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Chen Y, Dai S, Su D, Wang Y, Ning J, Liu Z. The complete mitochondrial genome and phylogenetic analysis of hydrozoan jellyfish Eirene ceylonensis (Cnidaria, Hydrozoa, Eirenidae) in the coastal sea of Qinhuangdao, China. Mitochondrial DNA B Resour 2023; 8:1381-1385. [PMID: 38189024 PMCID: PMC10768735 DOI: 10.1080/23802359.2023.2290845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Eirene ceylonensis, a hydrozoan jellyfish species with a complex polymorphic life cycle, is widely distributed in the Chinese coastal sea. In this study, we conducted sequencing and analysis of the first complete mitochondrial genome of E. ceylonensis, obtained from the coastal sea of Qinhuangdao, China. The linear mitochondrial genome is 14,997 bp in length with the overall AT content being 72.8%, encoding 13 protein-coding genes (PCGs), two transfer RNA (tRNA) genes (tRNA-Met and tRNA-Trp) and two ribosomal RNA (rRNA) genes (rrnS and rrnL). Phylogenetic analysis of 13 PCGs suggests that the E. ceylonensis is closely related to Laomedea flexuosa. The availability of the complete mitochondrial genome of E. ceylonensis will be useful for studying the evolutionary relationships of hydrozoan jellyfish species.
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Affiliation(s)
- Yang Chen
- Research Center for Marine Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Key Hebei Key Laboratory of Ocean Dynamics, Resources and Environments, Qinhuangdao, China
| | - Sheng Dai
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Du Su
- Research Center for Marine Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Key Hebei Key Laboratory of Ocean Dynamics, Resources and Environments, Qinhuangdao, China
| | - Yibo Wang
- Research Center for Marine Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Key Hebei Key Laboratory of Ocean Dynamics, Resources and Environments, Qinhuangdao, China
| | - Jiaqi Ning
- Research Center for Marine Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Key Hebei Key Laboratory of Ocean Dynamics, Resources and Environments, Qinhuangdao, China
| | - Zhiliang Liu
- Research Center for Marine Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Key Hebei Key Laboratory of Ocean Dynamics, Resources and Environments, Qinhuangdao, China
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2
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Lee HE, Ki JS. The complete mitochondrial genome of the mauve stinger jellyfish Pelagia noctiluca Forskål, 1775 (Cnidaria, Scyphozoa, Semaeostomeae) with phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1239-1242. [PMID: 38188449 PMCID: PMC10769544 DOI: 10.1080/23802359.2023.2281028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/02/2023] [Indexed: 01/09/2024] Open
Abstract
This study determined the complete mitochondrial genome of the jellyfish Pelagia noctiluca (Scyphozoa, Semaeostomeae) for the first time. The genome was a linear molecule of 16,390 bp in length and 59.3% AT. It comprised of 13 typical protein-coding genes (cox1-3, nd1-6, nd4L, atp6, atp8, and cytB), two ribosomal RNAs (16S and 12S rRNA), and two tRNAs (trnM and trnW). In addition, we detected two additional open reading frames (polB and ORF314) at one end of the genome. The gene-coding structures were identical to those of other scyphozoans. Based on a molecular phylogeny constructed using 13 protein-coding genes, P. noctiluca has the closest genetic relationship with the genus Chrysaora (Semaeostomeae).
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Affiliation(s)
- Ha-Eun Lee
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
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3
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Xia W, Jiang H, Fan W, Li X, Liu Y, Xu L, Gou X. Complete mitochondrial genome of Mastigias papua (Scyphozoa: Rhizostomeae: Mastigiidae) based on next-generation sequencing and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1294-1297. [PMID: 38188436 PMCID: PMC10769521 DOI: 10.1080/23802359.2023.2281033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/02/2023] [Indexed: 01/09/2024] Open
Abstract
We assembled the complete mitochondrial genome (mitogenome) of Mastigias papua (Scyphozoa: Rhizostomeae: Mastigiidae) by the data generated from the next-generation sequencing platform. The complete mitogenome of M. papua was 16,560 bp in length, containing 14 protein-coding genes, two transfer RNA genes, and two ribosomal RNA genes. The base compositions were A 30.65%, C 15.16%, G 16.34%, and T 37.86%, with a gene arrangement similar to the mitogenomes derived from other representatives of Scyphozoa. Based on the 13 common protein-coding genes of 16 species within Scyphozoa, we constructed the phylogenetic tree and found that M. papua has a close relationship with Cassiopea andromeda and Cassiopea xamachana. All these species belong to an order of jellyfish Rhizostomeae, which have similar morphological characteristics. This is agreement with the conclusion we got by the phylogenetic relationship analysis using molecular data. This research has practical implications for advancing understanding of the phylogenetic relationships, taxonomic classifications, and phylogeography within Scyphozoa.
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Affiliation(s)
- Wangxiao Xia
- Institute of Basic Translational Medicine, Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, China
- Department of Anesthesiology, School of Stomatology, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Air Force Military Medical University, Xi'an, China
| | - Hui Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Wenbo Fan
- Department of Anesthesiology, School of Stomatology, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Air Force Military Medical University, Xi'an, China
| | - Xiaomin Li
- Department of Anesthesiology, School of Stomatology, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Air Force Military Medical University, Xi'an, China
| | - Yaowen Liu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Lixian Xu
- Department of Anesthesiology, School of Stomatology, State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Air Force Military Medical University, Xi'an, China
| | - Xingchun Gou
- Institute of Basic Translational Medicine, Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an, China
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4
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Ling MK, Yap NWL, Iesa IB, Yip ZT, Huang D, Quek ZBR. Revisiting mitogenome evolution in Medusozoa with eight new mitochondrial genomes. iScience 2023; 26:108252. [PMID: 37965150 PMCID: PMC10641506 DOI: 10.1016/j.isci.2023.108252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Mitogenomics has improved our understanding of medusozoan phylogeny. However, sequenced medusozoan mitogenomes remain scarce, and Medusozoa phylogeny studies often analyze mitogenomic sequences without incorporating mitogenome rearrangements. To better understand medusozoan evolution, we analyzed Medusozoa mitogenome phylogeny by sequencing and assembling eight mitogenomes from three classes (Cubozoa, Hydrozoa, and Scyphozoa). We reconstructed the mitogenome phylogeny using these mitogenomes and 84 other existing cnidarian mitogenomes to study mitochondrial gene rearrangements. All reconstructed mitogenomes had 13 mitochondrial protein-coding genes and two ribosomal genes typical for Medusozoa. Non-cubozoan mitogenomes were all linear and had typical gene orders, while arrangement of genes in the fragmented Cubozoa (Morbakka sp.) mitogenome differed from other Cubozoa mitogenomes. Gene order comparisons and ancestral state reconstruction suggest minimal rearrangements within medusozoan classes except for Hydrozoa. Our findings support a staurozoan ancestral medusozoan gene order, expand the pool of available medusozoan mitogenomes, and enhance our understanding of medusozoan phylogenetic relationships.
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Affiliation(s)
- Min Kang Ling
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Nicholas Wei Liang Yap
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- St. John’s Island National Marine Laboratory, c/o Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Iffah Binte Iesa
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
| | - Zhi Ting Yip
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
| | - Zheng Bin Randolph Quek
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
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5
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Feng H, Lv S, Li R, Shi J, Wang J, Cao P. Mitochondrial genome comparison reveals the evolution of cnidarians. Ecol Evol 2023; 13:e10157. [PMID: 37325715 PMCID: PMC10261974 DOI: 10.1002/ece3.10157] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/18/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Cnidarians are the most primitive metazoans, but their evolutionary relationships are poorly understood, although recent studies present several phylogenetic hypotheses. Here, we collected 266 complete cnidarian mitochondrial genomes and re-evaluated the phylogenetic relationships between the major lineages. We described the gene rearrangement patterns of Cnidaria. Anthozoans had significantly greater mitochondrial genome size and lower A + T content than medusozoans. Most of the protein-coding genes in anthozoans such as COX 13, ATP6, and CYTB displayed a faster rate of evolution based on selection analysis. There were 19 distinct patterns of mitochondrial gene order, including 16 unique gene orders in anthozoans and 3 mtDNA gene orders pattern in medusozoans, were identified among cnidarians. The gene order arrangement suggested that a linearized mtDNA structure may be more conducive to Medusozoan mtDNA stability. Based on phylogenetic analyses, the monophyly of the Anthozoa was strongly supported compared to previous mitochondrial genome-based analyses rather than octocorals forming a sister group relationship with medusozoans. In addition, Staurozoa were more closely related to Anthozoa than to Medusozoa. In conclusion, these results largely support the traditional phylogenetic view of the relationships of cnidarians and provide new insights into the evolutionary processes for studying the most ancient animal radiations.
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Affiliation(s)
- Hui Feng
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Sitong Lv
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Rong Li
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Jing Shi
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Jianxing Wang
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Pinglin Cao
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
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6
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Shimpi GG, Bentlage B. Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes. Bioessays 2023; 45:e2200190. [PMID: 36412071 DOI: 10.1002/bies.202200190] [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: 09/24/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022]
Abstract
In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.
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Zhang N, Li Y, Halanych KM, Kong L, Li Q. A comparative analysis of mitochondrial ORFs provides new insights on expansion of mitochondrial genome size in Arcidae. BMC Genomics 2022; 23:809. [PMID: 36474182 PMCID: PMC9727918 DOI: 10.1186/s12864-022-09040-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Arcidae, comprising about 260 species of ark shells, is an ecologically and economically important lineage of bivalve mollusks. Interestingly, mitochondrial genomes of several Arcidae species are 2-3 times larger than those of most bilaterians, and are among the largest bilaterian mitochondrial genomes reported to date. The large mitochondrial genome size is mainly due to expansion of unassigned regions (regions that are functionally unassigned). Previous work on unassigned regions of Arcidae mtDNA genomes has focused on nucleotide-level analyses to observe sequence characteristics, however the origin of expansion remains unclear. RESULTS We assembled six new mitogenomes and sequenced six transcriptomes of Scapharca broughtonii to identify conserved functional ORFs that are transcribed in unassigned regions. Sixteen lineage-specific ORFs with different copy numbers were identified from seven Arcidae species, and 11 of 16 ORFs were expressed and likely biologically active. Unassigned regions of 32 Arcidae mitogenomes were compared to verify the presence of these novel mitochondrial ORFs and their distribution. Strikingly, multiple structural analyses and functional prediction suggested that these additional mtDNA-encoded proteins have potential functional significance. In addition, our results also revealed that the ORFs have a strong connection to the expansion of Arcidae mitochondrial genomes and their large-scale duplication play an important role in multiple expansion events. We discussed the possible origin of ORFs and hypothesized that these ORFs may originate from duplication of mitochondrial genes. CONCLUSIONS The presence of lineage-specific mitochondrial ORFs with transcriptional activity and potential functional significance supports novel features for Arcidae mitochondrial genomes. Given our observation and analyses, these ORFs may be products of mitochondrial gene duplication. These findings shed light on the origin and function of novel mitochondrial genes in bivalves and provide new insights into evolution of mitochondrial genome size in metazoans.
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Affiliation(s)
- Ning Zhang
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yuanning Li
- grid.27255.370000 0004 1761 1174Shandong University, Qingdao, China
| | - Kenneth M. Halanych
- grid.217197.b0000 0000 9813 0452Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC 28409 USA
| | - Lingfeng Kong
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qi Li
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa. Genes (Basel) 2021; 12:genes12122030. [PMID: 34946978 PMCID: PMC8700879 DOI: 10.3390/genes12122030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species Macrohectopus branickii. The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome’s size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.
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Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing. Nat Commun 2020; 11:3051. [PMID: 32561724 PMCID: PMC7305137 DOI: 10.1038/s41467-020-16801-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/22/2020] [Indexed: 12/30/2022] Open
Abstract
The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.
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Seo Y, Chae J, Ki JS. The complete mitochondrial genome of the jellyfish Aurelia coerulea ( Cnidaria and Scyphozoa) with phylogenetic analysis. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1749155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Yoseph Seo
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
| | - Jinho Chae
- Marine Environmental Research and Information Laboratory, Gunpo, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
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11
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Schultz DT, Eizenga JM, Corbett-Detig RB, Francis WR, Christianson LM, Haddock SH. Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii. PeerJ 2020; 8:e8356. [PMID: 32025367 PMCID: PMC6991124 DOI: 10.7717/peerj.8356] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 12/04/2019] [Indexed: 11/20/2022] Open
Abstract
To date, five ctenophore species' mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.
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Affiliation(s)
- Darrin T. Schultz
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Jordan M. Eizenga
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Warren R. Francis
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Steven H.D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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12
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Wang Y, Yin J. Complete mitochondrial genome of the jellyfish, Chrysaora pacifica (Goette, 1886) (Cnidaria, Scyphozoa) and the phylogenetic relationship in the related species. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:455-456. [PMID: 33366599 PMCID: PMC7748765 DOI: 10.1080/23802359.2019.1704648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The complete mitochondrial genome sequences of giant jellyfish Chrysaora pacifica, a scyphozoan species inhabiting the Bohai Sea water in China, is firstly described and analyzed in this research. The mitogenome is a circular molecule 16,964 bp in length, including 13 protein-coding genes (Cox 1, Cox2, Atp 8, Atp 6, Cox 3, ND2, ND5, ND 6, ND3, ND4L,ND1,ND4, Cob), 2 tRNAs (trnW, trnM), 2 rRNA genes (small subunit RNA and large subunit RNA). The neighbor-joining (NJ) phylogenetic tree in the related species showed that C. pacifica is close to Chrysaora quinquecirrha.
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Affiliation(s)
- Yantao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, P. R. China
| | - Jiehui Yin
- Ocean College Yan Tai University, Yan Tai, China
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13
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Lin J, Feng S, Wang L. Complete mitochondrial genome sequence of Aequorea coerulescens. Mitochondrial DNA B Resour 2019; 4:2882-2883. [PMID: 33365773 PMCID: PMC7706856 DOI: 10.1080/23802359.2019.1660257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 08/01/2019] [Indexed: 11/22/2022] Open
Abstract
The complete mitochondrial genome sequences of hydromedusa Aequorea coerulescens, a dominant giant jellyfish distributing in the Yellow Sea and northern East China Sea, China, is first reported in this research. Its mitochondrial DNA has 14,804 bp in length with a linear structure, containing 13 protein-coding genes (PCGs), 2rRNA (s-rRNA and l-rRNA), and 2tRNA (trnaW-TGA and tranM-AGT). The A + T content of the whole base composition of the genome is 72.8% (A: 30.15%; C: 12.33%; G: 14.87%; T: 42.64%). ATG, ATA, and ATT are start codons in five (ATP8, ATP6, COX3, NAD6, NAD4l), four (NAD2, NAD5, NAD1, COX1) and two PCGs (NAD3, NAD4), respectively. COB and COX2 began with GTG and CAA as start codon, respectively. TAA and ATA were the stop codon of ATP6 and NAD5 as well as NAD2 and NAD4, respectively. However, other PCGs were terminated with different stop codons. The NJ phylogenetic tree among the related 15 jellyfish species showed that A. coerulescens is close to Hydra spp.
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Affiliation(s)
- Jianing Lin
- Department of Riverine Ecological Conservation and Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Song Feng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Lijuan Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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Johri P, Marinov GK, Doak TG, Lynch M. Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. Genome Biol Evol 2019; 11:1398-1416. [PMID: 30980669 PMCID: PMC6505448 DOI: 10.1093/gbe/evz081] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
The evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate mitochondrial genomes exhibit a unique combination of characteristics, including a linear organization and the presence of multiple genes with no known function or detectable homologs in other eukaryotes. Here we study the variation of ciliate mitochondrial genomes both within and across 13 highly diverged Paramecium species, including multiple species from the P. aurelia species complex, with four outgroup species: P. caudatum, P. multimicronucleatum, and two strains that may represent novel related species. We observe extraordinary conservation of gene order and protein-coding content in Paramecium mitochondria across species. In contrast, significant differences are observed in tRNA content and copy number, which is highly conserved in species belonging to the P. aurelia complex but variable among and even within the other Paramecium species. There is an increase in GC content from ∼20% to ∼40% on the branch leading to the P. aurelia complex. Patterns of polymorphism in population-genomic data and mutation-accumulation experiments suggest that the increase in GC content is primarily due to changes in the mutation spectra in the P. aurelia species. Finally, we find no evidence of recombination in Paramecium mitochondria and find that the mitochondrial genome appears to experience either similar or stronger efficacy of purifying selection than the nucleus.
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Affiliation(s)
- Parul Johri
- Department of Biology, Indiana University, Bloomington
| | - Georgi K Marinov
- Department of Biology, Indiana University, Bloomington.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington.,National Center for Genome Analysis Support, Indiana University, Bloomington
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington.,Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe
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15
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Feng S, Lin J, Sun S, Liu Q. Complete mitochondrial genome sequence of Parumbrosa polylobata. Mitochondrial DNA B Resour 2019; 4:2262-2263. [PMID: 33365502 PMCID: PMC7687615 DOI: 10.1080/23802359.2019.1627925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/31/2019] [Indexed: 10/26/2022] Open
Abstract
The complete mitochondrial genome sequences of giant jellyfish Parumbrosa polylobata, a scyphozoan species inhabiting the Yellow Sea cold bottom water in China, is firstly described and analyzed in this research. It is 16,809 bp in length with a linear mitochondrial DNA. The base composition of the genome with A + T bias is 69.7%. There are 13 protein-coding genes (PCGs), 2 tRNAs, and 2 rRNAs. Another two special PCGs, ORF360 and ORF147 with telomeres were found at both ends. The neighbor-joining (NJ) phylogenetic tree among the related 13 species showed that P. polylobata is close to Aurelia spp.
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Affiliation(s)
- Song Feng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jianing Lin
- Department of Riverine Ecological Conservation and Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Song Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qing Liu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
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16
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Karagozlu MZ, Seo Y, Ki JS, Kim CB. The complete mitogenome of brownbranded moon jellyfish Aurelia limbata (Cnidaria, Semaeostomeae, Ulmaridae) with phylogenetic analysis. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1614494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
| | - Yoseph Seo
- Department of Biotechnology, Sangmyung University, Seoul, Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, Korea
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17
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O'Hanlon SJ, Rieux A, Farrer RA, Rosa GM, Waldman B, Bataille A, Kosch TA, Murray KA, Brankovics B, Fumagalli M, Martin MD, Wales N, Alvarado-Rybak M, Bates KA, Berger L, Böll S, Brookes L, Clare F, Courtois EA, Cunningham AA, Doherty-Bone TM, Ghosh P, Gower DJ, Hintz WE, Höglund J, Jenkinson TS, Lin CF, Laurila A, Loyau A, Martel A, Meurling S, Miaud C, Minting P, Pasmans F, Schmeller DS, Schmidt BR, Shelton JMG, Skerratt LF, Smith F, Soto-Azat C, Spagnoletti M, Tessa G, Toledo LF, Valenzuela-Sánchez A, Verster R, Vörös J, Webb RJ, Wierzbicki C, Wombwell E, Zamudio KR, Aanensen DM, James TY, Gilbert MTP, Weldon C, Bosch J, Balloux F, Garner TWJ, Fisher MC. Recent Asian origin of chytrid fungi causing global amphibian declines. Science 2018; 360:621-627. [PMID: 29748278 PMCID: PMC6311102 DOI: 10.1126/science.aar1965] [Citation(s) in RCA: 282] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.
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Affiliation(s)
- Simon J O'Hanlon
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK.
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Adrien Rieux
- CIRAD, UMR PVBMT, 97410 St. Pierre, Reunion, France
| | - Rhys A Farrer
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Gonçalo M Rosa
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Bruce Waldman
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Arnaud Bataille
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- CIRAD, UMR ASTRE, F-34398 Montpellier, France
| | - Tiffany A Kosch
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Kris A Murray
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Balázs Brankovics
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT Utrecht, Netherlands
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 49, NO-7012 Trondheim, Norway
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mario Alvarado-Rybak
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | - Kieran A Bates
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Lee Berger
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Susanne Böll
- Agency for Population Ecology and Nature Conservancy, Gerbrunn, Germany
| | - Lola Brookes
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Frances Clare
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Elodie A Courtois
- Laboratoire Ecologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, 97300 Cayenne, French Guiana
| | | | | | - Pria Ghosh
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
| | - David J Gower
- Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - William E Hintz
- Biology Department, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Jacob Höglund
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Thomas S Jenkinson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chun-Fu Lin
- Zoology Division, Endemic Species Research Institute, 1 Ming-shen East Road, Jiji, Nantou 552, Taiwan
| | - Anssi Laurila
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Adeline Loyau
- Department of Conservation Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Sara Meurling
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Claude Miaud
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, France
| | - Pete Minting
- Amphibian and Reptile Conservation (ARC) Trust, Boscombe, Bournemouth, Dorset BH1 4AP, UK
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Dirk S Schmeller
- Department of Conservation Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Benedikt R Schmidt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland, and Info Fauna Karch, UniMail-Bâtiment G, Bellevaux 51, 2000 Neuchâtel, Switzerland
| | - Jennifer M G Shelton
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Lee F Skerratt
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Freya Smith
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
- National Wildlife Management Centre, APHA, Woodchester Park, Gloucestershire GL10 3UJ, UK
| | - Claudio Soto-Azat
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | | | - Giulia Tessa
- Non-profit Association Zirichiltaggi-Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100 Sassari, Italy
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Unicamp, Campinas, Brazil
| | - Andrés Valenzuela-Sánchez
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
- ONG Ranita de Darwin, Nataniel Cox 152, Santiago, Chile
| | - Ruhan Verster
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
| | - Judit Vörös
- Collection of Amphibians and Reptiles, Department of Zoology, Hungarian Natural History Museum, Budapest, Baross u. 13., 1088, Hungary
| | - Rebecca J Webb
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Claudia Wierzbicki
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Emma Wombwell
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - David M Aanensen
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridgeshire, UK
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 49, NO-7012 Trondheim, Norway
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Ché Weldon
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, CSIC c/ Jose Gutierrez Abascal 2, 28006 Madrid, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Trenton W J Garner
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
- Non-profit Association Zirichiltaggi-Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100 Sassari, Italy
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK.
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18
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19
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Wang Y, Sun S. Complete mitochondrial genome of the jellyfish, Rhopilema esculentum Kishinouye 1891 (Cnidaria: Scyphozoa) and the phylogenetic relationship in the related species. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:167-168. [PMID: 33490444 PMCID: PMC7800393 DOI: 10.1080/23802359.2017.1303342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The complete mitochondrial genome of Rhopilema esculentum collected from Jiaozhou Bay, China, was determined by next-generation sequencing. The mitogenome is a circular molecule 15,855 bp in length, including 13 protein-coding genes (Cox 1, Cox2, Atp 8, Atp 6, Cox 3, ND2, ND5, ND 6, ND3, ND4L, ND1,ND4, Cytb), 5 tRNAs (tRNA-Trp, tRNA-Met, tRNA-Leu, tRNA-Ser, tRNA-Gln), 2 rRNA genes (small subunit RNA and large subunit RNA) and 1 putative control region. The phylogenetic tree in the related species showed that R. esculentum is close to Nemopilema nomurai.
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Affiliation(s)
- Yantao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Song Sun
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Jiaozhou Bay Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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20
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Wang Y, Sun S. Complete mitochondrial genome of the jellyfish, Nemopilema nomurai (Cnidaria: Scyphozoa) and the phylogenetic relationship in the related species. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:165-166. [PMID: 33473754 PMCID: PMC7800497 DOI: 10.1080/23802359.2017.1298417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The complete mitochondrial genome of giant jellyfish Nemopilema nomurai collected from East China Sea was determined by next-generation sequencing. The mitogenome is a circular molecule 17,024 bp in length, including 13 protein-coding genes (including Cox 1, Cox2, Atp 8, Atp 6, ND5, ND 6, ND3, ND41, ND1,ND4, Cytb), 6 tRNAs (tRNA-Trp, tRNA-Met, tRNA-Val, tRNA-Arg, tRNA-Glu, tRNA-Asn), 2 rRNA genes (small subunit RNA and large subunit RNA), and 1 putative control region. The phylogenetic tree in the related species showed that giant jellyfish is close to Hydraoligaclis.
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Affiliation(s)
- Yantao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Song Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Jiaozhou Bay Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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21
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Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
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22
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Pratlong M, Rancurel C, Pontarotti P, Aurelle D. Monophyly of Anthozoa (Cnidaria): why do nuclear and mitochondrial phylogenies disagree? ZOOL SCR 2016. [DOI: 10.1111/zsc.12208] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marine Pratlong
- Aix Marseille Univ; Univ Avignon; CNRS; IRD; IMBE; Marseille France
- Aix Marseille Univ; CNRS; Centrale Marseille, I2M, Equipe Evolution Biologique et Modélisation; Marseille France
| | - Corinne Rancurel
- INRA; University Nice Sophia Antipolis; CNRS; UMR 1355-7254 Institut Sophia Agrobiotech; Sophia Antipolis France
| | - Pierre Pontarotti
- Aix Marseille Univ; CNRS; Centrale Marseille, I2M, Equipe Evolution Biologique et Modélisation; Marseille France
| | - Didier Aurelle
- Aix Marseille Univ; Univ Avignon; CNRS; IRD; IMBE; Marseille France
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23
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Rizman-Idid M, Farrah-Azwa AB, Chong VC. Preliminary Taxonomic Survey and Molecular Documentation of Jellyfish Species (Cnidaria: Scyphozoa and Cubozoa) in Malaysia. Zool Stud 2016; 55:e35. [PMID: 31966180 PMCID: PMC6511900 DOI: 10.6620/zs.2016.55-35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 05/24/2016] [Indexed: 11/18/2022]
Abstract
Mohammed Rizman-Idid, Abu Bakar Farrah-Azwa, and Ving Ching Chong (2016) Scientific enquiries into jellyfish blooms and associated problems are often deterred by the lack of taxonomical and ecological studies worldwide. Taxonomic difficulty is attributed to the high degree of morphological variations among and within species. To date, only two scyphozoan jellyfish species have been documented from field surveys in Malaysian waters, whereas another four Malaysian scyphozoan and two cubozoan jellyfish species have been mentioned in toxicological studies. None of these species have; however, been verified. This study thus aimed to document and resolves the uncertainty of earlier identified species in the region using morphology and molecular DNA sequencing. Jellyfish specimens were collected from Malaysian waters in the Straits of Malacca, South-China Sea and the Sulu-Sulawesi Sea over two years (June 2008 to October 2010), and their DNA sequences were compared with those from the Atlantic and Pacific regions. Ten scyphozoan and two cubozoan species were recorded in Malaysian waters (South China Sea and Straits of Malacca). These jellyfish included eight species from the order Rhizostomeae (Rhizostomatidae, Lobonematidae, Mastigiidae, Catostylidae and Cepheidae), two species from Semaestomeae (Pelagiidae and Cyaneidae) and two species from class Cubozoa; one from order Carybdeida (family Carukiidae) and another from order Chirodropida (family Chiropsalmidae). Molecular identification of species using phylogenetic approaches was based on DNA sequences of partial cytochrome oxidase I (COI), 16S and internal transcribed spacer (ITS1) regions. The COI phylogenetic tree of Cubozoa and Scyphozoa species from the Atlantic and Pacific regions showed distinct clustering of six Malaysian jellyfish species. However, most of the deeper divergences and relationships between the families were unresolved, which were also observed in the 16S and ITS1 phylogenetic trees. The Malaysian edible species Lobonemoides robustus, Rhopilema hispidum and Rhopilema esculentum were grouped within Rhizostomeae, whereas other scyphozoans showed phylogenetic affinities to Semaestomeae and Kolpophorae. Chrysaora and Cyanea appeared non-monophyletic; however their paraphyly was not confirmed. This study has provided the much needed baseline information on the taxonomy of Malaysian jellyfish species which have been substantiated by partial COI, 16S and ITS1 sequences. A total of 12 putative species of jellyfish were identified, which encompassed 12 genera.
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Affiliation(s)
- Mohammed Rizman-Idid
- Institute of Ocean and Earth Sciences, University of
Malaya, 50603 Kuala Lumpur, Malaysia
| | - Abu Bakar Farrah-Azwa
- Institute of Biological Sciences, University of Malaya,
50603 Kuala Lumpur, Malaysia. E-mail: ,
| | - Ving Ching Chong
- Institute of Ocean and Earth Sciences, University of
Malaya, 50603 Kuala Lumpur, Malaysia
- Institute of Biological Sciences, University of Malaya,
50603 Kuala Lumpur, Malaysia. E-mail: ,
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24
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Kayal E, Bentlage B, Collins AG. Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa). RNA Biol 2016; 13:799-809. [PMID: 27267414 DOI: 10.1080/15476286.2016.1194161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In most animals, the mitochondrial genome is characterized by its small size, organization into a single circular molecule, and a relative conservation of the number of encoded genes. In box jellyfish (Cubozoa, Cnidaria), the mitochondrial genome is organized into 8 linear mito-chromosomes harboring between one and 4 genes each, including 2 extra protein-coding genes: mt-polB and orf314. Such an organization challenges the traditional view of mitochondrial DNA (mtDNA) expression in animals. In this study, we investigate the pattern of mitochondrial gene expression in the box jellyfish Alatina alata, as well as several key nuclear-encoded molecular pathways involved in the processing of mitochondrial gene transcription. RESULTS Read coverage of DNA-seq data is relatively uniform for all 8 mito-chromosomes, suggesting that each mito-chromosome is present in equimolar proportion in the mitochondrion. Comparison of DNA and RNA-seq based assemblies indicates that mito-chromosomes are transcribed into individual transcripts in which the beginning and ending are highly conserved. Expression levels for mt-polB and orf314 are similar to those of other mitochondrial-encoded genes, which provides further evidence for them having functional roles in the mitochondrion. Survey of the transcriptome suggests recognition of the mitochondrial tRNA-Met by the cytoplasmic aminoacyl-tRNA synthetase counterpart and C-to-U editing of the cytoplasmic tRNA-Trp after import into the mitochondrion. Moreover, several mitochondrial ribosomal proteins appear to be lost. CONCLUSIONS This study represents the first survey of mitochondrial gene expression of the linear multi-chromosomal mtDNA in box jellyfish (Cubozoa). Future exploration of small RNAs and the proteome of the mitochondrion will test the hypotheses presented herein.
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Affiliation(s)
- Ehsan Kayal
- a Department of Invertebrate Zoology , National Museum of Natural History, Smithsonian Institution , Washington DC , USA
| | - Bastian Bentlage
- a Department of Invertebrate Zoology , National Museum of Natural History, Smithsonian Institution , Washington DC , USA
| | - Allen G Collins
- a Department of Invertebrate Zoology , National Museum of Natural History, Smithsonian Institution , Washington DC , USA.,b National Systematics Laboratory of NOAA's Fisheries Service, National Museum of Natural History , Washington , DC , USA
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Review: can diet influence the selective advantage of mitochondrial DNA haplotypes? Biosci Rep 2015; 35:BSR20150232. [PMID: 26543031 PMCID: PMC4708006 DOI: 10.1042/bsr20150232] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 01/12/2023] Open
Abstract
This review explores the potential for changes in dietary macronutrients to differentially influence mitochondrial bioenergetics and thereby the frequency of mtDNA haplotypes in natural populations. Such dietary modification may be seasonal or result from biogeographic or demographic shifts. Mechanistically, mtDNA haplotypes may influence the activity of the electron transport system (ETS), retrograde signalling to the nuclear genome and affect epigenetic modifications. Thus, differential provisioning by macronutrients may lead to selection through changes in the levels of ATP production, modulation of metabolites (including AMP, reactive oxygen species (ROS) and the NAD+/NADH ratio) and potentially complex epigenetic effects. The exquisite complexity of dietary influence on haplotype frequency is further illustrated by the fact that macronutrients may differentially influence the selective advantage of specific mutations in different life-history stages. In Drosophila, complex I mutations may affect larval growth because dietary nutrients are fed through this complex in immaturity. In contrast, the majority of electrons are provided to complex III in adult flies. We conclude the review with a case study that considers specific interactions between diet and complex I of the ETS. Complex I is the first enzyme of the mitochondrial ETS and co-ordinates in the oxidation of NADH and transfer of electrons to ubiquinone. Although the supposition that mtDNA variants may be selected upon by dietary macronutrients could be intuitively consistent to some and counter intuitive to others, it must face a multitude of scientific hurdles before it can be recognized.
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Figueroa DF, Baco AR. Octocoral mitochondrial genomes provide insights into the phylogenetic history of gene order rearrangements, order reversals, and cnidarian phylogenetics. Genome Biol Evol 2014; 7:391-409. [PMID: 25539723 PMCID: PMC4316637 DOI: 10.1093/gbe/evu286] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2014] [Indexed: 11/24/2022] Open
Abstract
We use full mitochondrial genomes to test the robustness of the phylogeny of the Octocorallia, to determine the evolutionary pathway for the five known mitochondrial gene rearrangements in octocorals, and to test the suitability of using mitochondrial genomes for higher taxonomic-level phylogenetic reconstructions. Our phylogeny supports three major divisions within the Octocorallia and show that Paragorgiidae is paraphyletic, with Sibogagorgia forming a sister branch to the Coralliidae. Furthermore, Sibogagorgia cauliflora has what is presumed to be the ancestral gene order in octocorals, but the presence of a pair of inverted repeat sequences suggest that this gene order was not conserved but rather evolved back to this apparent ancestral state. Based on this we recommend the resurrection of the family Sibogagorgiidae to fix the paraphyly of the Paragorgiidae. This is the first study to show that in the Octocorallia, mitochondrial gene orders have evolved back to an ancestral state after going through a gene rearrangement, with at least one of the gene orders evolving independently in different lineages. A number of studies have used gene boundaries to determine the type of mitochondrial gene arrangement present. However, our findings suggest that this method known as gene junction screening may miss evolutionary reversals. Additionally, substitution saturation analysis demonstrates that while whole mitochondrial genomes can be used effectively for phylogenetic analyses within Octocorallia, their utility at higher taxonomic levels within Cnidaria is inadequate. Therefore for phylogenetic reconstruction at taxonomic levels higher than subclass within the Cnidaria, nuclear genes will be required, even when whole mitochondrial genomes are available.
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Affiliation(s)
- Diego F Figueroa
- Present address: Department of Biological Sciences, University of Texas, Brownsville, TX
| | - Amy R Baco
- Department of Earth, Ocean and Atmospheric Science, Florida State University
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Abstract
Since the unexpected discovery that mitochondria contain their own distinct DNA molecules, studies of the mitochondrial DNA (mtDNA) have yielded many surprises. In animals, transmission of the mtDNA genome is explicitly non-Mendelian, with a very high number of genome copies being inherited from the mother after a drastic bottleneck. Recent work has begun to uncover the molecular details of this unusual mode of transmission. Many surprising variations in animal mitochondrial biology are known; however, a series of recent studies have identified a core of evolutionarily conserved mechanisms relating to mtDNA inheritance, e.g., mtDNA bottlenecks during germ cell development, selection against specific mtDNA mutation types during maternal transmission, and targeted destruction of sperm mitochondria. In this review, we outline recent literature on the transmission of mtDNA in animals and highlight the implications for human health and ageing.
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Breton S, Milani L, Ghiselli F, Guerra D, Stewart DT, Passamonti M. A resourceful genome: updating the functional repertoire and evolutionary role of animal mitochondrial DNAs. Trends Genet 2014; 30:555-64. [PMID: 25263762 DOI: 10.1016/j.tig.2014.09.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 11/24/2022]
Abstract
Recent data from mitochondrial genomics and proteomics research demonstrate the existence of several atypical mitochondrial protein-coding genes (other than the standard set of 13) and the involvement of mtDNA-encoded proteins in functions other than energy production in several animal species including humans. These results are of considerable importance for evolutionary and cellular biology because they indicate that animal mtDNAs have a larger functional repertoire than previously believed. This review summarizes recent studies on animal species with a non-standard mitochondrial functional repertoire and discusses how these genetic novelties represent promising candidates for studying the role of the mitochondrial genome in speciation.
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Affiliation(s)
- Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, 90 Avenue Vincent d'Indy, Montréal, Québec H2V 2S9, Canada.
| | - Liliana Milani
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Fabrizio Ghiselli
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Davide Guerra
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Donald T Stewart
- Department of Biology, Acadia University, 24 University Avenue, Wolfville, Nova Scotia B4P 2R6, Canada
| | - Marco Passamonti
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
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Plazzi F, Cassano A, Passamonti M. The quest for Doubly Uniparental Inheritance in heterodont bivalves and its detection inMeretrix lamarckii(Veneridae: Meretricinae). J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12078] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Federico Plazzi
- Dipartimento di Scienze Biologiche; Geologiche e Ambientali; Bologna Italy
| | - Antonello Cassano
- Dipartimento di Scienze Biologiche; Geologiche e Ambientali; Bologna Italy
| | - Marco Passamonti
- Dipartimento di Scienze Biologiche; Geologiche e Ambientali; Bologna Italy
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31
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Milani L, Ghiselli F, Guerra D, Breton S, Passamonti M. A comparative analysis of mitochondrial ORFans: new clues on their origin and role in species with doubly uniparental inheritance of mitochondria. Genome Biol Evol 2013; 5:1408-34. [PMID: 23824218 PMCID: PMC3730352 DOI: 10.1093/gbe/evt101] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite numerous comparative mitochondrial genomics studies revealing that animal mitochondrial genomes are highly conserved in terms of gene content, supplementary genes are sometimes found, often arising from gene duplication. Mitochondrial ORFans (ORFs having no detectable homology and unknown function) were found in bivalve molluscs with Doubly Uniparental Inheritance (DUI) of mitochondria. In DUI animals, two mitochondrial lineages are present: one transmitted through females (F-type) and the other through males (M-type), each showing a specific and conserved ORF. The analysis of 34 mitochondrial major Unassigned Regions of Musculista senhousia F- and M-mtDNA allowed us to verify the presence of novel mitochondrial ORFs in this species and to compare them with ORFs from other species with ascertained DUI, with other bivalves and with animals showing new mitochondrial elements. Overall, 17 ORFans from nine species were analyzed for structure and function. Many clues suggest that the analyzed ORFans arose from endogenization of viral genes. The co-option of such novel genes by viral hosts may have determined some evolutionary aspects of host life cycle, possibly involving mitochondria. The structure similarity of DUI ORFans within evolutionary lineages may also indicate that they originated from independent events. If these novel ORFs are in some way linked to DUI establishment, a multiple origin of DUI has to be considered. These putative proteins may have a role in the maintenance of sperm mitochondria during embryo development, possibly masking them from the degradation processes that normally affect sperm mitochondria in species with strictly maternal inheritance.
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Affiliation(s)
- Liliana Milani
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Bologna, Italy.
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Abstract
Recently, it was shown that gene conversion between the ends of linear mitochondrial chromosomes can cause telomere expansion and the duplication of subtelomeric loci. However, it is not yet known how widespread this phenomenon is and how significantly it has impacted organelle genome architecture. Using linear mitochondrial DNAs and mitochondrial plasmids from diverse eukaryotes, we argue that telomeric recombination has played a major role in fashioning linear organelle chromosomes. We find that mitochondrial telomeres frequently expand into subtelomeric regions, resulting in gene duplications, homogenizations, and/or fragmentations. We suggest that these features are a product of subtelomeric gene conversion, provide a hypothetical model for this process, and employ genetic diversity data to support the idea that the greater the effective population size the greater the potential for gene conversion between subtelomeric loci.
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Affiliation(s)
- David Roy Smith
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada.
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Doublet V, Helleu Q, Raimond R, Souty-Grosset C, Marcadé I. Inverted repeats and genome architecture conversions of terrestrial isopods mitochondrial DNA. J Mol Evol 2013; 77:107-18. [PMID: 24068302 DOI: 10.1007/s00239-013-9587-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Abstract
Mitochondrial DNA (mtDNA) is usually depicted as a circular molecule, however, there is increasing evidence that linearization of mtDNA evolved independently many times in organisms such as fungi, unicellular eukaryotes, and animals. Recent observations in various models with linear mtDNA revealed the presence of conserved inverted repeats (IR) at both ends that, when they become single-stranded, may be able to fold on themselves to create telomeric-hairpins involved in genome architecture conversions. The atypical mtDNA of terrestrial isopods (Crustacea: Oniscidea) composed of linear monomers and circular dimers is an interesting model to study genome architecture conversions. Here, we present the mtDNA control region sequences of two species of the genus Armadillidium: A. vulgare and A. pelagicum. All features of arthropods mtDNA control regions are present (origin of replication, poly-T stretch, GA and TA-rich blocks and one variable domain), plus a conserved IR. This IR can potentially fold into a hairpin structure and is present in two different orientations among the A. vulgare populations: either in one sense or in its reverse complement. This polymorphism, also observed in a single individual (heteroplasmy), might be a signature of genome architecture conversions from linear to circular monomeric mtDNA via successive opening and closing of the molecules.
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Affiliation(s)
- Vincent Doublet
- Equipe Ecologie Evolution Symbiose, Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, 40 Avenue du Recteur Pineau, 86022, Poitiers Cedex, France,
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Osigus HJ, Eitel M, Bernt M, Donath A, Schierwater B. Mitogenomics at the base of Metazoa. Mol Phylogenet Evol 2013; 69:339-51. [PMID: 23891951 DOI: 10.1016/j.ympev.2013.07.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/29/2013] [Accepted: 07/09/2013] [Indexed: 11/25/2022]
Abstract
Unraveling the base of metazoan evolution is of crucial importance for rooting the metazoan Tree of Life. This subject has attracted substantial attention for more than a century and recently fueled a burst of modern phylogenetic studies. Conflicting scenarios from different studies and incongruent results from nuclear versus mitochondrial markers challenge current molecular phylogenetic approaches. Here we analyze the presently most comprehensive data sets of mitochondrial genomes from non-bilaterian animals to illuminate the phylogenetic relationships among early branching metazoan phyla. The results of our analyses illustrate the value of mitogenomics and support previously known topologies between animal phyla but also identify several problematic taxa, which are sensitive to long branch artifacts or missing data.
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Affiliation(s)
- Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology and Evolution, Buenteweg 17d, D-30559 Hannover, Germany.
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35
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Song S, Jiang F, Yuan J, Guo W, Miao Y. Exceptionally high cumulative percentage of NUMTs originating from linear mitochondrial DNA molecules in the Hydra magnipapillata genome. BMC Genomics 2013; 14:447. [PMID: 23826818 PMCID: PMC3716686 DOI: 10.1186/1471-2164-14-447] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 07/03/2013] [Indexed: 11/10/2022] Open
Abstract
Background In contrast to most animal genomes, mitochondrial genomes in species belonging to the phylum Cnidaria show distinct variations in genome structure, including the mtDNA structure (linear or circular) and the presence or absence of introns in protein-coding genes. Therefore, the analysis of nuclear insertions of mitochondrial sequences (NUMTs) in cnidarians allows us to compare the NUMT content in animals with different mitochondrial genome structures. Results NUMT identification in the Hydra magnipapillata, Nematostella vectensis and Acropora digitifera genomes showed that the NUMT density in the H. magnipapillata genome clearly exceeds that in other two cnidarians with circular mitochondrial genomes. We found that H. magnipapillata is an exceptional ancestral metazoan with a high NUMT cumulative percentage but a large genome, and its mitochondrial genome linearisation might be responsible for the NUMT enrichment. We also detected the co-transposition of exonic and intronic fragments within NUMTs in N. vectensis and provided direct evidence that mitochondrial sequences can be transposed into the nuclear genome through DNA-mediated fragment transfer. In addition, NUMT expression analyses showed that NUMTs are co-expressed with adjacent protein-coding genes, suggesting the relevance of their biological function. Conclusions Taken together, our results provide valuable information for understanding the impact of mitochondrial genome structure on the interaction of mitochondrial molecules and nuclear genomes.
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Affiliation(s)
- Shen Song
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
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36
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Beagley CT, Wolstenholme DR. Characterization and localization of mitochondrial DNA-encoded tRNAs and nuclear DNA-encoded tRNAs in the sea anemone Metridium senile. Curr Genet 2013; 59:139-52. [PMID: 23801360 DOI: 10.1007/s00294-013-0395-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/12/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
Abstract
The mitochondrial (mt) genome of the sea anemone Metridium senile contains genes for only two transfer RNAs (tRNAs), tRNAf-Met and tRNATrp. Experiments were conducted to seek evidence for the occurrence of functional tRNAs corresponding to these genes and for the participation of nuclear DNA-encoded tRNAs in mt-protein synthesis. RNA sequences corresponding to the two mt-tRNA genes were located in mitochondria and it was shown that 3'-CC (and possibly A, but no other nucleotide) is added post-transcriptionally to the 3' end of at least 50 % of mt-tRNAf-Met molecules and to a small fraction of the mt-tRNATrp molecules. Using specific oligonucleotide primers based on expected nuclear DNA-encoded tRNAs in a series of RACE experiments, we located the nuclear genes for tRNAGln, tRNAIle, tRNAi-Met, tRNAVal and tRNAThr. Data from Northern blot analyses indicated that mtDNA-encoded tRNAf-Met is limited to mitochondria but that nuclear DNA-encoded tRNAVal and tRNAi-Met are present in the cytoplasm and in mitochondria. These data provide direct evidence that in M. senile, mature, functional tRNAs are transcribed from the mtDNA-encoded tRNAf-Met and tRNATrp genes, and are consistent with the interpretation that both nuclear DNA-encoded tRNAVal and tRNAi-Met are utilized in mitochondrial and cytosolic protein synthesis.
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Affiliation(s)
- C Timothy Beagley
- Department of Biology, University of Utah, Salt Lake City, UT 84121, USA.
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37
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Plazzi F, Ribani A, Passamonti M. The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with conchifera. BMC Genomics 2013; 14:409. [PMID: 23777315 PMCID: PMC3704766 DOI: 10.1186/1471-2164-14-409] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 06/11/2013] [Indexed: 11/17/2022] Open
Abstract
Background Bivalve mitochondrial genomes exhibit a wide array of uncommon features, like extensive gene rearrangements, large sizes, and unusual ways of inheritance. Species pertaining to the order Solemyida (subclass Opponobranchia) show many peculiar evolutionary adaptations, f.i. extensive symbiosis with chemoautotrophic bacteria. Despite Opponobranchia are central in bivalve phylogeny, being considered the sister group of all Autobranchia, a complete mitochondrial genome has not been sequenced yet. Results In this paper, we characterized the complete mitochondrial genome of the Atlantic awning clam Solemya velum: A-T content, gene arrangement and other features are more similar to putative ancestral mollusks than to other bivalves. Two supranumerary open reading frames are present in a large, otherwise unassigned, region, while the origin of replication could be located in a region upstream to the cox3 gene. Conclusions We show that S. velum mitogenome retains most of the ancestral conchiferan features, which is unusual among bivalve mollusks, and we discuss main peculiarities of this first example of an organellar genome coming from the subclass Opponobranchia. Mitochondrial genomes of Solemya (for bivalves) and Haliotis (for gastropods) seem to retain the original condition of mollusks, as most probably exemplified by Katharina.
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Affiliation(s)
- Federico Plazzi
- Department of Biological Geological and Environmental Sciences, University of Bologna, Via Selmi, 3, Bologna 40126, Italy.
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de Paula WBM, Lucas CH, Agip ANA, Vizcay-Barrena G, Allen JF. Energy, ageing, fidelity and sex: oocyte mitochondrial DNA as a protected genetic template. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120263. [PMID: 23754815 PMCID: PMC3685464 DOI: 10.1098/rstb.2012.0263] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Oxidative phosphorylation couples ATP synthesis to respiratory electron transport. In eukaryotes, this coupling occurs in mitochondria, which carry DNA. Respiratory electron transport in the presence of molecular oxygen generates free radicals, reactive oxygen species (ROS), which are mutagenic. In animals, mutational damage to mitochondrial DNA therefore accumulates within the lifespan of the individual. Fertilization generally requires motility of one gamete, and motility requires ATP. It has been proposed that oxidative phosphorylation is nevertheless absent in the special case of quiescent, template mitochondria, that these remain sequestered in oocytes and female germ lines and that oocyte mitochondrial DNA is thus protected from damage, but evidence to support that view has hitherto been lacking. Here we show that female gametes of Aurelia aurita, the common jellyfish, do not transcribe mitochondrial DNA, lack electron transport, and produce no free radicals. In contrast, male gametes actively transcribe mitochondrial genes for respiratory chain components and produce ROS. Electron microscopy shows that this functional division of labour between sperm and egg is accompanied by contrasting mitochondrial morphology. We suggest that mitochondrial anisogamy underlies division of any animal species into two sexes with complementary roles in sexual reproduction. We predict that quiescent oocyte mitochondria contain DNA as an unexpressed template that avoids mutational accumulation by being transmitted through the female germ line. The active descendants of oocyte mitochondria perform oxidative phosphorylation in somatic cells and in male gametes of each new generation, and the mutations that they accumulated are not inherited. We propose that the avoidance of ROS-dependent mutation is the evolutionary pressure underlying maternal mitochondrial inheritance and the developmental origin of the female germ line.
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Affiliation(s)
- Wilson B M de Paula
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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Uda K, Komeda Y, Fujita T, Iwasaki N, Bavestrello G, Giovine M, Cattaneo-Vietti R, Suzuki T. Complete mitochondrial genomes of the Japanese pink coral (Corallium elatius) and the Mediterranean red coral (Corallium rubrum): a reevaluation of the phylogeny of the family Coralliidae based on molecular data. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2013; 8:209-19. [PMID: 23792378 DOI: 10.1016/j.cbd.2013.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/23/2013] [Accepted: 05/26/2013] [Indexed: 11/30/2022]
Abstract
Precious corals are soft corals belonging to the family Coralliidae (Anthozoa: Octocorallia: Alcyonacea) and class Anthozoa, whose skeletal axes are used for jewelry. The family Coralliidae includes ca. 40 species and was originally thought to comprise of the single genus Corallium. In 2003, Corallium was split into two genera, Corallium and Paracorallium, and seven species were moved to this newly identified genus on the bases of morphological features. Previously, we determined the complete mitochondrial genome sequence of two precious corals Paracorallium japonicum and Corallium konojoi, in order to clarify their systematic positions. The two genomes showed high nucleotide sequence identity, but their gene order arrangements were not identical. Here, we determined three complete mitochondrial genome sequences from the one specimen of Mediterranean Corallium rubrum and two specimens of Corallium elatius coming from Kagoshima (South Japan). The circular mitochondrial genomes of C. rubrum and C. elatius are 18,915bp and 18,969-18,970bp in length, respectively, and encode 14 typical octocorallian protein-coding genes (nad1-6, nad4L, cox1-3, cob, atp6, atp8, and mtMutS, which is an octocoral-specific mismatch repair gene homologue), two ribosomal RNA genes (rns and rnl), and one transfer RNA (trnM). The overall nucleotide differences between C. konojoi and each C. elatius haplotype (T2007 and I2011) are only 10 and 11 nucleotides, respectively; this degree of similarity indicates that C. elatius and C. konojoi are very closely related species. Notably, the C. rubrum mitochondrial genome shows more nucleotide sequence identity to P. japonicum (99.5%) than to its congeneric species C. konojoi (95.3%) and C. elatius (95.3%). Moreover, the gene order arrangement of C. rubrum was the same as that of P. japonicum, while that of C. elatius was the same as C. konojoi. Phylogenetic analysis based on three mitochondrial genes from 24 scleraxonian species shows that the family Coralliidae is separated into two distinct groups, recovering Corallium as a paraphyletic genus. Our results indicate that the currently accepted generic classification of Coralliidae should be reconsidered.
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Affiliation(s)
- Kouji Uda
- Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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40
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Hwang DS, Park E, Won YJ, Lee WJ, Shin K, Lee JS. Complete mitochondrial genome of the jellyfish, Chrysaora quinquecirrha (Cnidaria, Scyphozoa). ACTA ACUST UNITED AC 2013; 25:25-6. [PMID: 23488924 DOI: 10.3109/19401736.2013.775272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We sequenced 16,775 bp of the linear mitochondrial DNA of the jellyfish Chrysaora quinquecirrha and characterized them. C. quinquecirrha has 13 protein-coding genes (PCGs), 16S rRNA and 12S rRNA with 3 tRNAs (tRNA-Leu, tRNA-Ser(TGA), tRNA-Met) as shown in Aurelia sp. nov. Both have another two PCGs such as helicase and orf363 with telomeres at both ends. The PCGs of C. quinquecirrha shows anti-G bias on 2nd and 3rd positions of PCGs as well as anti-C bias on 1st and 3rd positions of PCGs.
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Affiliation(s)
- Dae-Sik Hwang
- Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University , Seoul , South Korea
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Hwang DS, Park E, Won YJ, Lee JS. Complete mitochondrial genome of the moon jellyfish, Aurelia sp. nov. (Cnidaria, Scyphozoa). ACTA ACUST UNITED AC 2013; 25:27-8. [PMID: 23488923 DOI: 10.3109/19401736.2013.775273] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We sequenced 16,971 bp of the linear mitochondrial DNA of the moon jellyfish Aurelia sp. nov. and characterized it by comparing with Aurelia aurita. They had 13 protein-coding genes (PCGs), 16S rRNA and 12S rRNA with three tRNAs (tRNA-Leu, tRNA-Ser(TGA), tRNA-Met). Both have another two PCGs, orf969 and orf324 with telomeres at both ends. After comparison of Aurelia sp. nov. with Aurelia aurita, we found low-protein similarity of orf969 (59%) and orf324 (75%), respectively, while the other 13 PCGs showed 80% to 98% protein similarities.
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Affiliation(s)
- Dae-Sik Hwang
- Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University , Seoul , South Korea
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Kayal E, Roure B, Philippe H, Collins AG, Lavrov DV. Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evol Biol 2013; 13:5. [PMID: 23302374 PMCID: PMC3598815 DOI: 10.1186/1471-2148-13-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 12/21/2012] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) - cnidarians with a reproductive polyp and the absence of a medusa stage - and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) - cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. RESULTS We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. CONCLUSIONS Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in these groups are plesiomorphies, originated in the branch leading to Medusozoa. The expansion of mitogenomic data along with improvements in phylogenetic inference methods and use of additional nuclear markers will further enhance our understanding of the phylogenetic relationships and character evolution within Cnidaria.
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Affiliation(s)
- Ehsan Kayal
- Dept. Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, Iowa, USA
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 20013-7012, Washington, DC, USA
| | - Béatrice Roure
- Dept. Biochimie, Fac. Médecine, Université de Montral, Pavillon Roger-Gaudry, C.P. 6128, Succ. Centre-Ville, H3C 3J7, Montral, QC, Canada
| | - Hervé Philippe
- Dept. Biochimie, Fac. Médecine, Université de Montral, Pavillon Roger-Gaudry, C.P. 6128, Succ. Centre-Ville, H3C 3J7, Montral, QC, Canada
| | - Allen G Collins
- National Systematics Laboratory of NOAA’s Fisheries Service, National Museum of Natural History, MRC-153, Smithsonian Institution, PO Box 37012, 20013-7012, Washington, DC, USA
| | - Dennis V Lavrov
- Dept. Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, Iowa, USA
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Beaudet D, Terrat Y, Halary S, de la Providencia IE, Hijri M. Mitochondrial genome rearrangements in glomus species triggered by homologous recombination between distinct mtDNA haplotypes. Genome Biol Evol 2013; 5:1628-43. [PMID: 23925788 PMCID: PMC3787672 DOI: 10.1093/gbe/evt120] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2013] [Indexed: 02/02/2023] Open
Abstract
Comparative mitochondrial genomics of arbuscular mycorrhizal fungi (AMF) provide new avenues to overcome long-lasting obstacles that have hampered studies aimed at understanding the community structure, diversity, and evolution of these multinucleated and genetically polymorphic organisms.AMF mitochondrial (mt) genomes are homogeneous within isolates, and their intergenic regions harbor numerous mobile elements that have rapidly diverged, including homing endonuclease genes, small inverted repeats, and plasmid-related DNA polymerase genes (dpo), making them suitable targets for the development of reliable strain-specific markers. However, these elements may also lead to genome rearrangements through homologous recombination, although this has never previously been reported in this group of obligate symbiotic fungi. To investigate whether such rearrangements are present and caused by mobile elements in AMF, the mitochondrial genomes from two Glomeraceae members (i.e., Glomus cerebriforme and Glomus sp.) with substantial mtDNA synteny divergence,were sequenced and compared with available glomeromycotan mitochondrial genomes. We used an extensive nucleotide/protein similarity network-based approach to investigated podiversity in AMF as well as in other organisms for which sequences are publicly available. We provide strong evidence of dpo-induced inter-haplotype recombination, leading to a reshuffled mitochondrial genome in Glomus sp. These findings raise questions as to whether AMF single spore cultivations artificially underestimate mtDNA genetic diversity.We assessed potential dpo dispersal mechanisms in AMF and inferred a robust phylogenetic relationship with plant mitochondrial plasmids. Along with other indirect evidence, our analyses indicate that members of the Glomeromycota phylum are potential donors of mitochondrial plasmids to plants.
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Affiliation(s)
- Denis Beaudet
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | | | | | - Ivan Enrique de la Providencia
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
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Zou H, Zhang J, Li W, Wu S, Wang G. Mitochondrial genome of the freshwater jellyfish Craspedacusta sowerbyi and phylogenetics of Medusozoa. PLoS One 2012; 7:e51465. [PMID: 23240028 PMCID: PMC3519871 DOI: 10.1371/journal.pone.0051465] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 11/05/2012] [Indexed: 12/24/2022] Open
Abstract
The 17,922 base pairs (bp) nucleotide sequence of the linear mitochondrial DNA (mtDNA) molecule of the freshwater jellyfish Craspedacusta sowerbyi (Hydrozoa, Trachylina, Limnomedusae) has been determined. This sequence exhibits surprisingly low A+T content (57.1%), containing genes for 13 energy pathway proteins, a small and a large subunit rRNAs, and methionine and tryptophan tRNAs. Mitochondrial ancestral medusozoan gene order (AMGO) was found in the C. sowerbyi, as those found in Cubaia aphrodite (Hydrozoa, Trachylina, Limnomedusae), discomedusan Scyphozoa and Staurozoa. The genes of C. sowerbyi mtDNA are arranged in two clusters with opposite transcriptional polarities, whereby transcription proceeds toward the ends of the DNA molecule. Identical inverted terminal repeats (ITRs) flank the ends of the mitochondrial DNA molecule, a characteristic typical of medusozoans. In addition, two open reading frames (ORFs) of 354 and 1611 bp in length were found downstream of the large subunit rRNA gene, similar to the two ORFs of ORF314 and polB discovered in the linear mtDNA of C. aphrodite, discomedusan Scyphozoa and Staurozoa. Phylogenetic analyses of C. sowerbyi and other cnidarians were carried out based on both nucleotide and inferred amino acid sequences of the 13 mitochondrial energy pathway genes. Our working hypothesis supports the monophyletic Medusozoa being a sister group to Octocorallia (Cnidaria, Anthozoa). Within Medusozoa, the phylogenetic analysis suggests that Staurozoa may be the earliest diverging class and the sister group of all other medusozoans. Cubozoa and coronate Scyphozoa form a clade that is the sister group of Hydrozoa plus discomedusan Scyphozoa. Hydrozoa is the sister group of discomedusan Scyphozoa. Semaeostomeae is a paraphyletic clade with Rhizostomeae, while Limnomedusae (Trachylina) is the sister group of hydroidolinans and may be the earliest diverging lineage among Hydrozoa.
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Affiliation(s)
- Hong Zou
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Graduate School of the Chinese Academy of Sciences, Beijing, P.R. China
| | - Jin Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Graduate School of the Chinese Academy of Sciences, Beijing, P.R. China
| | - Wenxiang Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
| | - Shangong Wu
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
| | - Guitang Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- * E-mail:
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Lavrov DV, Pett W, Voigt O, Wörheide G, Forget L, Lang BF, Kayal E. Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): six linear chromosomes, fragmented rRNAs, tRNA editing, and a novel genetic code. Mol Biol Evol 2012; 30:865-80. [PMID: 23223758 DOI: 10.1093/molbev/mss274] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sponges (phylum Porifera) are a large and ancient group of morphologically simple but ecologically important aquatic animals. Although their body plan and lifestyle are relatively uniform, sponges show extensive molecular and genetic diversity. In particular, mitochondrial genomes from three of the four previously studied classes of Porifera (Demospongiae, Hexactinellida, and Homoscleromorpha) have distinct gene contents, genome organizations, and evolutionary rates. Here, we report the mitochondrial genome of Clathrina clathrus (Calcinea, Clathrinidae), a representative of the fourth poriferan class, the Calcarea, which proves to be the most unusual. Clathrina clathrus mitochondrial DNA (mtDNA) consists of six linear chromosomes 7.6-9.4 kb in size and encodes at least 37 genes: 13 protein codings, 2 ribosomal RNAs (rRNAs), and 24 transfer RNAs (tRNAs). Protein genes include atp9, which has now been found in all major sponge lineages, but no atp8. Our analyses further reveal the presence of a novel genetic code that involves unique reassignments of the UAG codons from termination to tyrosine and of the CGN codons from arginine to glycine. Clathrina clathrus mitochondrial rRNAs are encoded in three (srRNA) and ≥6 (lrRNA) fragments distributed out of order and on several chromosomes. The encoded tRNAs contain multiple mismatches in the aminoacyl acceptor stems that are repaired posttranscriptionally by 3'-end RNA editing. Although our analysis does not resolve the phylogenetic position of calcareous sponges, likely due to their high rates of mitochondrial sequence evolution, it confirms mtDNA as a promising marker for population studies in this group. The combination of unusual mitochondrial features in C. clathrus redefines the extremes of mtDNA evolution in animals and further argues against the idea of a "typical animal mtDNA."
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, USA.
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Brockman SA, McFadden CS. The mitochondrial genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports intramolecular recombination as the primary mechanism of gene rearrangement in octocoral mitochondrial genomes. Genome Biol Evol 2012; 4:994-1006. [PMID: 22975720 PMCID: PMC3468961 DOI: 10.1093/gbe/evs074] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene content and nucleotide composition are, however, identical to most other octocorals, and the additional length is due to the presence of two large, noncoding intergenic regions. Relative to the presumed ancestral octocoral gene order, in P. aldersladei a block of three protein-coding genes (nad6–nad3–nad4l) has been translocated and inverted. Mapping the distribution of mt gene arrangements onto a taxonomically comprehensive phylogeny of Octocorallia suggests that all of the known octocoral gene orders have evolved by successive inversions of one or more evolutionarily conserved blocks of protein-coding genes. This mode of genome evolution is unique among Metazoa, and contrasts strongly with that observed in Hexacorallia, in which extreme gene shuffling has occurred among taxonomic orders. Two of the four conserved gene blocks found in Octocorallia are, however, also conserved in the linear mt genomes of Medusozoa and in one group of Demospongiae. We speculate that the rate and mechanism of gene rearrangement in octocorals may be influenced by the presence in their mt genomes of mtMutS, a putatively active DNA mismatch repair protein that may also play a role in mediating intramolecular recombination.
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Nardi F, Carapelli A, Frati F. Repeated regions in mitochondrial genomes: Distribution, origin and evolutionary significance. Mitochondrion 2012; 12:483-91. [DOI: 10.1016/j.mito.2012.07.105] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 04/05/2012] [Accepted: 07/10/2012] [Indexed: 10/28/2022]
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Doublet V, Raimond R, Grandjean F, Lafitte A, Souty-Grosset C, Marcadé I. Widespread atypical mitochondrial DNA structure in isopods (Crustacea, Peracarida) related to a constitutive heteroplasmy in terrestrial species. Genome 2012; 55:234-44. [PMID: 22376074 DOI: 10.1139/g2012-008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Metazoan mitochondrial DNA (mtDNA) is generally composed of circular monomeric molecules. However, a few exceptions do exist and among them two terrestrial isopods Armadillidium vulgare and Porcellionides pruinosus have an atypical mtDNA composed of linear monomers associated with circular "head-to-head" dimers: a very unusual structure for animal mtDNA genome. To assess the distribution of this atypical mtDNA among isopods, we performed RFLP and Southern blot analyses on mtDNA of 16 terrestrial (Oniscidea family) and two aquatic isopod species: the marine Sphaeroma serratum (suborder Flabellifera, sister group of Oniscidea) and the freshwater Asellus aquaticus (Asellota, early derived taxon of isopod). The atypical mtDNA structure was observed in 15 terrestrial isopod species and A. aquaticus, suggesting a wide distribution of atypical mtDNA among isopods. However, a typical metazoan mtDNA structure was detected in the marine isopod S. serratum and the Oniscidea Ligia oceanica . Our results suggest two possible scenarios: an early origin of the atypical mtDNA in isopods followed by reversion to the typical ancestral mtDNA structure for several species, or a convergent appearance of the atypical mtDNA structure in two isopod suborders. We compare this distribution of the atypical mtDNA structure with the presence of a heteroplasmy also observed in the mtDNA of several terrestrial isopod species. We discuss if this transmitted heteroplasmy is vectored by the atypical mtDNA and its impact on the maintenance of the atypical mtDNA in isopods.
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Affiliation(s)
- Vincent Doublet
- Université de Poitiers, UMR CNRS 7267, Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 40 Avenue du Recteur Pineau, 86022 Poitiers CEDEX, France.
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Park E, Hwang DS, Lee JS, Song JI, Seo TK, Won YJ. Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. Mol Phylogenet Evol 2012; 62:329-45. [DOI: 10.1016/j.ympev.2011.10.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 10/01/2011] [Accepted: 10/04/2011] [Indexed: 01/18/2023]
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Smith DR, Kayal E, Yanagihara AA, Collins AG, Pirro S, Keeling PJ. First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution. Genome Biol Evol 2011; 4:52-8. [PMID: 22117085 PMCID: PMC3268669 DOI: 10.1093/gbe/evr127] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Animal mitochondrial DNAs (mtDNAs) are typically single circular chromosomes, with the exception of those from medusozoan cnidarians (jellyfish and hydroids), which are linear and sometimes fragmented. Most medusozoans have linear monomeric or linear bipartite mitochondrial genomes, but preliminary data have suggested that box jellyfish (cubozoans) have mtDNAs that consist of many linear chromosomes. Here, we present the complete mtDNA sequence from the winged box jellyfish Alatina moseri (the first from a cubozoan). This genome contains unprecedented levels of fragmentation: 18 unique genes distributed over eight 2.9- to 4.6-kb linear chromosomes. The telomeres are identical within and between chromosomes, and recombination between subtelomeric sequences has led to many genes initiating or terminating with sequences from other genes (the most extreme case being 150 nt of a ribosomal RNA containing the 5′ end of nad2), providing evidence for a gene conversion–based model of telomere evolution. The silent-site nucleotide variation within the A. moseri mtDNA is among the highest observed from a eukaryotic genome and may be associated with elevated rates of recombination.
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Affiliation(s)
- David Roy Smith
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada.
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