1
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Gendron EMS, Qing X, Sevigny JL, Li H, Liu Z, Blaxter M, Powers TO, Thomas WK, Porazinska DL. Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection. BMC Genomics 2024; 25:615. [PMID: 38890582 PMCID: PMC11184840 DOI: 10.1186/s12864-024-10500-1] [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: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. RESULTS Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. CONCLUSIONS Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.
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Affiliation(s)
- Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA.
| | - Xue Qing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Hongmei Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyin Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | | | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - W Kelly Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
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2
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Valencia M P, Baeza JA, López-Cuamatzi IL, Ortega J. Characterization of the mitochondrial genomes of the Mexican endemic bats Corynorhinus mexicanus and Corynorhinus leonpaniaguae (Chiroptera: Vespertilionidae). Mol Biol Rep 2024; 51:760. [PMID: 38874795 DOI: 10.1007/s11033-024-09700-5] [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: 03/19/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND The genus Corynorhinus is composed of four recognized species: C. rafinesquii, C. townsendii, C. mexicanus, and C. leonpaniaguae, the latter two being endemic to Mexico. According to the IUCN, C. mexicanus is considered "Near Threatened", as its populations are dwindling and habitats are affected by anthropogenic disturbance. Corynorhinus leonpaniaguae has not been assigned to an IUCN Red List risk category due to its recent description. METHODS AND RESULTS In this study, the mitochondrial genomes of C. mexicanus and C. leonpaniaguae were assembled and characterized in detail. The mitochondrial genomes (mtDNA) of C. mexicanus and C. leonpaniaguae have lengths of 16,470 and 16,581 bp respectively, with a predominant nucleotide usage of adenine (31.670% and 31.729%, respectively) and thymine (26.15% and 26.18%, respectively). The mtDNA of C. mexicanus and C. leonpaniaguae is composed of 37 coding and non-coding elements: 22 transfer RNAs (tRNA), 13 protein-coding genes (PCGs), two ribosomal RNAs and a non-coding region, the control region, which has a length of 933 bp and 1,149 bp, respectively. All tRNAs exhibited a cloverleaf secondary structure, with the exception of trn-Ser1 which showed a deletion of the dihydrouridine arm in the two species. All PCGs are subjected to purifying selection, with atp8 being the gene showing the highest Ka/Ks value. CONCLUSIONS These are the first whole mitogenomic resources developed for C. mexicanus and C. leonpaniaguae and enhance our knowledge of the ecology of these species and aid in their conservation.
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Affiliation(s)
- Pablo Valencia M
- Laboratorio de Bioconservación y Manejo, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Manuel Carpio y Plan de Ayala s/n, Col. Santo Tomás C.P. 11340 Alcaldía Miguel Hidalgo, Ciudad de México, México
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281, Coquimbo, Chile
| | - Issachar L López-Cuamatzi
- Centro de Investigaciones Tropicales, Universidad Veracruzana, José María Morelos 44, Zona Centro, Centro, Xalapa-Enríquez, 91000, México
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Manuel Carpio y Plan de Ayala s/n, Col. Santo Tomás C.P. 11340 Alcaldía Miguel Hidalgo, Ciudad de México, México.
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3
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Cao ML, Nie Y, Fu YT, Li R, Yi XL, Xiong J, Liu GH. Characterization of the complete mitochondrial genomes of five hard ticks and phylogenetic implications. Parasitol Res 2023:10.1007/s00436-023-07891-7. [PMID: 37329345 DOI: 10.1007/s00436-023-07891-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 05/27/2023] [Indexed: 06/19/2023]
Abstract
Ticks are blood-sucking ectoparasites with significant medical and veterinary importance, capable of transmitting bacteria, protozoa, fungi, and viruses that cause a variety of human and animal diseases worldwide. In the present study, we sequenced the complete mitochondrial (mt) genomes of five hard tick species and analyzed features of their gene contents and genome organizations. The complete mt genomes of Haemaphysalis verticalis, H. flava, H. longicornis, Rhipicephalus sanguineus and Hyalomma asiaticum were 14855 bp, 14689 bp, 14693 bp, 14715 bp and 14722 bp in size, respectively. Their gene contents and arrangements are the same as those of most species of metastriate Ixodida, but distinct from species of genus Ixodes. Phylogenetic analyses using concatenated amino acid sequences of 13 protein-coding genes with two different computational algorithms (Bayesian inference and maximum likelihood) revealed the monophylies of the genera Rhipicephalus, Ixodes and Amblyomma, however, rejected the monophyly of the genus Haemaphysalis. To our knowledge, this is the first report of the complete mt genome of H. verticalis. These datasets provide useful mtDNA markers for further studies of the identification and classification of hard ticks.
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Affiliation(s)
- Mei-Ling Cao
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Hunan, 410128, Changsha, China
| | - Yu Nie
- College of Biotechnology, Hunan University of Environment and Biology, Hengyang, 421001, Hunan, China
| | - Yi-Tian Fu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Hunan, 410128, Changsha, China
| | - Rong Li
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Hunan, 410128, Changsha, China
| | - Xi-Long Yi
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Hunan, 410128, Changsha, China
| | - Jun Xiong
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Hunan, 410128, Changsha, China
| | - Guo-Hua Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Hunan, 410128, Changsha, China.
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4
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Li LY, Deng YP, Zhang Y, Wu Y, Fu YT, Liu GH, Liu JH. Characterization of the complete mitochondrial genome of Culex vishnui (Diptera: Culicidae), one of the major vectors of Japanese encephalitis virus. Parasitol Res 2023; 122:1403-1414. [PMID: 37072585 DOI: 10.1007/s00436-023-07840-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/05/2023] [Indexed: 04/20/2023]
Abstract
Culex mosquitoes (Diptera: Culicidae) can transmit a variety of arthropod-borne viruses (arboviruses), causing human and animal diseases. Cx. vishnui, Cx. pseudovishnui, and Cx. tritaeniorhynchus are three representative species in Culex vishnui subgroup, which are widely distributed in southeast Asia, and they have been proved as the main vectors transmitting Japanese encephalitis virus (JEV) that could cause human infectious mosquito-borne disease across Asia. However, the epidemiology, biology, and even molecular information of those mosquitos remain poorly understood, and only the mitochondrial genome (mitogenome) of Cx. tritaeniorhynchus has been reported in these species. In the present study, we sequenced and annotated the complete mitogenome sequence of Cx. vishnui which was 15,587 bp in length, comprising 37 genes. Comparisons of nucleotide and amino acid sequences between Cx. vishnui and Cx. tritaeniorhynchus revealed that most genes within Culex vishnui subgroup were conserved, except atp8, nad1, atp6, and nad6, with differences of 0.4 (rrnS) - 15.1% (tRNAs) and 0 (nad4L) - 9.4% (atp8), respectively, interestingly suggesting the genes nad4L and rrnS were the most conserved but atp8 gene was the least. The results based on nucleotide diversity also supported a relatively uniform distribution of the intraspecific differences in Cx. vishnui and Cx. tritaeniorhynchus with only one highly pronounced peak of divergence centered at the control region. Phylogenetic analyses using concatenated amino acid sequences of 13 protein-coding genes supported the previous taxonomic classification of the family Culicidae and the monophyly of tribes Aedini, Culicini, Mansoniini, and Sabethini. The present study revealed detailed information on the subgroup Culex vishnui, reanalyzed the relationships within the family Culicidae, provided better markers to identify and distinguish Culex species, and offered more markers for studying the molecular epidemiology, population genetics, and molecular phylogenetics of Cx. vishnui.
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Affiliation(s)
- Le-Yan Li
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Yuan-Ping Deng
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Yu Zhang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - You Wu
- Hunan Engineering Research Center of Livestock and Poultry Health Care, Hunan Agricultural University, Hunan Province, Changsha, 410128, China
| | - Yi-Tian Fu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Guo-Hua Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Jin-Hui Liu
- Hunan Co-Innovation Center of Animal Production Safety, Hunan Agricultural University, Changsha, 410128, Hunan Province, China.
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5
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Xu M, Gu Z, Huang J, Guo B, Jiang L, Xu K, Ye Y, Li J. The Complete Mitochondrial Genome of Mytilisepta virgata (Mollusca: Bivalvia), Novel Gene Rearrangements, and the Phylogenetic Relationships of Mytilidae. Genes (Basel) 2023; 14:910. [PMID: 37107667 PMCID: PMC10137486 DOI: 10.3390/genes14040910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/10/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
The circular mitochondrial genome of Mytilisepta virgata spans 14,713 bp, which contains 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. Analysis of the 13 PCGs reveals that the mitochondrial gene arrangement of Mytilisepta is relatively conserved at the genus level. The location of the atp8 gene in Mytilisepta keenae differs from that of other species. However, compared with the putative molluscan ancestral gene order, M. virgata exhibits a high level of rearrangement. We constructed phylogenetic trees based on concatenated 12 PCGs from Mytilidae. As a result, we found that M. virgata is in the same clade as other Mytilisepta spp. The result of estimated divergence times revealed that M. virgata and M. keenae diverged around the early Paleogene period, although the oldest Mytilisepta fossil was from the late or upper Eocene period. Our results provide robust statistical evidence for a sister-group relationship within Mytilida. The findings not only confirm previous results, but also provide valuable insights into the evolutionary history of Mytilidae.
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Affiliation(s)
- Minhui Xu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhongqi Gu
- Shengsi Marine Science and Technology Institute, Shengsi, Zhoushan 202450, China
| | - Ji Huang
- Shengsi Marine Science and Technology Institute, Shengsi, Zhoushan 202450, China
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Lihua Jiang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
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6
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Montaña-Lozano P, Balaguera-Reina SA, Prada-Quiroga CF. Comparative analysis of codon usage of mitochondrial genomes provides evolutionary insights into reptiles. Gene 2023; 851:146999. [DOI: 10.1016/j.gene.2022.146999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/30/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022]
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7
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Deng YP, Suleman, Zhang XL, Li R, Li LY, Fu YT, Liu GH, Yao C. Aonchotheca (Nematoda: Capillariidae) is validated as a separated genus from Capillaria by both mitochondrial and nuclear ribosomal DNA. Parasit Vectors 2022; 15:493. [PMID: 36585724 PMCID: PMC9805247 DOI: 10.1186/s13071-022-05609-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/03/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The family Capillariidae is a group of thread-like nematodes of 27 genera and over 300 species that infect a great variety of hosts including humans. Among these, some taxa such as the genus Aonchotheca have remained controversial regarding their systematic status for decades. The aim of the current study was to verify Aonchotheca's systemic status and to further determine whether it is a distinct genus from Capillaria using molecular and phylogenetic analyses. RESULTS We sequenced the mitochondrial (mt) genome and nuclear small subunit (18S) rRNA gene of Aonchotheca putorii, a representative species of the genus, and investigated its systematic status in Trichinellida using maximum likelihood and Bayesian inference. The differences in amino acid sequences of 13 protein-coding genes were 12.69-67.35% among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillaria with cox1 (12.69%) and atp8 (67.35%) as the most and the least conserved gene, respectively, and the difference of two mt rRNAs was 18.61-34.15%. Phylogenetic analyses of the complete mt genome and 18S rRNAs unequivocally showed that Aonchotheca was a distinct genus from Capillaria. CONCLUSIONS Large difference exists among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillarias. Aonchotheca putorii is the first species in the genus Aonchotheca for which a complete mitogenome has been sequenced. These data are useful for phylogenetics, systematics and the evolution of Capillariidae.
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Affiliation(s)
- Yuan-Ping Deng
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Suleman
- grid.502337.00000 0004 4657 4747Department of Zoology, University of Swabi, Swabi, 23561 Khyber Pakhtunkhwa Pakistan
| | - Xue-Ling Zhang
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Rong Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Le-Yan Li
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Yi-Tian Fu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Guo-Hua Liu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Chaoqun Yao
- grid.412247.60000 0004 1776 0209Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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8
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Andaman local goat: mitochondrial genome characterization and lineage analysis. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01234-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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9
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Ding L, Luo G, Zhou Q, Sun Y, Liao J. Comparative Mitogenome Analysis of Gerbils and the Mitogenome Phylogeny of Gerbillinae (Rodentia: Muridae). Biochem Genet 2022; 60:2226-2249. [PMID: 35314913 DOI: 10.1007/s10528-022-10213-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 02/24/2022] [Indexed: 11/02/2022]
Abstract
To enrich the mitogenomic database of Gerbillinae (Rodentia: Muridae), mitogenomes of three gerbils from different genera, Meriones tamariscinus (16,393 bp), Brachiones przewalskii (16,357 bp), and Rhombomys opimus (16,352 bp), were elaborated and compared with those of other gerbils in the present study. The three gerbil mitogenomes consisted of 2 ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes, and one control region. Here, gerbil mitogenomes have shown unique characteristics in terms of base composition, codon usage, non-coding region, and the replication origin of the light strand. There was no significant correlation between the nucleotide percentage of G + C and the phylogenetic status in gerbils, and between the GC content of PCGs and the leucine count. Phylogenetic relationships of the subfamily Gerbillinae were reconstructed by 7 gerbils that represented four genera based on concatenated mitochondrial DNA data using both Bayesian Inference and Maximum Likelihood. The phylogenetic analysis indicated that M. tamariscinus was phylogenetically distant from the genus Meriones, but has a close relationship with R. opimus. B. przewalskii was closely related to the genus Meriones rather than that of R. opimus.
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Affiliation(s)
- Li Ding
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.,School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Guangjie Luo
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Quan Zhou
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yuanhai Sun
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jicheng Liao
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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10
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Cejp B, Ravara A, Aguado MT. First mitochondrial genomes of Chrysopetalidae (Annelida) from shallow-water and deep-sea chemosynthetic environments. Gene 2022; 815:146159. [PMID: 34995739 DOI: 10.1016/j.gene.2021.146159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023]
Abstract
Among Annelida, Chrysopetalidae is an ecologically and morphologically diverse group, which includes shallow-water, deep-sea, free-living, and symbiotic species. Here, the four first mitochondrial genomes of this group are presented and described. One of the free-living shallow-water species Chrysopetalum debile (Chrysopetalinae), one of the yet undescribed free-living deep-sea species Boudemos sp., and those of the two deep-sea bivalve endosymbionts Craseoschema thyasiricola and Iheyomytilidicola lauensis (Calamyzinae). An updated phylogeny of Chrysopetalidae is performed, which supports previous phylogenetic hypotheses within Chrysopetalinae and indicates a complex ecological evolution within Calamyzinae. Additionally, analyses of natural selection pressure in the four mitochondrial genomes and additional genes from the two shallow-water species Bhawania goodei and Arichlidon gathofi were performed. Relaxed selection pressure in the mitochondrion of deep-sea and symbiotic species was found, with many sites under selection identified in the COX3 gene of deep-sea species.
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Affiliation(s)
- Benjamin Cejp
- Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, 37073, Germany.
| | - Ascensão Ravara
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
| | - M Teresa Aguado
- Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, 37073, Germany.
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11
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Fan Y, Wang W. Using multi-layer perceptron to identify origins of replication in eukaryotes via informative features. BMC Bioinformatics 2021; 22:516. [PMID: 34688247 PMCID: PMC8542328 DOI: 10.1186/s12859-021-04431-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The origin is the starting site of DNA replication, an extremely vital part of the informational inheritance between parents and children. More importantly, accurately identifying the origin of replication has great application value in the diagnosis and treatment of diseases related to genetic information errors, while the traditional biological experimental methods are time-consuming and laborious. RESULTS We carried out research on the origin of replication in a variety of eukaryotes and proposed a unique prediction method for each species. Throughout the experiment, we collected data from 7 species, including Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, Kluyveromyces lactis, Pichia pastoris and Schizosaccharomyces pombe. In addition to the commonly used sequence feature extraction methods PseKNC-II and Base-content, we designed a feature extraction method based on TF-IDF. Then the two-step method was utilized for feature selection. After comparing a variety of traditional machine learning classification models, the multi-layer perceptron was employed as the classification algorithm. Ultimately, the data and codes involved in the experiment are available at https://github.com/Sarahyouzi/EukOriginPredict . CONCLUSIONS The prediction accuracy of the training set of the above-mentioned seven species after 100 times fivefold cross validation reach 92.60%, 90.80%, 91.22%, 96.15%, 96.72%, 99.86%, 96.72%, respectively. It denotes that compared with other methods, the methods we designed could accomplish superior performance. In addition, our experiments reveals that the models of multiple species could predict each other with high accuracy, and the results of STREME shows that they have a certain common motif.
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Affiliation(s)
- Yongxian Fan
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China.
| | - Wanru Wang
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China
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12
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Jakovlić I, Zou H, Chen JH, Lei HP, Wang GT, Liu J, Zhang D. Slow crabs - fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes. Mol Ecol 2021; 30:5488-5502. [PMID: 34418213 DOI: 10.1111/mec.16138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 02/05/2023]
Abstract
Base composition skews (G-C/G+C) of mitochondrial genomes are believed to be primarily driven by mutational pressure, which is positively correlated with metabolic rate. In marine animals, metabolic rate is also positively correlated with locomotory capacity. Given the central role of mitochondria in energy metabolism, we hypothesised that selection for locomotory capacity should be positively correlated with the strength of purifying selection (dN/dS), and thus be negatively correlated with the skew magnitude. Therefore, these two models assume diametrically opposite associations between the metabolic rate and skew magnitude: positive correlation in the prevailing paradigm, and negative in our working hypothesis. We examined correlations between the skew magnitude, metabolic rate, locomotory capacity, and several other variables previously associated with mitochondrial evolution on 287 crustacean mitogenomes. Weakly locomotory taxa had higher skew magnitude and ω (dN/dS) values, but not the gene order rearrangement rate. Skew and ω magnitudes were correlated. Multilevel regression analyses indicated that three competing variables, body size, gene order rearrangement rate, and effective population size, had negligible impacts on the skew magnitude. In most crustacean lineages selection for locomotory capacity appears to be the primary factor determining the skew magnitude. Contrary to the prevailing paradigm, this implies that adaptive selection outweighs nonadaptive selection (mutation pressure) in crustaceans. However, we found indications that effective population size (nonadaptive factor) may outweigh the impact of locomotory capacity in sessile crustaceans (Thecostraca). In conclusion, skew magnitude is a product of the interplay between adaptive and nonadaptive factors, the balance of which varies among lineages.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Hai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong-Peng Lei
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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Jakovlić I, Zou H, Zhao XM, Zhang J, Wang GT, Zhang D. Evolutionary History of Inversions in Directional Mutational Pressures in Crustacean Mitochondrial Genomes: Implications for Evolutionary Studies. Mol Phylogenet Evol 2021; 164:107288. [PMID: 34365015 DOI: 10.1016/j.ympev.2021.107288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 01/29/2023]
Abstract
Inversions of the origin of replication (ORI) in mitochondrial genomes produce asymmetrical mutational pressures that can cause strong base composition skews. Due to skews often being overlooked, the total number of crustacean lineages that underwent ORI events remains unknown. We analysed skews, cumulative skew plots, conserved sequence motifs, and mitochondrial architecture of all 965 available crustacean mitogenomes (699 unique species). We found indications of an ORI in 159 (22.7%) species, and mapped these to 23 ORI events: 16 identified with confidence and 7 putative (13 newly proposed, and for 5 we improved the resolution). Two ORIs occurred at or above the order level: Isopoda and Copepoda. Shifts in skew plots are not a precise tool for identifying the replication mechanism. We discuss how ORIs can produce mutational bursts in mitogenomes and show how these can interfere with various types of evolutionary studies. Phylogenetic analyses were plagued by artefactual clustering, and ORI lineages exhibited longer branches, a higher number of synonymous substitutions, higher mutational saturation, and higher compositional heterogeneity. ORI events also affected codon usage and protein properties. We discuss how this may have caused erroneous interpretation of data in previous studies that did not account for skew patterns.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xu-Mao Zhao
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Jin Zhang
- Bio-Transduction Lab, Wuhan 430075, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China.
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Berná L, Greif G, Pita S, Faral-Tello P, Díaz-Viraqué F, Souza RDCMD, Vallejo GA, Alvarez-Valin F, Robello C. Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex. PLoS Negl Trop Dis 2021; 15:e0009719. [PMID: 34437557 PMCID: PMC8425572 DOI: 10.1371/journal.pntd.0009719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/08/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022] Open
Abstract
We sequenced maxicircles from T. cruzi strains representative of the species evolutionary diversity by using long-read sequencing, which allowed us to uncollapse their repetitive regions, finding that their real lengths range from 35 to 50 kb. T. cruzi maxicircles have a common architecture composed of four regions: coding region (CR), AT-rich region, short (SR) and long repeats (LR). Distribution of genes, both in order and in strand orientation are conserved, being the main differences the presence of deletions affecting genes coding for NADH dehydrogenase subunits, reinforcing biochemical findings that indicate that complex I is not functional in T. cruzi. Moreover, the presence of complete minicircles into maxicircles of some strains lead us to think about the origin of minicircles. Finally, a careful phylogenetic analysis was conducted using coding regions of maxicircles from up to 29 strains, and 1108 single copy nuclear genes from all of the DTUs, clearly establishing that taxonomically T. cruzi is a complex of species composed by group 1 that contains clades A (TcI), B (TcIII) and D (TcIV), and group 2 (1 and 2 do not coincide with groups I and II described decades ago) containing clade C (TcII), being all hybrid strains of the BC type. Three variants of maxicircles exist in T. cruzi: a, b and c, in correspondence with clades A, B, and C from mitochondrial phylogenies. While A and C carry maxicircles a and c respectively, both clades B and D carry b maxicircle variant; hybrid strains also carry the b- variant. We then propose a new nomenclature that is self-descriptive and makes use of both the phylogenetic relationships and the maxicircle variants present in T. cruzi.
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Affiliation(s)
- Luisa Berná
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Sección Biomatemática—Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Greif
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Sebastián Pita
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Sección Genética, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Paula Faral-Tello
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Florencia Díaz-Viraqué
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Gustavo Adolfo Vallejo
- Laboratorio de investigaciones en Parasitología Tropical (LIPT), Facultad de Ciencias, Universidad del Tolima, Tolima, Colombia
| | - Fernando Alvarez-Valin
- Sección Biomatemática—Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Carlos Robello
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail:
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The complete mitochondrial genome of capillariid nematodes (Eucoleus annulatus): A novel gene arrangement and phylogenetic implications. Vet Parasitol 2021; 296:109476. [PMID: 34089993 DOI: 10.1016/j.vetpar.2021.109476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/28/2021] [Accepted: 05/24/2021] [Indexed: 11/20/2022]
Abstract
Capillariid nematode is a group of endoparasites of vertebrates with a complex taxonomy, causing significant economic losses to poultry industry. The taxonomic status of the genus Eucoleus remained controversial for several decades. Mitochondrial (mt) DNA provides useful genetic markers for accurate identification of species, but complete mt genome sequences have been lacking for any Capillariid nematodes. In the present study, we decoded the complete mt genome of E. annulatus and examined its phylogenetic relationship with selected members of the class Enoplea nematodes. The circular mt genome of E. annulatus was 14,118 bp, encoded 37 genes with a single non-coding region and showed substantial gene rearrangements (especially tRNA genes) compared to other nematodes studied to date. The complete mt genome of E. annulatus showed a clear A + T bias in nucleotide composition. The number of A (5404) was approximately equal to T (5405) and the GC-skew was negative on average (-0.073). Phylogenetic analyses based on 18S rDNA placed Eucoleus spp. well apart from each other and supported the proposal that Eucoleus and Capillaria are two distinct genera. Similarly, Bayesian inference (BI) and Maximum likelihood (ML) phylogenies based on mtDNA sequences revealed that the family Capillariidae is more closely related to the family Trichuridae than to the family Trichinellidae. This is the first report of the complete mt genome of capillariid nematodes, and it will provide additional genetic markers for studying the molecular epidemiology, population genetics and systematics of capillariid nematodes and should have implications for the molecular diagnosis, prevention, and control of capillariosis in animals.
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Gonzalez BC, Martínez A, Worsaae K, Osborn KJ. Morphological convergence and adaptation in cave and pelagic scale worms (Polynoidae, Annelida). Sci Rep 2021; 11:10718. [PMID: 34021174 PMCID: PMC8139957 DOI: 10.1038/s41598-021-89459-y] [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: 01/29/2021] [Accepted: 04/27/2021] [Indexed: 02/07/2023] Open
Abstract
Across Annelida, accessing the water column drives morphological and lifestyle modifications-yet in the primarily "benthic" scale worms, the ecological significance of swimming has largely been ignored. We investigated genetic, morphological and behavioural adaptations associated with swimming across Polynoidae, using mitogenomics and comparative methods. Mitochondrial genomes from cave and pelagic polynoids were highly similar, with non-significant rearrangements only present in cave Gesiella. Gene orders of the new mitogenomes were highly similar to shallow water species, suggestive of an underlying polynoid ground pattern. Being the first phylogenetic analyses to include the holopelagic Drieschia, we recovered this species nested among shallow water terminals, suggesting a shallow water ancestry. Based on these results, our phylogenetic reconstructions showed that swimming evolved independently three times in Polynoidae, involving convergent adaptations in morphology and motility patterns across the deep sea (Branchipolynoe), midwater (Drieschia) and anchialine caves (Pelagomacellicephala and Gesiella). Phylogenetic generalized least-squares (PGLS) analyses showed that holopelagic and anchialine cave species exhibit hypertrophy of the dorsal cirri, yet, these morphological modifications are achieved along different evolutionary pathways, i.e., elongation of the cirrophore versus style. Together, these findings suggest that a water column lifestyle elicits similar morphological adaptations, favouring bodies designed for drifting and sensing.
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Affiliation(s)
- Brett C Gonzalez
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, P.O. Box 37012, Washington, DC, USA.
| | - Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Largo Tonolli, 50, Pallanza, Italy
| | - Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, Copenhagen Ø, Denmark
| | - Karen J Osborn
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, P.O. Box 37012, Washington, DC, USA
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, USA
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iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC. PLoS One 2020; 15:e0228479. [PMID: 32413030 PMCID: PMC7228126 DOI: 10.1371/journal.pone.0228479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/01/2020] [Indexed: 11/19/2022] Open
Abstract
Terminator is a DNA sequence that gives the RNA polymerase the transcriptional termination signal. Identifying terminators correctly can optimize the genome annotation, more importantly, it has considerable application value in disease diagnosis and therapies. However, accurate prediction methods are deficient and in urgent need. Therefore, we proposed a prediction method "iterb-PPse" for terminators by incorporating 47 nucleotide properties into PseKNC-Ⅰ and PseKNC-Ⅱ and utilizing Extreme Gradient Boosting to predict terminators based on Escherichia coli and Bacillus subtilis. Combing with the preceding methods, we employed three new feature extraction methods K-pwm, Base-content, Nucleotidepro to formulate raw samples. The two-step method was applied to select features. When identifying terminators based on optimized features, we compared five single models as well as 16 ensemble models. As a result, the accuracy of our method on benchmark dataset achieved 99.88%, higher than the existing state-of-the-art predictor iTerm-PseKNC in 100 times five-fold cross-validation test. Its prediction accuracy for two independent datasets reached 94.24% and 99.45% respectively. For the convenience of users, we developed a software on the basis of "iterb-PPse" with the same name. The open software and source code of "iterb-PPse" are available at https://github.com/Sarahyouzi/iterb-PPse.
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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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The chloroplast genome sequence of the green macroalga Caulerpa okamurae (Ulvophyceae, Chlorophyta): Its structural features, organization and phylogenetic analysis. Mar Genomics 2020; 53:100752. [PMID: 32014385 DOI: 10.1016/j.margen.2020.100752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 12/05/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022]
Abstract
To clarify evolutionary characteristics, phylogenetic relationships as well as species identification of C. okamurae, we determined the cpDNA sequence of Caulerpa okamurae using de novo sequencing in the present study. The cpDNA of C. okamurae was 148,274 bp in length, and it lacked the inverted repeat commonly found in vascular green plants. The cpDNA of C. okamurae was highly compact with a gene density of 71.7%. Moreover, it was an AT-rich genome (65.5%) consisting 76 protein-coding genes (PCGs), 27 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 32 putative open reading frames (ORFs) and six introns. Additionally, the six introns were annotated in six genes as follows: psbA, rpoB, ftsH, psbD, atpF and cysA. The overall base composition of its cpDNA was 65.46% for AT. A total of 56 genes were encoded on the light strand, while all the other 50 chloroplast genes were encoded on the heavy strand. All of the PCGs had ATG as their start codon and employed TAA, TGA or TAG as their termination codon. Phylogenetic analyses suggested that the complete cpDNA sequence of C. okamurae fell in the Chlorophyta, Ulvophyceae, Bryopsidales, and Caulerpaceae and more resembled the cpDNAs of C. racemosa, C. cliftonii voucher and Tydemania expeditionis. Taken together, our data offered useful information for the studies of C.okamurae on evolutionary characteristics, phylogenetic relationships as well as species identification.
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Xiao L, Zhang S, Long C, Guo Q, Xu J, Dai X, Wang J. Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications. Genes (Basel) 2019; 10:E992. [PMID: 31805706 PMCID: PMC6947639 DOI: 10.3390/genes10120992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/16/2022] Open
Abstract
A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and -0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.
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Affiliation(s)
- Lifang Xiao
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Shengdi Zhang
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Chengpeng Long
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Qingyun Guo
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Jiasheng Xu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Jianguo Wang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
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Ding L, Zhou Q, Sun Y, Feoktistova NY, Liao J. Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae). Genomics 2019; 112:1716-1725. [PMID: 31669701 DOI: 10.1016/j.ygeno.2019.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 01/30/2023]
Abstract
Both Cricetus cricetus and Phodopus sungorus mitochondrial genomes (mitogenomes) were sequenced and elaborated for the first time in the present study. Their mitogenomes contained 37 genes and showed typical characteristics of the vertebrate mitogenome. Comparative analysis of 10 cricetine mitogenomes indicated that they shared similar characteristics with those of other cricetines in terms of genes arrangement, nucleotide composition, codon usage, tRNA structure, nucleotide skew and the origin of replication of light strand. Phylogenetic relationship of the subfamily Cricetinae was reconstructed using mitogenomes data with the methods of Bayesian Inference and Maximum Likelihood. Phylogenetic analysis indicated that Cricetulus kamensis was at basal position and phylogenetically distant from all other Cricetulus species but had a close relationship with the group of Phodopus, and supported that the genus Urocricetus deserved as a separate genus rank. The phylogenetic status of Tscherskia triton represented a separate clade corresponding to a diversified cricetine lineage (Cricetulus, Allocricetulus, and Cricetus).
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Affiliation(s)
- Li Ding
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
| | - Quan Zhou
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Yuanhai Sun
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Natalia Yu Feoktistova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Jicheng Liao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
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Tang Y, Zheng X, Zhong H, Li Q. Phylogenetics and comparative analysis of the mitochondrial genomes of three violet‐ringed octopuses. ZOOL SCR 2019. [DOI: 10.1111/zsc.12359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yan Tang
- Key Laboratory of Mariculture Ocean University of China Qingdao China
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture Ocean University of China Qingdao China
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
| | - Hong Zhong
- Shenzhen BGTX Foods Co., Ltd. Shenzhen China
| | - Qi Li
- Key Laboratory of Mariculture Ocean University of China Qingdao China
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23
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Xia X. Is there a mutation gradient along vertebrate mitochondrial genome mediated by genome replication? Mitochondrion 2019; 46:30-40. [DOI: 10.1016/j.mito.2018.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/07/2018] [Accepted: 06/13/2018] [Indexed: 11/29/2022]
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Gao B, Peng C, Chen Q, Zhang J, Shi Q. Mitochondrial genome sequencing of a vermivorous cone snail Conus quercinus supports the correlative analysis between phylogenetic relationships and dietary types of Conus species. PLoS One 2018; 13:e0193053. [PMID: 30059499 PMCID: PMC6066214 DOI: 10.1371/journal.pone.0193053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/02/2018] [Indexed: 12/15/2022] Open
Abstract
Complete mitochondrial genome (mitogenome) sequence of a worm-hunting cone snail, Conus quercinus, was reported in this study. Its mitogenome, the longest one (16,460 bp) among reported Conus specie, is composed of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one D-loop region. The mitochondrial gene arrangement is highly-conserved and identical to other reported. However, the D-loop region of C. quercinus is the longest (943 bp) with the higher A+T content (71.3%) and a long AT tandem repeat stretch (68 bp). Subsequent phylogenetic analysis demonstrated that three different dietary types (vermivorous, molluscivorous and piscivorous) of cone snails are clustered separately, suggesting that the phylogenetics of cone snails is related to their dietary types. In conclusion, our current work improves our understanding of the mitogenomic structure and evolutionary status of the vermivorous C. quercinus, which support the putative hypothesis that the Conus ancestor was vermivorous.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou, China
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Qin Chen
- School of Agricultural and Forestry Science and Technology, Hainan Radio & TV University, Haikou, China
| | - Junqing Zhang
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
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Zheng F, Liu H, Jiang M, Xu Z, Wang Z, Wang C, Du F, Shen Z, Wang B. The complete mitochondrial genome of the Caulerpa lentillifera (Ulvophyceae, Chlorophyta): Sequence, genome content, organization structure and phylogenetic consideration. Gene 2018; 673:225-238. [PMID: 29933020 DOI: 10.1016/j.gene.2018.06.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 04/21/2018] [Accepted: 06/15/2018] [Indexed: 11/19/2022]
Abstract
The complete mitochondrial genome is greatly important for studies on genetic structure and phylogenetic relationship at various taxonomic levels. To obtain information about the evolutionary trends of mtDNA in the Ulvophyceae and also to gain insights into the phylogenetic relationships between ulvophytes and other chlorophytes, we determined the mtDNA sequence of Caulerpa lentillifera (sea grape) using de novo mitochondrial genome sequencing. The complete genomic DNA of C. lentillifera was circular and 209,034 bp in length, and it was the largest green-algal mitochondrial genome sequenced to date, with a low gene density of 65.2%, which is reminiscent of the "expanded" pattern of evolution exhibited by embryophyte mtDNAs. The C. lentillifera mtDNA consisted of a typical set of 17 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 42 putative open reading frames (ORFs) and 29 introns, which had homologs in green-algal mtDNAs displaying an "ancestral" or a "reduced-derived" pattern of evolution. The overall base composition of its mitochondrial genome was 24.19% for A, 24.94% for T, 25.80% for G, 25.07% for C and 50.87% for GC. The mitochondrial genome of C. lentillifera was characterized by numerous small intergenic regions and introns, which was clearly different from other green algae. With the exception of the NADH dehydrogenase subunit 6 (ND6), ND1, ATP and three tRNA genes (tRNA-His, tRNA-Thr and tRNA-Ala), all other mitochondrial genes were encoded on the heavy strand. All of the PCGs had ATG as their start codon and employed TAA, TGA or TAG as their termination codon. To gain insights into the evolutionary trends of mtDNA in the Ulvophyceae, we inferred the complete mtDNA sequence of C. lentillifera, an ulvophyte belonging to a distinct, early-diverging lineage. Taken together, our data offered useful information for the studies on phylogenetic hypotheses and phylogenetic relationships of C. lentillifera within the Chlorophyta.
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Affiliation(s)
- Fengrong Zheng
- First Institute of Oceanography SOA, Qingdao 266061, China; Key laboratory of Marine Bioactive substance SOA, Qingdao 266061, China
| | - Hongzhan Liu
- Marine College of Shandong University, Weihai 264209, China.
| | - Meijing Jiang
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Zongjun Xu
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Zongxing Wang
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Claire Wang
- Qingdao Haiputao Organic Green Algae Research and Development Breed CO., LTD, Qingdao 266000, China
| | - Fei Du
- Qingdao Haiputao Organic Green Algae Research and Development Breed CO., LTD, Qingdao 266000, China
| | - Zhen Shen
- First Institute of Oceanography SOA, Qingdao 266061, China; Key laboratory of Marine Bioactive substance SOA, Qingdao 266061, China
| | - Bo Wang
- First Institute of Oceanography SOA, Qingdao 266061, China.
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Kolora SR, Faria R, Weigert A, Schaffer S, Grimm A, Henle K, Sahyoun AH, Stadler PF, Nowick K, Bleidorn C, Schlegel M. The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:116-118. [PMID: 26709540 DOI: 10.3109/19401736.2015.1111349] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We sequenced the mitochondrial genome of the Western green lizard (Lacerta bilineata) using Illumina technology and additional Sanger sequencing. The assembled 17 086 bp mitogenome had a GC content of 40.32% and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region (CR), with a gene order identical to the chordate consensus. In addition, we re-sequenced the mitogenome of the closely related Eastern green lizard L. viridis using the same techniques as for L. bilineata. The mitogenomes of L. bilineata and L. viridis showed a sequence identity of 94.4% and 99.9%, respectively, relative to the previously published L. viridis mitogenome. The phylogenetic reconstruction based on 17 Lacertinae mitogenomes using Anolis carolinensis as the outgroup supported L. bilineata and its sister species L. viridis as distinct lineages.
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Affiliation(s)
- Sree Rohit Kolora
- a German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig , Germany.,b Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig , Leipzig , Germany.,c Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig , Leipzig , Germany
| | - Rui Faria
- d CIBIO, Centro De Investigacßao Em Biodiversidade E Recursos Geneticos, InBio, Laboratorio Associado, Universidade Do Porto , Campus Agrário De Vairão , Vairão , Portugal.,e Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC) , PRBB, Barcelona , Catalonia , Spain
| | - Anne Weigert
- b Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig , Leipzig , Germany.,f Max Planck Institute for Evolutionary Anthropology , Deutscher Platz 6 , Leipzig , Germany
| | - Stefan Schaffer
- b Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig , Leipzig , Germany
| | - Annegret Grimm
- g Department of Conservation Biology , UFZ - Helmholtz Center for Environmental Research , Leipzig , Germany
| | - Klaus Henle
- g Department of Conservation Biology , UFZ - Helmholtz Center for Environmental Research , Leipzig , Germany
| | - Abdullah H Sahyoun
- c Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig , Leipzig , Germany
| | - Peter F Stadler
- c Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig , Leipzig , Germany.,h Paul-Flechsig-Institute for Brain Research, University of Leipzig , Leipzig , Germany.,i Max-Planck-Institute for Mathematics in the Sciences , Leipzig , Germany.,j Fraunhofer Institut Für Zelltherapie Und Immunologie , Leipzig , Germany.,k Department of Theoretical Chemistry , University of Vienna , Wien , Austria.,l Center for non-Coding RNA In Technology and Health, University of Copenhagen , Frederiksberg , Denmark.,m Santa Fe Institute , Santa Fe , NM , USA , and
| | - Katja Nowick
- c Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig , Leipzig , Germany.,h Paul-Flechsig-Institute for Brain Research, University of Leipzig , Leipzig , Germany.,n TFome Research Group, Bioinformatics Group, Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig , Leipzig , Germany
| | - Christoph Bleidorn
- a German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig , Germany.,b Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig , Leipzig , Germany
| | - Martin Schlegel
- a German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig , Germany.,b Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig , Leipzig , Germany
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Complete mitochondrial genome of Anadara vellicata (Bivalvia: Arcidae): A unique gene order and large atypical non-coding region. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 16:73-82. [DOI: 10.1016/j.cbd.2015.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/04/2015] [Accepted: 08/17/2015] [Indexed: 11/19/2022]
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Aguado MT, Glasby CJ, Schroeder PC, Weigert A, Bleidorn C. The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata. Sci Rep 2015; 5:12072. [PMID: 26183383 PMCID: PMC4505326 DOI: 10.1038/srep12072] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/12/2015] [Indexed: 12/13/2022] Open
Abstract
Ramisyllis multicaudata is a member of Syllidae (Annelida, Errantia, Phyllodocida) with a remarkable branching body plan. Using a next-generation sequencing approach, the complete mitochondrial genomes of R. multicaudata and Trypanobia sp. are sequenced and analysed, representing the first ones from Syllidae. The gene order in these two syllids does not follow the order proposed as the putative ground pattern in Errantia. The phylogenetic relationships of R. multicaudata are discerned using a phylogenetic approach with the nuclear 18S and the mitochondrial 16S and cox1 genes. Ramisyllis multicaudata is the sister group of a clade containing Trypanobia species. Both genera, Ramisyllis and Trypanobia, together with Parahaplosyllis, Trypanosyllis, Eurysyllis, and Xenosyllis are located in a long branched clade. The long branches are explained by an accelerated mutational rate in the 18S rRNA gene. Using a phylogenetic backbone, we propose a scenario in which the postembryonic addition of segments that occurs in most syllids, their huge diversity of reproductive modes, and their ability to regenerate lost parts, in combination, have provided an evolutionary basis to develop a new branching body pattern as realised in Ramisyllis.
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Affiliation(s)
- M. Teresa Aguado
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Christopher J. Glasby
- Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin, N.T., Australia
| | - Paul C. Schroeder
- School of Biological Sciences, Washington State University, Pullman, Washington 99163-4236, USA
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Christoph Bleidorn
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
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Fonseca MM, Harris DJ, Posada D. The inversion of the Control Region in three mitogenomes provides further evidence for an asymmetric model of vertebrate mtDNA replication. PLoS One 2014; 9:e106654. [PMID: 25268704 PMCID: PMC4182315 DOI: 10.1371/journal.pone.0106654] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 08/04/2014] [Indexed: 11/29/2022] Open
Abstract
Mitochondrial genomes are known to have a strong strand-specific compositional bias that is more pronounced at fourfold redundant sites of mtDNA protein-coding genes. This observation suggests that strand asymmetries, to a large extent, are caused by mutational asymmetric mechanisms. In vertebrate mitogenomes, replication and not transcription seems to play a major role in shaping compositional bias. Hence, one can better understand how mtDNA is replicated – a debated issue – through a detailed picture of mitochondrial genome evolution. Here, we analyzed the compositional bias (AT and GC skews) in protein-coding genes of almost 2,500 complete vertebrate mitogenomes. We were able to identify three fish mitogenomes with inverted AT/GC skew coupled with an inversion of the Control Region. These findings suggest that the vertebrate mitochondrial replication mechanism is asymmetric and may invert its polarity, with the leading-strand becoming the lagging-strand and vice-versa, without compromising mtDNA maintenance and expression. The inversion of the strand-specific compositional bias through the inversion of the Control Region is in agreement with the strand-displacement model but it is also compatible with the RITOLS model of mtDNA replication.
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Affiliation(s)
- Miguel M. Fonseca
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- * E-mail:
| | - D. James Harris
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
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