1
|
Jakovlić I, Ye T, Zou H, Zhu F, Shi Y, Ma Y, Wang GT, Li WX, Zhang D. Drivers of interlineage variability in mitogenomic evolutionary rates in Platyhelminthes. Heredity (Edinb) 2024:10.1038/s41437-024-00712-2. [PMID: 39095653 DOI: 10.1038/s41437-024-00712-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
Studies of forces driving interlineage variability in the evolutionary rates (both sequence and architecture) of mitochondrial genomes often produce contradictory results. Flatworms (Platyhelminthes) exhibit the fastest-evolving mitogenomic sequences among all bilaterian phyla. To test the effects of multiple factors previously associated with different aspects of mitogenomic evolution, we used mitogenomes of 223 flatworm species, phylogenetic multilevel regression models, and causal inference. Thermic host environment (endothermic vs. ectothermic) had nonsignificant impacts on both sequence evolution and mitogenomic size. Mitogenomic gene order rearrangements (GORR) were mostly positively correlated with mitogenomic size (R2 ≈ 20-30%). Longevity was not (negatively) correlated with sequence evolution in flatworms. The predominantly free-living "turbellaria" exhibited much shorter branches and faster-evolving mitogenomic architecture than parasitic Neodermata. As a result, "parasitism" had a strong explanatory power on the branch length variability (>90%), and there was a negative correlation between GORR and branch length. However, the stem branch of Neodermata comprised 63.6% of the total average branch length. This evolutionary period was also marked by a high rate of gene order rearrangements in the ancestral Neodermata. We discuss how this period of rapid evolution deep in the evolutionary history may have decoupled sequence evolution rates from longevity and GORR, and overestimated the explanatory power of "parasitism". This study shows that impacts of variables often vary across lineages, and stresses the importance accounting for the episodic nature of evolutionary patterns in studies of mitogenomic evolution.
Collapse
Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Tong Ye
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, 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
| | - Fengyue Zhu
- National Agricultural Science Observing and Experimental Station of Chongqing, Chongqing, 401329, China
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, 430073, China
| | - Yuying Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yiwen Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, 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
| | - Wen-Xiang Li
- 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
| | - Dong Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, 850011, China.
| |
Collapse
|
2
|
Jiang C, Kang H, Zhou Y, Zhu W, Zhao X, Mohamed N, Li B. Selected Lark Mitochondrial Genomes Provide Insights into the Evolution of Second Control Region with Tandem Repeats in Alaudidae (Aves, Passeriformes). Life (Basel) 2024; 14:881. [PMID: 39063634 PMCID: PMC11278119 DOI: 10.3390/life14070881] [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: 05/22/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
The control region (CR) regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two CRs, and the second control region (CR2) may enhance replication and transcription; however, the CR2 in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from Alaudala cheleensis, Eremophila alpestris, Alauda razae, and Calandrella cinerea and reconstructed the phylogeny of Passerida. Through further comparative analysis among larks, we traced the evolutionary process of CR2. The mitochondrial gene orders were conserved in all published lark mitogenomes, with Cytb-trnT-CR1-trnP-ND6-trnE-remnant CR2 with tandem repeat-trnF-rrnS. Phylogenetic analysis revealed Alaudidae and Panuridae are sister groups at the base of Sylvioidea, and sporadic losses of CR2 may occur in their common ancestor. CR sequence and phylogeny analysis indicated CR2 tandem repeats were generated within CR2, originating in the ancestor of all larks, rather than inherited from CR1. The secondary structure comparison of tandem repeat units within and between species suggested slipped-strand mispairing and DNA turnover as suitable models for explaining the origin and evolution of these repeats. This study reveals the evolutionary process of the CR2 containing tandem repeat in Alaudidae, providing reference for understanding the evolutionary characteristics and dynamics of tandem repeats.
Collapse
Affiliation(s)
- Chuan Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Hui Kang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Yang Zhou
- BGI Research, Shenzhen 518083, China;
- BGI Research, Wuhan 430074, China
| | - Wenwen Zhu
- School of Life Sciences, Heilongjiang University, Harbin 150080, China;
| | - Xilong Zhao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Nassoro Mohamed
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Bo Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin 150040, China
| |
Collapse
|
3
|
Yang YX, Kang Y, Ge XY, Yuan SL, Li XY, Liu HY. A Mysterious Asian Firefly Genus, Oculogryphus Jeng, Engel & Yang (Coleoptera, Lampyridae): The First Complete Mitochondrial Genome and Its Phylogenetic Implications. INSECTS 2024; 15:464. [PMID: 39057197 PMCID: PMC11277304 DOI: 10.3390/insects15070464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024]
Abstract
The firefly genus Oculogryphus Jeng, Engel & Yang, 2007 is a rare-species group endemic to Asia. Since its establishment, its position has been controversial but never rigorously tested. To address this perplexing issue, we are the first to present the complete mitochondrial sequence of Oculogryphus, using the material of O. chenghoiyanae Yiu & Jeng, 2018 determined through a comprehensive morphological identification. Our analyses demonstrate that its mitogenome exhibits similar characteristics to that of Stenocladius, including a rearranged gene order between trnC and trnW, and a long intergenic spacer (702 bp) between the two rearranged genes, within which six remnants (29 bp) of trnW were identified. Further, we incorporated this sequence into phylogenetic analyses of Lampyridae based on different molecular markers and datasets using ML and BI analyses. The results consistently place Oculogryphus within the same clade as Stenocladius in all topologies, and the gene rearrangement is a synapomorphy for this clade. It suggests that Oculogryphus should be classified together with Stenocladius in the subfamily Ototretinae at the moment. This study provides molecular evidence confirming the close relationship between Oculogryphus and Stenocladius and discovers a new phylogenetic marker helpful in clarifying the monophyly of Ototretinae, which also sheds a new light on firefly evolution.
Collapse
Affiliation(s)
- Yu-Xia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China
| | - Ya Kang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
| | - Xue-Ying Ge
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
| | - Shuai-Long Yuan
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hao-Yu Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China
| |
Collapse
|
4
|
Cardoso DC, Baldez BCL, Pereira AH, Kalapothakis E, Rosse IC, Cristiano MP. De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes. Mol Genet Genomics 2024; 299:16. [PMID: 38411741 DOI: 10.1007/s00438-024-02099-5] [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: 05/30/2023] [Accepted: 12/10/2023] [Indexed: 02/28/2024]
Abstract
Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.
Collapse
Affiliation(s)
- Danon Clemes Cardoso
- Genetics and Evolution of Ants Research Group - GEF, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil.
| | - Brenda Carla Lima Baldez
- Programa de Pós-Graduação em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil
| | - Adriana Heloísa Pereira
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-010, Brazil
| | - Evanguedes Kalapothakis
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-010, Brazil
| | - Izinara Cruz Rosse
- Departamento de Farmácia, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | - Maykon Passos Cristiano
- Genetics and Evolution of Ants Research Group - GEF, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil
| |
Collapse
|
5
|
Meng X, Wang D, Pang Q, Wang H, Zhou H. Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22087. [PMID: 38288498 DOI: 10.1002/arch.22087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/20/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age-related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P123 and P4FD between the single and multiple-CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips.
Collapse
Affiliation(s)
| | - Dong Wang
- Qingdao Technical College, Qingdao, China
| | - Qiang Pang
- Qingdao Technical College, Qingdao, China
| | - Heng Wang
- Rizhao Agricultural Technology Service Center, Rizhao, China
| | - Hongxu Zhou
- Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Fiedler L, Bernt M, Middendorf M, Stadler PF. Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs. BMC Bioinformatics 2023; 24:235. [PMID: 37277700 DOI: 10.1186/s12859-023-05371-4] [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: 03/20/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Identifying the locations of gene breakpoints between species of different taxonomic groups can provide useful insights into the underlying evolutionary processes. Given the exact locations of their genes, the breakpoints can be computed without much effort. However, often, existing gene annotations are erroneous, or only nucleotide sequences are available. Especially in mitochondrial genomes, high variations in gene orders are usually accompanied by a high degree of sequence inconsistencies. This makes accurately locating breakpoints in mitogenomic nucleotide sequences a challenging task. RESULTS This contribution presents a novel method for detecting gene breakpoints in the nucleotide sequences of complete mitochondrial genomes, taking into account possible high substitution rates. The method is implemented in the software package DeBBI. DeBBI allows to analyze transposition- and inversion-based breakpoints independently and uses a parallel program design, allowing to make use of modern multi-processor systems. Extensive tests on synthetic data sets, covering a broad range of sequence dissimilarities and different numbers of introduced breakpoints, demonstrate DeBBI 's ability to produce accurate results. Case studies using species of various taxonomic groups further show DeBBI 's applicability to real-life data. While (some) multiple sequence alignment tools can also be used for the task at hand, we demonstrate that especially gene breaks between short, poorly conserved tRNA genes can be detected more frequently with the proposed approach. CONCLUSION The proposed method constructs a position-annotated de-Bruijn graph of the input sequences. Using a heuristic algorithm, this graph is searched for particular structures, called bulges, which may be associated with the breakpoint locations. Despite the large size of these structures, the algorithm only requires a small number of graph traversal steps.
Collapse
Affiliation(s)
- Lisa Fiedler
- Department of Computer Science, University Leipzig, Augustusplatz 10-11, 04109, Leipzig, Germany.
| | - Matthias Bernt
- Helmholtz Centre for Environmental Research -UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Martin Middendorf
- Department of Computer Science, University Leipzig, Augustusplatz 10-11, 04109, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04109, Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090, Vienna, Austria
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Ciudad Universitaria, 111321, Bogotá, D.C., Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA
| |
Collapse
|
8
|
Xu S, Li W, Liu Q, Wang Y, Li X, Duan X, He J, Song F. The mitochondrial genome of Binodoxys acalephae (Hymenoptera: Braconidae) with unique gene rearrangement and phylogenetic implications. Mol Biol Rep 2023; 50:2641-2649. [PMID: 36639523 PMCID: PMC10011326 DOI: 10.1007/s11033-022-08232-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023]
Abstract
BACKGROUND Species in the subfamily Aphidiinae from the Braconidae of Hymenoptera are endoparasitic wasps that exclusively utilize aphids as hosts. Some Aphidiinae species are widely used as biological agents. However, there were only one species with determined complete mitochondrial genome from this subfamily. METHODS AND RESULTS In this study, we sequenced and annotated the mitochondrial genome (mitogenome) of Binodoxys acalephae, which was 15,116 bp in size and contained 37 genes. The start codon of 13 protein-coding genes was ATN, and the complete stop codon TAA and TAG was widely assigned to 11 protein-coding genes. The lrRNA contains 43 stem-loop structures, and srRNA contains 25 stem-loop structures. Translocation and inversion of tRNA genes was found to be dominant in B. acalephae. In contrast to Aphidius gifuensis from the same subfamily Aphidiinae, inverted tRNALeu1 was translocated to the gene cluster between tRNALeu2 and COX2, and the control region between tRNAIle and tRNAMet was deleted in the mitogenome of B. acalephae. Within Braconidae, gene clusters tRNATrp-tRNACys-tRNATyr and CR-tRNAIle-tRNAGln-tRNAMet were hotspots for gene rearrangement. Phylogenetic analysis showed that both Bayesian and maximum-likelihood methods recovered the monophyly of Aphidiinae and suggested that Aphidiinae formed sister clades with the remaining subfamilies. The phylogenetic analyses of nine subfamilies supported the monophyly of Cyclostomes and Noncyclostomes in Braconidae. CONCLUSION The arrangement of mitochondrial genes and the phylogenetic relationships among nine Braconidae subfamilies were constructed better to understand the diversity and evolution of Aphidiinae mitogenomes.
Collapse
Affiliation(s)
- Shiwen Xu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Weiwei Li
- Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Yunnan Agricultural University, 650201 Kunming, China
| | - Qiannan Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Yunming Wang
- Yuxi Branch, Yunnan Tobacco Company, 653100 Yuxi, China
| | - Xiaoling Li
- Yuxi Branch, Yunnan Tobacco Company, 653100 Yuxi, China
| | - Xiaoqian Duan
- Yuxi Branch, Yunnan Tobacco Company, 653100 Yuxi, China
| | - Jia He
- Institute of Plant Protection, Academy of Ningxia Agriculture and Forestry Science, 750002 Yinchuan, China
- Ningxia Key Laboratory of Plant Disease and Pest Control, 750002 Yinchuan, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| |
Collapse
|
9
|
Yang T, Liu Y, Ning Z. Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae. Animals (Basel) 2023; 13:ani13030362. [PMID: 36766251 PMCID: PMC9913227 DOI: 10.3390/ani13030362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The family Ophichthidae has the largest number and the most various species (about 359 valid species) in the order Anguilliformes worldwide. Both morphological and molecular characteristics have been used to assess their taxonomic status. However, due to the ambiguous morphological features, molecular data such as mitochondrial DNA sequences have been implemented for the correct identification and classification of these fishes. In this study, the gene arrangement and structure characteristics of two Ophichthidae mitochondrial genomes were investigated for the first time. The total mitogenome lengths of O. evermanni and O. erabo were 17,759 bp and 17,856 bp, respectively. Comparing with the ancestral mitochondrial gene order, the irregular gene rearrangement happened between ND6 and tRNA-Pro (P) genes with another similar control region emerging between tRNA-Thr (T) and ND6 genes, which could be explained by the tandem duplication and random loss (TDRL) model appropriately. ML phylogenetic tree demonstrated that the family Ophichthidae was monophyletic origin, but genus Ophichthus might be polyphyletic because of the confused cluster relationships among different species.
Collapse
|
10
|
The complete mitochondrial genome and novel gene arrangement in Nesodiprion zhejiangensis Zhou & Xiao (Hymenoptera: Diprionidae). Funct Integr Genomics 2023; 23:41. [PMID: 36650401 DOI: 10.1007/s10142-022-00959-0] [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: 11/19/2022] [Revised: 12/29/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023]
Abstract
The complete mitochondrial genome (mitogenome) of the sawfly, Nesodiprion zhejiangensis Zhou & Xiao, was sequenced, assembled, and deposited in GenBank (Accession Number: OM501121). The 15,660 bp N. zhejiangensis mitogenome encodes for 2 ribosomal RNAs (rrnL and rrnS), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and an AT-rich region of 450 bp in length. The nucleotide composition is biased toward adenine and thymine (A + T = 81.8%). Each PCG is initiated by an ATN codon, except for cox2, which starts with a TTG. Of 13 PCGs, 9 have a TAA termination codon, while the remainder terminate with a TAG or a single T. All tRNAs have the classic cloverleaf structure, except for the dihydrouridine (DHU) arm of tRNAval, which forms a simple loop. There are 49 helices belonging to 6 domains in rrnL and 30 helices belonging to 4 domains in rrnS. In comparison to the ancestral architecture, N. zhejiangensis has the most rearranged mitogenome in Symphyta, in which rearrangement events of local inversion and transposition are identified in three gene clusters. Specifically, the main hotspot of gene rearrangement occurred between rrnS and trnY, and rearranged from rrnS-(AT-rich region)-I-Q-M-nd2-W-C-Y to rrnS-Q-W-C-nd2-I-M-(AT-rich region)-Y, involving a local inversion event of a large gene cluster and transposition events of some tRNAs. Transposition of trnA and trnR (rearranged from A-R to R-A) was observed at the nd3-nd5 gene junction while shuffling of trnP and trnT (rearranged from T-P to P-T) occurred at the nd4l-nd6 gene junction. While illegitimate inter-mtDNA recombination might explain the opposite orientations of transcription between rrnS and trnY, transposition events of tRNA in some gene blocks can be accounted for by the tandem duplication/random loss (TDRL) model. Our phylogenetic analysis suggests that N. zhejiangensis is closely related to congeneric species N. biremis and N. japonicus, which together form a sister lineage with the European pine sawfly, Neodiprion sertifer.
Collapse
|
11
|
Xu S, Duan Y, Ma L, Song F, Tian L, Cai W, Li H. Full-Length Transcriptome Profiling of Coridius chinensis Mitochondrial Genome Reveals the Transcription of Genes with Ancestral Arrangement in Insects. Genes (Basel) 2023; 14:225. [PMID: 36672965 PMCID: PMC9859431 DOI: 10.3390/genes14010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Coridius chinensis (Hemiptera: Dinidoridae) is a medicinal insect. Its mitochondrial gene arrangement is consistent with that of Drosophila melanogaster and Erthesina fullo, the two insects with well-studied mitochondrial transcription. To investigate whether the structural consistency of mitochondrial genes leads to similarities in transcription and post-transcriptional processing, we improved the gene annotation and constructed a quantitative transcription map for the C. chinensis mitochondrial genome (mitogenome) using full-length transcriptome sequencing. The size of this mitogenome was 16,214 bp and the proposed model of mitochondrial transcription was similar to that of Drosophila. Both strands were nearly entirely transcribed except for the antisense genes downstream of trnS2 on N strand. The expression of cytochrome c subunit genes is higher than that of NADH-dehydrogenase subunit genes. The post-transcriptional cleavage process followed the "tRNA punctuation" model, and both the "reverse cleavage" model in Drosophila and "forward cleavage" model in E. fullo were found in C. chinensis. In addition, we found that long non-coding RNAs from the control region contained tandem repeats. Polyadenylation was performed after CCA triplet at the 3' end of tRNA. The isoform diversity of lrRNA was identified. Our study sheds light on the transcriptional regulation and RNA processing of insect mitogenomes with the putative ancestral gene arrangement.
Collapse
Affiliation(s)
| | | | | | | | | | | | - 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
| |
Collapse
|
12
|
Park D, Kim IH, Park IK, Grajal-Puche A, Park J. A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA. Zookeys 2022; 1129:21-35. [PMID: 36761844 PMCID: PMC9836557 DOI: 10.3897/zookeys.1129.82981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/16/2022] [Indexed: 11/12/2022] Open
Abstract
Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.
Collapse
Affiliation(s)
- Daesik Park
- Kangwon National University, Chuncheon, Republic of KoreaKangwon National UniversityChuncheonRepublic of Korea
| | - Il-Hun Kim
- National Marine Biodiversity Institute of Korea, Seochun, Republic of KoreaNational Marine Biodiversity Institute of KoreaSeochunRepublic of Korea
| | - Il-Kook Park
- Kangwon National University, Chuncheon, Republic of KoreaKangwon National UniversityChuncheonRepublic of Korea
| | - Alejandro Grajal-Puche
- Northern Arizona University, Flagstaff, Arizona, USANorthern Arizona UniversityFlagstaffUnited States of America
| | - Jaejin Park
- Kangwon National University, Chuncheon, Republic of KoreaKangwon National UniversityChuncheonRepublic of Korea
| |
Collapse
|
13
|
Wang W, Wang H, Huang H, Zhao Y, Zhou Z. Mitochondrial genomes of 10 Mantidae species and their phylogenetic implications. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21874. [PMID: 35112399 DOI: 10.1002/arch.21874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/20/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
This article aims to present a phylogenetic evaluation of Mantidae based on a mitochondrial genome (mitogenome) data set. The mitogenome of 10 Mantidae species were sequenced using next-generation sequencing. The length of nine the complete mitogenomes ranged from 15,371 bp in Tenodera aridifolia to 16,063 bp in Hierodula longa. Mantidae mitogenomes have 37 genes and control region with two exceptions: five trnR copies in Statilia maculata, and H. zhangi was incomplete missing trnI, trnQ, trnM and a portion of the control region. There was a large noncoding region (LNC) between trnM and nad2 in H. chinensis, H. longa, H. maculata and Titanodula sp. Most of protein-coding genes (PCGs) used the typical start ATN codon and TAA/TAG stop codons. All tRNAs fold into the typical clover-leaf secondary structure except trnS1 which lacks a dihydrouracil (DHU) arm. Nucleotide diversity and Ka/Ks analysis of 13 PCGs showed that atp8 had the highest variability and fastest evolutionary rate. Phylogenetic relationships among 42 Mantidae species were reconstructed using the 13 PCGs and two rRNA genes using Bayesian Inference (BI) and Maximum Likelihood (ML) methods. Of the seven mantid subfamilies included in this analysis, only four had multiple exemplars, and of those only Mantinae and Vatinae formed monophyletic groups in BI and ML trees. Consistent with previous studies, the monophyly of the Hierudulinae and Tenoderinae were not been supported. The present results imply that it is necessary to combine nuclear molecular markers and external characteristic to understand the phylogenetic relationships within Mantidae.
Collapse
Affiliation(s)
- Wenjing Wang
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Hui Wang
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Huimin Huang
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Yizheng Zhao
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Zhijun Zhou
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, China
- The Key Laboratory of Zoological Systematics and Application of Hebei Province, Hebei University, Baoding, China
| |
Collapse
|
14
|
Inverted base composition skews and discontinuous mitochondrial genome architecture evolution in the Enoplea (Nematoda). BMC Genomics 2022; 23:376. [PMID: 35585506 PMCID: PMC9115964 DOI: 10.1186/s12864-022-08607-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/25/2022] [Indexed: 11/26/2022] Open
Abstract
Background Within the class Enoplea, the earliest-branching lineages in the phylum Nematoda, the relatively highly conserved ancestral mitochondrial architecture of Trichinellida is in stark contrast to the rapidly evolving architecture of Dorylaimida and Mermithida. To better understand the evolution of mitogenomic architecture in this lineage, we sequenced the mitogenome of a fish parasite Pseudocapillaria tomentosa (Trichinellida: Capillariidae) and compared it to all available enoplean mitogenomes. Results P. tomentosa exhibited highly reduced noncoding regions (the largest was 98 bp), and a unique base composition among the Enoplea. We attributed the latter to the inverted GC skew (0.08) in comparison to the ancestral skew in Trichinellidae (-0.43 to -0.37). Capillariidae, Trichuridae and Longidoridae (Dorylaimida) generally exhibited low negative or low positive skews (-0.1 to 0.1), whereas Mermithidae exhibited fully inverted low skews (0 to 0.05). This is indicative of inversions in the strand replication order or otherwise disrupted replication mechanism in the lineages with reduced/inverted skews. Among the Trichinellida, Trichinellidae and Trichuridae have almost perfectly conserved architecture, whereas Capillariidae exhibit multiple rearrangements of tRNA genes. In contrast, Mermithidae (Mermithida) and Longidoridae (Dorylaimida) exhibit almost no similarity to the ancestral architecture. Conclusions Longidoridae exhibited more rearranged mitogenomic architecture than the hypervariable Mermithidae. Similar to the Chromadorea, the evolution of mitochondrial architecture in enoplean nematodes exhibits a strong discontinuity: lineages possessing a mostly conserved architecture over tens of millions of years are interspersed with lineages exhibiting architectural hypervariability. As Longidoridae also have some of the smallest metazoan mitochondrial genomes, they contradict the prediction that compact mitogenomes should be structurally stable. Lineages exhibiting inverted skews appear to represent the intermediate phase between the Trichinellidae (ancestral) and fully derived skews in Chromadorean mitogenomes (GC skews = 0.18 to 0.64). Multiple lines of evidence (CAT-GTR analysis in our study, a majority of previous mitogenomic results, and skew disruption scenarios) support the Dorylaimia split into two sister-clades: Dorylaimida + Mermithida and Trichinellida. However, skew inversions produce strong base composition biases, which can hamper phylogenetic and other evolutionary studies, so enoplean mitogenomes have to be used with utmost care in evolutionary studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08607-4.
Collapse
|
15
|
Wang C, Lai T, Ye P, Yan Y, Feutry P, He B, Huang Z, Zhu T, Wang J, Chen X. Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae. Gene 2022; 820:146232. [PMID: 35114282 DOI: 10.1016/j.gene.2022.146232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/22/2021] [Accepted: 01/18/2022] [Indexed: 01/08/2023]
Abstract
In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.
Collapse
Affiliation(s)
- Chen Wang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China
| | - Tinghe Lai
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Peiyuan Ye
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yunrong Yan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524000, China
| | - Pierre Feutry
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania 7000, Australia
| | - Binyuan He
- Guangxi Academy of Oceanography, Nanning 530000, China
| | | | - Ting Zhu
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiao Chen
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; Guangxi Mangrove Research Center, Beihai 536000, China.
| |
Collapse
|
16
|
Liu D, Basso A, Babbucci M, Patarnello T, Negrisolo E. Macrostructural Evolution of the Mitogenome of Butterflies (Lepidoptera, Papilionoidea). INSECTS 2022; 13:insects13040358. [PMID: 35447800 PMCID: PMC9031222 DOI: 10.3390/insects13040358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Papilionoidea is a superfamily of Lepidoptera encompassing about 19,000 species. In the present work, we study the evolution of the structure of the mitogenome of these lepidopterans. The mechanisms generating the eight arrangements known for Papilionoidea were investigated analysing the movements of different mitochondrial genes. Five newly sequenced/assembled mitogenomes were included in our analysis involving more than 600 genomes. We provide new findings that help to understand the evolution of the gene orders MIQGO, IMQGO, 2S1GO, ES1GO and S1NGO in different butterflies. We demonstrate that the evolution of the 2S1GO in Lycaenidae followed a complicated pathway with multiple events of duplication and loss of trnS1 and changes in anticodon. We describe two new gene orders 2FFGO and 4QGO for Ampittia subvittatus (Hesperiidae) and Bhutanitis thaidina (Papilionidae). Abstract The mitogenome of the species belonging to the Papilionodea (Lepidoptera) is a double stranded circular molecule containing the 37 genes shared by Metazoa. Eight mitochondrial gene orders are known in the Papilionoidea. MIQGO is the plesiomorphic gene order for this superfamily, while other mitochondrial arrangements have a very limited distribution. 2S1GO gene order is an exception and is present in several Lycaenidae and one species of Hesperiidae. We studied the macrostructural changes generating the gene orders of butterflies by analysing a large data set (611 taxa) containing 5 new mitochondrial sequences/assemblies and 87 de novo annotated mitogenomes. Our analysis supports a possible origin of the intergenic spacer trnQ-nad2, characterising MIQGO, from trnM. We showed that the homoplasious gene order IMQGO, shared by butterflies, species of ants, beetles and aphids, evolved through different transformational pathways. We identify a complicated evolutionary scenario for 2S1GO in Lycaenidae, characterised by multiple events of duplication/loss and change in anticodon of trnS1. We show that the gene orders ES1GO and S1NGO originated through a tandem duplication random loss mechanism. We describe two novel gene orders. Ampittia subvittatus (Hesperiidae) exhibits the gene order 2FFGO, characterised by two copies of trnF, one located in the canonical position and a second placed in the opposite strand between trnR and trnN. Bhutanitis thaidina (Papilionidae) exhibits the gene order 4QGO, characterised by the quadruplication of trnQ.
Collapse
Affiliation(s)
- Di Liu
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (D.L.); (M.B.); (T.P.)
| | - Andrea Basso
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35020 Legnaro, Italy;
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (D.L.); (M.B.); (T.P.)
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (D.L.); (M.B.); (T.P.)
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (D.L.); (M.B.); (T.P.)
- Correspondence:
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Ge XY, Liu T, Kang Y, Liu HY, Yang YX. First complete mitochondrial genomes of Ototretinae (Coleoptera, Lampyridae) with evolutionary insights into the gene rearrangement. Genomics 2022; 114:110305. [DOI: 10.1016/j.ygeno.2022.110305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 01/09/2022] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
|
19
|
Urantówka AD, Kroczak A, Strzała T, Zaniewicz G, Kurkowski M, Mackiewicz P. Mitogenomes of Accipitriformes and Cathartiformes Were Subjected to Ancestral and Recent Duplications Followed by Gradual Degeneration. Genome Biol Evol 2021; 13:evab193. [PMID: 34432018 PMCID: PMC8435663 DOI: 10.1093/gbe/evab193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2021] [Indexed: 11/25/2022] Open
Abstract
The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus, as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14-47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately.
Collapse
Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
| | - Tomasz Strzała
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Grzegorz Zaniewicz
- Department of Vertebrate Ecology and Zoology, Avian Ecophysiology Unit, University of Gdańsk, Poland
| | - Marcin Kurkowski
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
| |
Collapse
|
20
|
Lv SS, Zhang YJ, Gong N, Chen XS. Characterization and Phylogenetic Analysis of the Mitochondrial Genome Sequence of Nisia fuliginosa (Hemiptera: Fulgoroidea: Meenoplidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:8. [PMID: 34327530 PMCID: PMC8322432 DOI: 10.1093/jisesa/ieab050] [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] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 06/13/2023]
Abstract
We explored characterization of the mitochondrial genome (mitogenome or mtGenome) and phylogenetic analysis between 32 Fulgoroid species by sequencing and analyzing the mitogenome of Nisia fuliginosa Yang and Hu, 1985 (Hemiptera: Fulgoroidea: Meenoplidae), thereby making it the first determined mitogenome from the family Meenoplidae. The mitogenome was found to be 15,754 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, two ribosomal RNA genes (rRNAs), and a control region. All PCGs started with typical ATN codons, except for nad1, which used GTG as the start codon. Canonical TAA termination codons were found in 10 PCGs and the remaining three genes (cox2, nad6, and nad1) had incomplete stop codons T. All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnC, trnV, and trnS1. Additionally, we compared the AT and GC skews of 13 PCGs of 32 Fulgoroidea mitogenomes, on the L-strand, the AT and GC skews were negative and positive, respectively. However, on the H-strand, the AT skew could be positive or negative and the GC skew was always negative. Phylogenetic results showed that the eight families of Fulgoroidea were divided into two large groups. Delphacidae formed a monophyletic group sister to a clade comprising Meenoplidae and other six families (Fulgoridae, Ricaniidae, Flatidae, Issidae, Caliscelidae, and Achilidae). Meenoplidae was located near the clade of Delphacidae, and Fulgoridae was located near the clade of Meenoplidae. Furthermore, Caliscelidae, Issidae, Ricaniidae, and Flatidae are closely related and they collectively formed a sister group to Achilidae.
Collapse
Affiliation(s)
| | - Yu-Jie Zhang
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang 550025, China
| | - Nian Gong
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang 550025, China
| | - Xiang-Sheng Chen
- Institute of Entomology and Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guizhou University, Guiyang 550025, China
| |
Collapse
|
21
|
Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved. Sci Rep 2021; 11:13552. [PMID: 34193932 PMCID: PMC8245539 DOI: 10.1038/s41598-021-92994-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/18/2021] [Indexed: 12/15/2022] Open
Abstract
Contrary to the early evidence, which indicated that the mitochondrial architecture in one of the two major annelida clades, Sedentaria, is relatively conserved, a handful of relatively recent studies found evidence that some species exhibit elevated rates of mitochondrial architecture evolution. We sequenced complete mitogenomes belonging to two congeneric shell-boring Spionidae species that cause considerable economic losses in the commercial marine mollusk aquaculture: Polydora brevipalpa and Polydora websteri. The two mitogenomes exhibited very similar architecture. In comparison to other sedentarians, they exhibited some standard features, including all genes encoded on the same strand, uncommon but not unique duplicated trnM gene, as well as a number of unique features. Their comparatively large size (17,673 bp) can be attributed to four non-coding regions larger than 500 bp. We identified an unusually large (putative) overlap of 14 bases between nad2 and cox1 genes in both species. Importantly, the two species exhibited completely rearranged gene orders in comparison to all other available mitogenomes. Along with Serpulidae and Sabellidae, Polydora is the third identified sedentarian lineage that exhibits disproportionally elevated rates of mitogenomic architecture rearrangements. Selection analyses indicate that these three lineages also exhibited relaxed purifying selection pressures.
Collapse
|
22
|
Ghiselli F, Gomes-Dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. Molluscan mitochondrial genomes break the rules. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200159. [PMID: 33813887 DOI: 10.1098/rstb.2020.0159] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Collapse
Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - André Gomes-Dos-Santos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, and Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, USA
| | - Manuel Lopes-Lima
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Jeffrey L Boore
- Providence St Joseph Health and the Institute for Systems Biology, Seattle, USA
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Zhang H, Liu Q, Lu C, Deng J, Huang X. The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region. INSECTS 2021; 12:55. [PMID: 33440807 PMCID: PMC7828084 DOI: 10.3390/insects12010055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.
Collapse
Affiliation(s)
| | | | | | | | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (Q.L.); (C.L.); (J.D.)
| |
Collapse
|
25
|
Li J, Lv Q, Zhang XM, Han HL, Zhang AB. Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Laelia suffusa (Lepidoptera: Erebidae, Lymantriinae). JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:5. [PMID: 33428744 PMCID: PMC7799433 DOI: 10.1093/jisesa/ieaa138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Indexed: 06/02/2023]
Abstract
In this study, the complete mitochondrial genome of a white tussock moth, Laelia suffusa (Walker, 1855) (Lepidoptera: Erebidae, Lymantriinae), was sequenced and annotated. The genome sequence was 15,502 bp in length and comprised 13 PCGs, 2 rRNAs, 22 tRNAs, and a single noncoding control region (CR). The nucleotide composition of the genome was highly A + T biased, accounting for 79.04% of the whole genome and with a slightly positive AT skewness (0.015). Comparing the gene order with the basal species of Lepidoptera, a typical trnM rearrangement was detected in the mitogenome of L. suffusa. Besides, the trnM rearrangement was found at the head of trnI and trnQ, rather than at the back. The 13 PCGs used ATN as their start codons, except for the cox1 which used CGA. Out of the 22 tRNAs, only 1 tRNA (trnS1) failed to fold in a typical cloverleaf secondary structure. The conserved motif 'ATAGA + poly-T' was detected at the start of the control region which was similar to other Lepidoptera species. In total, 10 overlapping regions and 19 intergenic spacers were identified, ranging from 1 to 41 and 2 to 73 bp, respectively. Phylogenetic analysis showed that Lymantriinae was a monophyletic group with a high support value and L. suffusa was closely related to tribe Orgyiini (Erebidae, Lymantriinae). Moreover, the phylogenetic relationship of Noctuoidea (Lepidoptera) species was reconstructed using two datasets (13 PCGs and 37 genes) and these supported the topology of (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))).
Collapse
Affiliation(s)
- Jing Li
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
| | - Qing Lv
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
| | - Xiao-man Zhang
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
| | - Hui-lin Han
- School of Forestry, Northeast Forestry University, Harbin Heilongjiang, P. R. China
| | - Ai-bing Zhang
- College of Life Sciences, Capital Normal University, Beijing, P. R. China
| |
Collapse
|
26
|
An J, Zheng W, Liang J, Xi Q, Chen R, Jia J, Lu X, Jakovlić I. Disrupted architecture and fast evolution of the mitochondrial genome of Argeia pugettensis (Isopoda): implications for speciation and fitness. BMC Genomics 2020; 21:607. [PMID: 32883208 PMCID: PMC7469299 DOI: 10.1186/s12864-020-07021-y] [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: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Argeia pugettensis is an isopod species that parasitizes other crustaceans. Its huge native geographic range spans the Pacific from China to California, but molecular data are available only for a handful of specimens from North-American populations. We sequenced and characterised the complete mitogenome of a specimen collected in the Yellow Sea. RESULTS It exhibited a barcode (cox1) similarity level of only 87-89% with North-American populations, which is unusually low for conspecifics. Its mitogenome is among the largest in isopods (≈16.5 Kbp), mostly due to a large duplicated palindromic genomic segment (2 Kbp) comprising three genes. However, it lost a segment comprising three genes, nad4L-trnP-nad6, and many genes exhibited highly divergent sequences in comparison to isopod orthologues, including numerous mutations, deletions and insertions. Phylogenetic and selection analyses corroborated that this is one of the handful of most rapidly evolving available isopod mitogenomes, and that it evolves under highly relaxed selection constraints (as opposed to positive selection). However, its nuclear 18S gene is highly conserved, which suggests that rapid evolution is limited to its mitochondrial genome. The cox1 sequence analysis indicates that elevated mitogenomic evolutionary rates are not shared by North-American conspecifics, which suggests a breakdown of cox1 barcoding in this species. CONCLUSIONS A highly architecturally disrupted mitogenome and decoupling of mitochondrial and nuclear rates would normally be expected to have strong negative impacts on the fitness of the organism, so the existence of this lineage is a puzzling evolutionary question. Additional studies are needed to assess the phylogenetic breadth of this disrupted mitochondrial architecture and its impact on fitness.
Collapse
Affiliation(s)
- Jianmei An
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China.
| | - Wanrui Zheng
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Jielong Liang
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Qianqian Xi
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ruru Chen
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Junli Jia
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Xia Lu
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan, 430075, Hubei, PR China
| |
Collapse
|
27
|
Novel gene rearrangement pattern in Cynoglossus melampetalus mitochondrial genome: New gene order in genus Cynoglossus (Pleuronectiformes: Cynoglossidae). Int J Biol Macromol 2020; 149:1232-1240. [DOI: 10.1016/j.ijbiomac.2020.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 11/24/2022]
|
28
|
An exceptional case of mitochondrial tRNA duplication-deletion events in blood-feeding leeches. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00431-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
29
|
Irisarri I, Uribe JE, Eernisse DJ, Zardoya R. A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora). BMC Evol Biol 2020; 20:22. [PMID: 32024460 PMCID: PMC7003433 DOI: 10.1186/s12862-019-1573-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/30/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and evolution remain unclear due to the few morphological, molecular, or combined phylogenetic analyses, particularly those addressing the relationships among the major chiton lineages. RESULTS Here, we present a mitogenomic phylogeny of chitons based on 13 newly sequenced mitochondrial genomes along with eight available ones and RNAseq-derived mitochondrial sequences from four additional species. Reconstructed phylogenies largely agreed with the latest advances in chiton systematics and integrative taxonomy but we identified some conflicts that call for taxonomic revisions. Despite an overall conserved gene order in chiton mitogenomes, we described three new rearrangements that might have taxonomic utility and reconstructed the most likely scenario of gene order change in this group. Our phylogeny was time-calibrated using various fossils and relaxed molecular clocks, and the robustness of these analyses was assessed with several sensitivity analyses. The inferred ages largely agreed with previous molecular clock estimates and the fossil record, but we also noted that the ambiguities inherent to the chiton fossil record might confound molecular clock analyses. CONCLUSIONS In light of the reconstructed time-calibrated framework, we discuss the evolution of key morphological features and call for a continued effort towards clarifying the phylogeny and evolution of chitons.
Collapse
Affiliation(s)
- Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/ José Gutiérrez Abascal 2, 28006, Madrid, Spain.
- Department of Organismal Biology (Systematic Biology Program), Evolutionary Biology Centre, Uppsala University, Norbyv. 18C, 75236, Uppsala, Sweden.
| | - Juan E Uribe
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/ José Gutiérrez Abascal 2, 28006, Madrid, Spain
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, 10th St. & Constitutional Ave. NW, Washington, DC, 20560, USA
| | - Douglas J Eernisse
- Department of Biological Science, California State University Fullerton, 800 N. State College Blvd, Fullerton, CA, 92831-3599, USA
| | - Rafael Zardoya
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/ José Gutiérrez Abascal 2, 28006, Madrid, Spain
| |
Collapse
|
30
|
Phylogenetic implications of mitogenome rearrangements in East Asian potamiscine freshwater crabs (Brachyura: Potamidae). Mol Phylogenet Evol 2020; 143:106669. [DOI: 10.1016/j.ympev.2019.106669] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 11/18/2022]
|
31
|
Tyagi K, Chakraborty R, Cameron SL, Sweet AD, Chandra K, Kumar V. Rearrangement and evolution of mitochondrial genomes in Thysanoptera (Insecta). Sci Rep 2020; 10:695. [PMID: 31959910 PMCID: PMC6971079 DOI: 10.1038/s41598-020-57705-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/21/2019] [Indexed: 11/11/2022] Open
Abstract
Prior to this study, complete mitochondrial genomes from Order Thysanoptera were restricted to a single family, the Thripidae, resulting in a biased view of their evolution. Here we present the sequences for the mitochondrial genomes of four additional thrips species, adding three extra families and an additional subfamily, thus greatly improving taxonomic coverage. Thrips mitochondrial genomes are marked by high rates of gene rearrangement, duplications of the control region and tRNA mutations. Derived features of mitochondrial tRNAs in thrips include gene duplications, anticodon mutations, loss of secondary structures and high gene translocation rates. Duplicated control regions are found in the Aeolothripidae and the 'core' Thripinae clade but do not appear to promote gene rearrangement as previously proposed. Phylogenetic analysis of thrips mitochondrial sequence data supports the monophyly of two suborders, a sister-group relationship between Stenurothripidae and Thripidae, and suggests a novel set of relationships between thripid genera. Ancestral state reconstructions indicate that genome rearrangements are common, with just eight gene blocks conserved between any thrips species and the ancestral insect mitochondrial genome. Conversely, 71 derived rearrangements are shared between at least two species, and 24 of these are unambiguous synapomorphies for clades identified by phylogenetic analysis. While the reconstructed sequence of genome rearrangements among the protein-coding and ribosomal RNA genes could be inferred across the phylogeny, direct inference of phylogeny from rearrangement data in MLGO resulted in a highly discordant set of relationships inconsistent with both sequence-based phylogenies and previous morphological analysis. Given the demonstrated rates of genomic evolution within thrips, extensive sampling is needed to fully understand these phenomena across the order.
Collapse
Affiliation(s)
- Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 750053, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 750053, India
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Andrew D Sweet
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 750053, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 750053, India.
| |
Collapse
|
32
|
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]
|
33
|
Froufe E, Bolotov I, Aldridge DC, Bogan AE, Breton S, Gan HM, Kovitvadhi U, Kovitvadhi S, Riccardi N, Secci-Petretto G, Sousa R, Teixeira A, Varandas S, Zanatta D, Zieritz A, Fonseca MM, Lopes-Lima M. Mesozoic mitogenome rearrangements and freshwater mussel (Bivalvia: Unionoidea) macroevolution. Heredity (Edinb) 2020; 124:182-196. [PMID: 31201385 PMCID: PMC6906506 DOI: 10.1038/s41437-019-0242-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 11/08/2022] Open
Abstract
Using a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female mitogenome (i.e., gene orders MF1 and UF1). Our results suggest that this macroevolutionary jump was completed within a relatively short time interval (95% HPD 201-226 Ma) that coincided with the Triassic-Jurassic mass extinction. Both gene orders have persisted within these clades for ~200 Ma. The monophyly of the so-called "problematic" Gonideinae taxa was supported by all the inferred phylogenies in this study using, for the first time, the M- and F-type mitogenomes either singly or combined. Within Gonideinae, two additional splits in the gene order (UF1 to UF2, UF2 to UF3) occurred in the Mesozoic and have persisted for ~150 and ~100 Ma, respectively. Finally, the mitogenomic results suggest ancient connections between freshwater basins of East Asia and Europe near the Cretaceous-Paleogene boundary, probably via a continuous paleo-river system or along the Tethys coastal line, which are well supported by at least three independent but almost synchronous divergence events.
Collapse
Affiliation(s)
- Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal.
| | - Ivan Bolotov
- IBIGER - Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk, 163000, Russian Federation
- Northern Arctic Federal University, Severnaya Dvina Emb. 17, Arkhangelsk, 163000, Russian Federation
| | - David C Aldridge
- Department of Zoology, University of Cambridge, The David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK
| | - Arthur E Bogan
- North Carolina State Museum of Natural Sciences, 11 West Jones St., Raleigh, NC, 27601, USA
| | - Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, H2V 2S9, Canada
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3220, VIC, Australia
| | - Uthaiwan Kovitvadhi
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Satit Kovitvadhi
- Department of Agriculture, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok, 10600, Thailand
| | | | - Giulia Secci-Petretto
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal
| | - Ronaldo Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
| | - Amilcar Teixeira
- CIMO/ESA/IPB - Mountain Research Centre, School of Agriculture, Polytechnic Institute of Bragança, Campus de Santa Apolónia, Apartado 1172, Bragança, 5301-854, Portugal
| | - Simone Varandas
- CITAB/UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, Vila Real, 5000-801, Portugal
| | - David Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Biosciences Bldg. 2408, Mount Pleasant, MI, 48859, USA
| | - Alexandra Zieritz
- School of Environmental and Geographical Sciences, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, 43500, Malaysia
| | - Miguel M Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal
| | - Manuel Lopes-Lima
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, Vairão, Porto, 4485-661, Portugal
- SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, c/o The David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK
| |
Collapse
|
34
|
Zheng C, Ye Z, Zhu X, Zhang H, Dong X, Chen P, Bu W. Integrative taxonomy uncovers hidden species diversity in the rheophilic genus
Potamometra
(Hemiptera: Gerridae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chenguang Zheng
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Xiuxiu Zhu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | | | - Xue Dong
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Pingping Chen
- Netherlands Biodiversity Centre – Naturalis Leiden The Netherlands
| | - Wenjun Bu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| |
Collapse
|
35
|
Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D. Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications. Genome Biol Evol 2019; 11:2824-2849. [PMID: 31580435 PMCID: PMC6795242 DOI: 10.1093/gbe/evz209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.
Collapse
Affiliation(s)
- Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
| | - Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Dorota Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
| |
Collapse
|
36
|
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).
Collapse
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
| |
Collapse
|
37
|
Li WN, Xue XF. Mitochondrial genome reorganization provides insights into the relationship between oribatid mites and astigmatid mites (Acari: Sarcoptiformes: Oribatida). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Oribatida s.l. represents one of the most species-rich mite lineages, including two recognized groups: oribatid mites (Oribatida s.s., non-astigmatan oribatids) and astigmatid mites (Astigmata). However, the relationship between these two groups has been debated. Here, we sequenced the complete mitochondrial (mt) genome of one oribatid mite and one astigmatid mite, retrieved complete mt genomes of three oribatid mites, and compared them with two other oribatid mites and 12 astigmatid mites sequenced previously. We find that gene orders in the mt genomes of both oribatid mites and astigmatid mites are rearranged relative to the hypothetical ancestral arrangement of the arthropods. Based on the shared derived gene clusters in each mt genome group, rearranged mt genomes are roughly divided into two groups corresponding to each mite group (oribatid mites or astigmatid mites). Phylogenetic results show that Astigmata nested in Oribatida. The monophyly of Astigmata is recovered, while paraphyly of Oribatida s.s. is observed. Our results show that rearranged gene orders in the mt genomes characterize various lineages of oribatid mites and astigmatid mites, and have potential phylogenetic information for resolving the high-level (cohort or supercohort) phylogeny of Oribatida.
Collapse
Affiliation(s)
- Wei-Ning Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | | |
Collapse
|
38
|
Song R, Zhang D, Gao JW, Cheng XF, Xie M, Li H, Wu YA. Characterization of the complete mitochondrial genome of Brentisentisyangtzensis Yu & Wu, 1989 (Acanthocephala, Illiosentidae). Zookeys 2019; 861:1-14. [PMID: 31363345 PMCID: PMC6656981 DOI: 10.3897/zookeys.861.34809] [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: 03/24/2019] [Accepted: 05/31/2019] [Indexed: 11/12/2022] Open
Abstract
The mitogenome of Brentisentisyangtzensis is 13,864 bp in length and has the circular structure typical of metazoans. It contains 36 genes: 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and 12 protein-encoding genes (PCGs). All genes are transcribed from the same strand. Thirteen overlapping regions were found in the mitochondrial genome. The overall A+T content of B.yangtzensis is 68.3% versus 31.7% of G+C content (A = 27.8%, T = 40.5%, C = 9.0%, G = 22.7%). B.yangtzenensis (Illiosentidae) and Leptorhynchoidesthecatus (Rhadinorhynchidae) form a sister clade, showing the relatively close relationship between the Illiosentidae and the Rhadinorhynchidae. The mitochondrial gene arrangements of acanthocephalan species are relatively conserved, with only a few translocations of tRNAs (trnS1, trnS2, trnV, and trnK) detected. An identical gene order was found both in a sister clade (Centrorhynchusaluconis and Plagiorhynchustransversus) and across different classes (B.yangtzensis (Palaeacanthocephala), Acanthosentischeni (Eoacanthocephala) and Macracanthorhynchushirudinaceus (Archiacanthocephala), Oncicolaluehei and L.thecatus (Palaeacanthocephala)). More studies and more sequences of acanthocephalan species are needed to gain a clear understanding of the phylogenetic relationships.
Collapse
Affiliation(s)
- Rui Song
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, 415000, ChinaCollaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan ProvinceChangdeChina
| | - Dong Zhang
- 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, ChinaInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
| | - Jin-Wei Gao
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
| | - Xiao-Fei Cheng
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
| | - Min Xie
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
| | - Hong Li
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
| | - Yuan-An Wu
- Hunan Fisheries Science Institute, Changsha 410153, ChinaHunan Fisheries Science InstituteChangshaChina
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, 415000, ChinaCollaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan ProvinceChangdeChina
| |
Collapse
|
39
|
Cole LW, Guo W, Mower JP, Palmer JD. High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants. Mol Biol Evol 2019; 35:2773-2785. [PMID: 30202905 DOI: 10.1093/molbev/msy176] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
For 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) not only take place at generally high rates in these genomes but also uncover significant variation in rearrangement rates. For example, the hyperactive mitochondrial genome of Monsonia ciliata has accumulated at least 30 rearrangements over the last million years, whereas the branch leading to M. ciliata and its sister species has sustained rearrangement at a rate that is at least ten times lower. Furthermore, our analysis of published data shows that rates of mitochondrial genome rearrangement in seed plants vary by at least 600-fold. We find that sites of rearrangement are highly preferentially located in very close proximity to repeated sequences in Monsonia. This provides strong support for the hypothesis that rearrangement in angiosperm mitochondrial genomes occurs largely through repeat-mediated recombination. Because there is little variation in the amount of repeat sequence among Monsonia genomes, the variable rates of rearrangement in Monsonia probably reflect variable rates of mitochondrial recombination itself. Finally, we show that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.
Collapse
Affiliation(s)
- Logan W Cole
- Department of Biology, Indiana University, Bloomington, IN
| | | | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE
| | | |
Collapse
|
40
|
Prada CF, Boore JL. Gene annotation errors are common in the mammalian mitochondrial genomes database. BMC Genomics 2019; 20:73. [PMID: 30669991 PMCID: PMC6341679 DOI: 10.1186/s12864-019-5447-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/10/2019] [Indexed: 11/13/2022] Open
Abstract
Background Although animal mitochondrial DNA sequences are known to evolve rapidly, their gene arrangements often remain unchanged over long periods of evolutionary time. Therefore, comparisons of mitochondrial genomes may result in significant insights into the evolution both of organisms and of genomes. Mammalian mitochondrial genomes recently published in the GenBank database of NCBI show numerous rearrangements in various regions of the genome, from which it may be inferred that the mammalian mitochondrial genome is more dynamic than expected. However, it is alternatively possible that these are errors of annotation and, if so, are misleading our interpretations. In order to verify these possible errors of annotation, we performed a comparative genomic analysis of mammalian mitochondrial genomes available in the NCBI database. Results Using a combination of bioinformatics methods to carefully examine the mitochondrial gene arrangements in 304 mammalian species, we determined that there are only two sets of gene arrangements, one that is shared by all of the marsupials and another that is shared by all of the monotremes and eutherians, with these two arrangements differing only by the positions of tRNA genes in the region commonly designated as “WANCY” for the genes it comprises. All of the 68 other cases of reported gene rearrangements are errors. We note that there are also numerous errors of impossibly short, incorrect gene annotations, cases where genomes that are reported as complete are actually missing portions of the sequence, and genes that are clearly present but were not annotated in these records. Conclusions We judge that the application of simple bioinformatic tools in the verification of gene annotation, particularly for organelle genomes, would be a very useful enhancement for the curation of genome sequences submitted to GenBank. Electronic supplementary material The online version of this article (10.1186/s12864-019-5447-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Carlos F Prada
- Departamento de Biología, Facultad de ciencias, Universidad del Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA
| |
Collapse
|
41
|
Zhang D, Li WX, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Wang GT. Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements. Parasit Vectors 2018; 11:601. [PMID: 30458858 PMCID: PMC6245931 DOI: 10.1186/s13071-018-3144-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/10/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent mitochondrial phylogenomics studies have reported a sister-group relationship of the orders Capsalidea and Dactylogyridea, which is inconsistent with previous morphology- and molecular-based phylogenies. As Dactylogyridea mitochondrial genomes (mitogenomes) are currently represented by only one family, to improve the phylogenetic resolution, we sequenced and characterized two dactylogyridean parasites, Lamellodiscus spari and Lepidotrema longipenis, belonging to a non-represented family Diplectanidae. RESULTS The L. longipenis mitogenome (15,433 bp) contains the standard 36 flatworm mitochondrial genes (atp8 is absent), whereas we failed to detect trnS1, trnC and trnG in L. spari (14,614 bp). Both mitogenomes exhibit unique gene orders (among the Monogenea), with a number of tRNA rearrangements. Both long non-coding regions contain a number of different (partially overlapping) repeat sequences. Intriguingly, these include putative tRNA pseudogenes in a tandem array (17 trnV pseudogenes in L. longipenis, 13 trnY pseudogenes in L. spari). Combined nucleotide diversity, non-synonymous/synonymous substitutions ratio and average sequence identity analyses consistently showed that nad2, nad5 and nad4 were the most variable PCGs, whereas cox1, cox2 and cytb were the most conserved. Phylogenomic analysis showed that the newly sequenced species of the family Diplectanidae formed a sister-group with the Dactylogyridae + Capsalidae clade. Thus Dactylogyridea (represented by the Diplectanidae and Dactylogyridae) was rendered paraphyletic (with high statistical support) by the nested Capsalidea (represented by the Capsalidae) clade. CONCLUSIONS Our results show that nad2, nad5 and nad4 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in the Diplectanidae. The unique gene order pattern further suggests discontinuous evolution of mitogenomic gene order arrangement in the Class Monogenea. This first report of paraphyly of the Dactylogyridea highlights the need to generate more molecular data for monogenean parasites, in order to be able to clarify their relationships using large datasets, as single-gene markers appear to provide a phylogenetic resolution which is too low for the task.
Collapse
Affiliation(s)
- Dong Zhang
- 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 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wen X. Li
- 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 People’s Republic of 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 People’s Republic of China
| | - Shan G. Wu
- 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 People’s Republic of China
| | - Ming Li
- 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 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Jin Zhang
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Gui T. 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 People’s Republic of China
| |
Collapse
|
42
|
Hartmann T, Wieseke N, Sharan R, Middendorf M, Bernt M. Genome Rearrangement with ILP. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1585-1593. [PMID: 28574364 DOI: 10.1109/tcbb.2017.2708121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The weighted Genome Sorting Problem (wGSP) is to find a minimum-weight sequence of rearrangement operations that transforms a given gene order into another given gene order using rearrangement operations that are associated with a predefined weight. This paper presents a polynomial sized Integer Linear Program -called GeRe-ILP- for solving the wGSP for the following three types of rearrangement operations: inversion , transposition, and inverse transposition. GeRe-ILP uses variables and constraints for gene orders of length . It is studied experimentally on simulated data how different weighting schemes influence the reconstructed scenarios. The influences of the length of the gene orders and of the size of the reconstructed scenarios on the runtime of GeRe-ILP are studied as well.
Collapse
|
43
|
The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum. ACTA ACUST UNITED AC 2018; 4. [PMID: 30105092 DOI: 10.1017/pao.2018.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.
Collapse
|
44
|
The complete mitochondrial genome of Vanessa indica and phylogenetic analyses of the family Nymphalidae. Genes Genomics 2018; 40:1011-1022. [PMID: 29949077 DOI: 10.1007/s13258-018-0709-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/29/2018] [Indexed: 02/02/2023]
Abstract
Vanessa indica is a small butterfly lacking historical molecular and biological research. Vanessa indica belongs to the family Nymphalidae (Lepidoptera: Papilionoidea), which is the largest group of butterflies and are nearly ubiquitous. However, after more than a century of taxonomic and molecular studies, there is no consensus for family classification, and the phylogenetic relationships within Nymphalidae are controversial. The first objective was to sequence and characterize the complete mitochondrial genome of V. indica. The most important objective was to completely reconstruct the phylogenetic relationships for family members within Nymphalidae. The mitochondrial genomic DNA (mtDNA) of V. indica was extracted and amplified by polymerase chain reaction. The complete mitochondrial sequence was annotated and characterized by analyzing sequences with SeqMan program. The phylogenetic analyses were conducted on thirteen protein coding genes (PCGs) in 95 mtDNA of Nymphalidae downloaded from GenBank for reference using the maximum likelihood method and Bayesian inference to ensure the validity of the results. The complete mitogenome was a circular molecule with 15,191 bp consisting of 13 protein coding genes, two ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA (tRNA) genes, and an A + T-rich region (D-loop). The nucleotide composition of the genome was highly biased for A + T content, which accounts for 80.0% of the nucleotides. All the tRNAs have putative secondary structures that are characteristic of mitochondrial tRNAs, except tRNASer(AGN). All the PCGs started with ATN codons, except cytochrome c oxidase subunit 1 (COX1), which was found to start with an unusual CGA codon. Four genes were observed to have unusual codons: COX1 terminated with atypical TT and the other three genes terminated with a single T. The A + T rich region of 327 bp consisted of repetitive sequences, including a ATAGA motif, a 19-bp poly-T stretch, and two microsatellite-like regions (TA)8. The phylogenetic analyses consistently placed Biblidinae as a sister cluster to Heliconiinae and Calinaginae as a sister clade to Satyrinae. Moreover, the phylogenetic tree identified Libytheinae as a monophyletic group within Nymphalidae. The complete mitogenome of V. indica was 15,191 bp with mitochondrial characterizations common for lepidopteran species, which enriched the mitochondria data of Nymphalid species. And the phylogenetic analysis revealed different classifications and relationships than those previously described. Our results are significant because they would be useful in further understanding of the evolutionary biology of Nymphalidae.
Collapse
|
45
|
Qian L, Wang H, Yan J, Pan T, Jiang S, Rao D, Zhang B. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes. BMC Genomics 2018; 19:354. [PMID: 29747572 PMCID: PMC5946542 DOI: 10.1186/s12864-018-4717-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. RESULTS In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. CONCLUSIONS The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.
Collapse
Affiliation(s)
- Lifu Qian
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Shanqun Jiang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.
| |
Collapse
|
46
|
Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources. Genomics 2018; 111:343-355. [PMID: 29486209 DOI: 10.1016/j.ygeno.2018.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 11/23/2022]
Abstract
For their apparent morphological simplicity, the Platyhelminthes or "flatworms" are a diverse clade found in a broad range of habitats. Their body plans have however made them difficult to robustly classify. Molecular evidence is only beginning to uncover the true evolutionary history of this clade. Here we present nine novel mitochondrial genomes from the still undersampled orders Polycladida and Rhabdocoela, assembled from short Illumina reads. In particular we present for the first time in the literature the mitochondrial sequence of a Rhabdocoel, Bothromesostoma personatum (Typhloplanidae, Mesostominae). The novel mitochondrial genomes examined generally contained the 36 genes expected in the Platyhelminthes, with all possessing 12 of the 13 protein-coding genes normally found in metazoan mitochondrial genomes (ATP8 being absent from all Platyhelminth mtDNA sequenced to date), along with two ribosomal RNA genes. The majority presented possess 22 transfer RNA genes, and a single tRNA gene was absent from two of the nine assembled genomes. By comparison of mitochondrial gene order and phylogenetic analysis of the protein coding and ribosomal RNA genes contained within these sequences with those of previously sequenced species we are able to gain a firm molecular phylogeny for the inter-relationships within this clade. Our phylogenetic reconstructions, using both nucleotide and amino acid sequences under several models and both Bayesian and Maximum Likelihood methods, strongly support the monophyly of Polycladida, and the monophyly of Acotylea and Cotylea within that clade. They also allow us to speculate on the early emergence of Macrostomida, the monophyly of a "Turbellarian-like" clade, the placement of Rhabditophora, and that of Platyhelminthes relative to the Lophotrochozoa (=Spiralia). The data presented here therefore represent a significant advance in our understanding of platyhelminth phylogeny, and will form the basis of a range of future research in the still-disputed classifications within this taxon.
Collapse
|
47
|
Hartmann T, Chu AC, Middendorf M, Bernt M. Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:83-95. [PMID: 28114075 DOI: 10.1109/tcbb.2016.2613522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The tandem duplication random loss operation (TDRL) is an important genome rearrangement operation in metazoan mitochondrial genomes. A TDRL consists of a duplication of a contiguous set of genes in tandem followed by a random loss of one copy of each duplicated gene. This paper presents an analysis of the combinatorics of TDRLs on circular genomes, e.g., the mitochondrial genome. In particular, results on TDRLs for circular genomes and their linear representatives are established. Moreover, the distance between gene orders with respect to linear TDRLs and circular TDRLs is studied. An analysis of the available animal mitochondrial gene orders shows the practical relevance of the theoretical results.
Collapse
|
48
|
Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches. Methods Mol Biol 2018; 1704:261-289. [PMID: 29277869 DOI: 10.1007/978-1-4939-7463-4_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Genome rearrangements are mutations that change the gene content of a genome or the arrangement of the genes on a genome. Several years of research on genome rearrangements have established different algorithmic approaches for solving some fundamental problems in comparative genomics based on gene order information. This review summarizes the literature on genome rearrangement analysis along two lines of research. The first line considers rearrangement models that are particularly well suited for a theoretical analysis. These models use rearrangement operations that cut chromosomes into fragments and then join the fragments into new chromosomes. The second line works with rearrangement models that reflect several biologically motivated constraints, e.g., the constraint that gene clusters have to be preserved. In this chapter, the border between algorithmically "easy" and "hard" rearrangement problems is sketched and a brief review is given on the available software tools for genome rearrangement analysis.
Collapse
|
49
|
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.
Collapse
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.
| | | |
Collapse
|
50
|
Du C, Zhang L, Lu T, Ma J, Zeng C, Yue B, Zhang X. Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera. BMC Genomics 2017; 18:698. [PMID: 28874137 PMCID: PMC5585954 DOI: 10.1186/s12864-017-4102-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very little is known about mitogenomes of Meloidae. RESULTS We determined complete or nearly complete mitogenomes of seven meloid species. The circular genomes encode 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) and two ribosomal RNAs (rRNAs), and contain a control region, with gene arrangement identical to the ancestral type for insects. The evolutionary rates of all PCGs indicate that their evolution is based on purifying selection. The comparison of tRNA secondary structures indicates diverse substitution patterns in Meloidae. Remarkably, all mitogenomes of the three studied Hycleus species contain two large intergenic spacers (IGSs). IGS1 is located between trnW and trnC, including a 9 bp consensus motif. IGS2 is located between trnS2 (UCN) and nad1, containing discontinuous repeats of a pentanucleotide motif and two 18-bp repeat units in both ends. To date, IGS2 is found only in genera Hycleus across all published Coleopteran mitogenomes. The duplication/random loss model and slipped-strand mispairing are proposed as evolutionary mechanisms for the two IGSs (IGS1, IGS2). The phylogenetic analyses using MrBayes, RAxML, and PhyloBayes methods based on nucleotide and amino acid datasets of 13 PCGs from all published mitogenomes of Tenebrionoids, consistently recover the monophylies of Meloidae and Tenebrionidae. Within Meloidae, the genus Lytta clusters with Epicauta rather than with Mylabris. Although data collected thus far could not resolve the phylogenetic relationships within Meloidae, this study will assist in future mapping of the Meloidae phylogeny. CONCLUSIONS This study presents mitogenomes of seven meloid beetles. New mitogenomes retain the genomic architecture of the Coleopteran ancestor, but contain two IGSs in the three studied Hycleus species. Comparative analyses of two IGSs suggest that their evolutionary mechanisms are duplication/random loss model and slipped-strand mispairing.
Collapse
Affiliation(s)
- Chao Du
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.,Nanchong Vocational and Technical College, Nanchong, 637131, Sichuan, People's Republic of China
| | - Lifang Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Ting Lu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jingnan Ma
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Chenjuan Zeng
- Sichuan Key Laboratory of Medicinal American Cockroach, Chengdu, 610041, People's Republic of China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
| |
Collapse
|