using three different assembly strategies: (1) reference-based (using bowtie2); (2) de novo (using abyss, soapdenovo2 and velvet); and (3) baiting and iterative mapping (using mira and mitobim). Mitogenomes were assembled exclusively with strategy 3, which we employed to assemble the remaining mitogenomes. Annotations were performed with mitos and confirmed by comparison with published amphibian mitochondria. In most cases, we recovered all 13 coding genes, 22 tRNAs, and two ribosomal subunit genes, with minor gene rearrangements. Our results show that few raw reads can be sufficient to generate high-quality scaffolds, making any Illumina machine run using genomic multiplex libraries a potential source of data for organelle assemblies as by-catch.
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Affiliation(s)
- D J Machado
- Department of Zoology, Institute of Biosciences, University of São Paulo, R. do Matão 101, São Paulo, SP, CEP 05508-090, Brazil
| | - M L Lyra
- Department of Zoology, Institute of Biosciences, São Paulo State University, Campus Rio Claro, Av. 24-A 1515, Rio Claro, SP, CEP 13506-900, Brazil
| | - T Grant
- Department of Zoology, Institute of Biosciences, University of São Paulo, R. do Matão 101, São Paulo, SP, CEP 05508-090, Brazil
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Xue R, Liu J, Yu J, Yang J. The complete mitogenome of Amolops loloensis and related phylogenetic relationship among Ranidae. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4629-4630. [PMID: 26681370 DOI: 10.3109/19401736.2015.1101589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Rufous-spotted Torrent Frog (Amolops loloensis) is a vulnerable species, which belongs to the family Ranidae and is distributed in high-gradient streams of Sichuan and Yunnan, China. In this study, we first determined the complete mitochondrial DNA sequence of A. loloensis (GenBank accession no. KT750963). The mitogenome sequence of A. loloensis was 18 926 bp in size. It contained 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and a D-loop region. Amolops loloensis shared the same gene arrangement pattern with A. mantzorum. The OL structures of A. loloensis and A. mantzorum were both located at the upstream of trnA-trnN, while the OL structures of A. ricketti and A. wuyiensis were both located at the downstream of trnA-trnN. It is of great interest to discuss the gene rearrangement mechanisms in the following study.
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Affiliation(s)
- Rui Xue
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Jiabin Liu
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Jiaojiao Yu
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Jiandong Yang
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
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Zhang C, Xia Y, Zeng X. Characterization of the mitochondrial genome of Amolops tuberodepressus (Anura: Ranidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2893-4. [PMID: 26153745 DOI: 10.3109/19401736.2015.1060425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Amolops tuberodepressus is a vulnerable torrent frog, and only know distributed in the Wuliang Mountain in southwestern China. In the present study, the mitochondrial DNA (mtDNA) sequence of A. tuberodepressus was determined. The genome was 18 348 bp in length, and it contained 37 genes (13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs), one partial control region and one light strand replication origin. The gene rearrangement was observed within the WANCY tRNA gene cluster region, which similar to other Amolops species. In this paper, we utilized 13 protein-coding genes of A. tuberodepressus and other 10 closely ranid species to construct the species phylogenetic tree to verify the A. tuberodepressus was accuracy.
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Affiliation(s)
- Chaohua Zhang
- a Department of Herpetology , Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China and.,b University of Chinese Academy of Sciences , Beijing , China
| | - Yun Xia
- a Department of Herpetology , Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China and
| | - Xiaomao Zeng
- a Department of Herpetology , Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China and
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Yu D, Zhang J, Li P, Zheng R, Shao C. Do cryptic species exist in Hoplobatrachus rugulosus? An examination using four nuclear genes, the cyt b gene and the complete MT genome. PLoS One 2015; 10:e0124825. [PMID: 25875761 PMCID: PMC4395372 DOI: 10.1371/journal.pone.0124825] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 03/18/2015] [Indexed: 11/18/2022] Open
Abstract
he Chinese tiger frog Hoplobatrachus rugulosus is widely distributed in southern China, Malaysia, Myanmar, Thailand, and Vietnam. It is listed in Appendix II of CITES as the only Class II nationally-protected frog in China. The bred tiger frog known as the Thailand tiger frog, is also identified as H. rugulosus. Our analysis of the Cyt b gene showed high genetic divergence (13.8%) between wild and bred samples of tiger frog. Unexpected genetic divergence of the complete mt genome (14.0%) was also observed between wild and bred samples of tiger frog. Yet, the nuclear genes (NCX1, Rag1, Rhod, Tyr) showed little divergence between them. Despite this and their very similar morphology, the features of the mitochondrial genome including genetic divergence of other genes, different three-dimensional structures of ND5 proteins, and gene rearrangements indicate that H. rugulosus may be a cryptic species complex. Using Bayesian inference, maximum likelihood, and maximum parsimony analyses, Hoplobatrachus was resolved as a sister clade to Euphlyctis, and H. rugulosus (BT) as a sister clade to H. rugulosus (WT). We suggest that we should prevent Thailand tiger frogs (bred type) from escaping into wild environments lest they produce hybrids with Chinese tiger frogs (wild type).
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Affiliation(s)
- Danna Yu
- Institute of Ecology, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Jiayong Zhang
- Institute of Ecology, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Rongquan Zheng
- Institute of Ecology, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
- Institute of Special Aquaculture Source, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
| | - Chen Shao
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
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