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Jakovlić I, Ye T, Zou H, Zhu F, Shi Y, Ma Y, Wang GT, Li WX, Zhang D. Drivers of interlineage variability in mitogenomic evolutionary rates in Platyhelminthes. Heredity (Edinb) 2024:10.1038/s41437-024-00712-2. [PMID: 39095653 DOI: 10.1038/s41437-024-00712-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
Studies of forces driving interlineage variability in the evolutionary rates (both sequence and architecture) of mitochondrial genomes often produce contradictory results. Flatworms (Platyhelminthes) exhibit the fastest-evolving mitogenomic sequences among all bilaterian phyla. To test the effects of multiple factors previously associated with different aspects of mitogenomic evolution, we used mitogenomes of 223 flatworm species, phylogenetic multilevel regression models, and causal inference. Thermic host environment (endothermic vs. ectothermic) had nonsignificant impacts on both sequence evolution and mitogenomic size. Mitogenomic gene order rearrangements (GORR) were mostly positively correlated with mitogenomic size (R2 ≈ 20-30%). Longevity was not (negatively) correlated with sequence evolution in flatworms. The predominantly free-living "turbellaria" exhibited much shorter branches and faster-evolving mitogenomic architecture than parasitic Neodermata. As a result, "parasitism" had a strong explanatory power on the branch length variability (>90%), and there was a negative correlation between GORR and branch length. However, the stem branch of Neodermata comprised 63.6% of the total average branch length. This evolutionary period was also marked by a high rate of gene order rearrangements in the ancestral Neodermata. We discuss how this period of rapid evolution deep in the evolutionary history may have decoupled sequence evolution rates from longevity and GORR, and overestimated the explanatory power of "parasitism". This study shows that impacts of variables often vary across lineages, and stresses the importance accounting for the episodic nature of evolutionary patterns in studies of mitogenomic evolution.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Tong Ye
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fengyue Zhu
- National Agricultural Science Observing and Experimental Station of Chongqing, Chongqing, 401329, China
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, 430073, China
| | - Yuying Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yiwen Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Dong Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, 850011, China.
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Cheng WX, Wang J, Mao ML, Lu YB, Zou JX. The mitochondrial genome of Bottapotamon fukienense (Brachiura: Potamidae) is fragmented into two chromosomes. BMC Genomics 2024; 25:755. [PMID: 39095713 PMCID: PMC11295360 DOI: 10.1186/s12864-024-10657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND China is the hotspot of global freshwater crab diversity, but their wild populations are facing severe pressures associated with anthropogenic factors, necessitating the need to map their taxonomic and genetic diversity and design conservation policies. RESULTS Herein, we sequenced the mitochondrial genome of a Chinese freshwater crab species Bottapotamon fukienense, and found that it is fragmented into two chromosomes. We confirmed that fragmentation was not limited to a single specimen or population. Chromosome 1 comprised 15,111 base pairs (bp) and there were 26 genes and one pseudogene (pseudo-nad1) encoded on it. Chromosome 2 comprised 8,173 bp and there were 12 genes and two pseudogenes (pseudo-trnL2 and pseudo-rrnL) encoded on it. Combined, they comprise the largest mitogenome (23,284 bp) among the Potamidae. Bottapotamon was the only genus in the Potamidae dataset exhibiting rearrangements of protein-coding genes. Bottapotamon fukienense exhibited average rates of sequence evolution in the dataset and did not differ in selection pressures from the remaining Potamidae. CONCLUSIONS This is the first experimentally confirmed fragmentation of a mitogenome in crustaceans. While the mitogenome of B. fukienense exhibited multiple signs of elevated mitogenomic architecture evolution rates, including the exceptionally large size, duplicated genes, pseudogenisation, rearrangements of protein-coding genes, and fragmentation, there is no evidence that this is matched by elevated sequence evolutionary rates or changes in selection pressures.
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Affiliation(s)
- Wang-Xinjun Cheng
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Jun Wang
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Mei-Lin Mao
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Yuan-Biao Lu
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Jie-Xin Zou
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China.
- Provincial Key Laboratory for Drug Targeting and Drug Screening, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
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Gendron EMS, Qing X, Sevigny JL, Li H, Liu Z, Blaxter M, Powers TO, Thomas WK, Porazinska DL. Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection. BMC Genomics 2024; 25:615. [PMID: 38890582 PMCID: PMC11184840 DOI: 10.1186/s12864-024-10500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. RESULTS Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. CONCLUSIONS Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.
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Affiliation(s)
- Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA.
| | - Xue Qing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Hongmei Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyin Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | | | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - W Kelly Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
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Zhang D, Chen X, Yang J, Yi W, Xie Q, Yang H, Sweet MH, Bu W, Li T. Phylogenetic placement and comparative analysis of the mitochondrial genomes of Idiostoloidea (Hemiptera: Heteroptera). Ecol Evol 2024; 14:e11328. [PMID: 38698924 PMCID: PMC11063732 DOI: 10.1002/ece3.11328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024] Open
Abstract
The classification system and the higher level phylogenetic relationships of Pentatomomorpha, the second largest infraorder of Heteroptera (Insecta: Hemiptera), have been debated and remain controversial over decades. In particular, the placement and phylogenetic relationship of Idiostoloidea are not well resolved, which hampers a better understanding of the evolutionary history of Pentatomomorpha. In this study, for the first time, we reported the complete mitochondrial genome for two narrowly distributed families of Idiostoloidea (including Idiostolidae and Henicocoridae), respectively. The length of the mitochondrial genome of Monteithocoris hirsutus and Henicocoris sp. is 16,632 and 16,013 bp, respectively. The content of AT is ranging from 75.15% to 80.48%. The mitogenomic structure of Idiostoloidea is highly conservative and there are no gene arrangements. By using the Bayesian inference, maximum likelihood, and Bayesian site-heterogeneous mixture model, we inferred the phylogenetic relationships within Pentatomomorpha and estimated their divergence times based on concatenated mitogenomes and nuclear ribosomal genes. Our results support the classification system of six superfamilies within Pentatomomorpha and confirm the monophyletic groups of each superfamily, with the following phylogenetic relationships: (Aradoidea + (Pentatomoidea + (Idiostoloidea + (Coreoidea + (Pyrrhocoroidea + Lygaeoidea))))). Furthermore, estimated divergence times revealed that most pentatomomorphan superfamilies and families diverged during the Late Jurassic to Early Cretaceous, which coincides with the explosive radiation of angiosperms.
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Affiliation(s)
- Danli Zhang
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - XiaoYan Chen
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Jingjing Yang
- College of Biological Sciences and TechnologyTaiyuan Normal UniversityJinzhongChina
| | - Wenbo Yi
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Qiang Xie
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - HuanHuan Yang
- School of BioengineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Merrill H. Sweet
- Department of Entomology, Plant Pathology, and Weed ScienceNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Wenjun Bu
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Teng Li
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
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Liang QR, Shi L. The first complete mitochondrial DNA of Tenuidactylus dadunensis (Squamata: Gekkonidae) and its phylogeny. Mitochondrial DNA B Resour 2024; 9:442-446. [PMID: 38586508 PMCID: PMC10993739 DOI: 10.1080/23802359.2024.2333566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
The complete mitochondrial DNA (mtDNA) of Tenuidactylus dadunensis (Squamata: Gekkonidae) was described by using next-generation sequencing. The total length of mtDNA was 16,893 bp, which contained 13 PCGs (COX1-3, ND1-6, ND4L, ATP6, ATP8, and CYTB), 22 transfer RNA(tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region (D-loop). The Bayesian inference tree showed that T. dadunensis was included in Gekkonidae and was a sister taxon to Cyrtopodion scabrum. The complete mtDNA of T. dadunensis will be an important genetic resource to the studies of conservation and research of geckonids.
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Affiliation(s)
- Qian-Ru Liang
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Lei Shi
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
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Lin X, Song N, Wang M. Six complete mitochondrial genomes of ground beetles from the Harpalinae and Carabinae (Coleoptera, Carabidae) with phylogenetic analysis based on mitogenomic data. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22108. [PMID: 38572532 DOI: 10.1002/arch.22108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024]
Abstract
In this study, we employed high-throughput sequencing technology to determine the complete mitochondrial genomes of six ground beetles, encompassing five Harpalinae species and one Carabinae species. The sizes of mitochondrial genomes ranged from 15,334 to 16,972 bp, encompassing 37 genes, including 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. Furthermore, each species was found to possess a putative control region. Combining with 65 published mitochondrial genome sequences of Carabidae as ingroups and four species from Trachypachidae, Gyrinidae and Dytiscidae as outgroups, we conducted phylogenetic analyses utilizing Maximum likelihood and Bayesian inference methods. Moreover, we reconstructed a species tree of Carabidae based on mitochondrial genome data using the coalescent-based species tree method (ASTRAL). The results revealed that the family Carabidae was not a monophyletic group. The subfamily Harpalinae was supported to be a monophyletic group in Maximum likelihood analysis. Although the subfamily Carabinae was found to be nonmonophyletic in the concatenation analyses under both Maximum likelihood and Bayesian inference criteria, it was identified as a monophyletic group in the species tree analysis.
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Affiliation(s)
- Xingyu Lin
- Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Nan Song
- Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Miaomiao Wang
- Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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Zhang D, Jakovlić I, Zou H, Liu F, Xiang CY, Gusang Q, Tso S, Xue S, Zhu WJ, Li Z, Wu J, Wang GT. Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea. Int J Parasitol 2024; 54:213-223. [PMID: 38185351 DOI: 10.1016/j.ijpara.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/03/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China.
| | - Ivan Jakovlić
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fei Liu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Institute of Aquatic Sciences, Tibet Academy of Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850032, China
| | - Chuan-Yu Xiang
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qunzong Gusang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Sonam Tso
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Shenggui Xue
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Wen-Jin Zhu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Zhenxin Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Jihua Wu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Gui-Tang Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Ma Y, Zheng B, Li J, Meng W, Xu K, Ye Y. Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha. PLoS One 2024; 19:e0301389. [PMID: 38547307 PMCID: PMC10977763 DOI: 10.1371/journal.pone.0301389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNASer1 and tRNASer2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNAAla lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.
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Affiliation(s)
- Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Biqi Zheng
- Department of Natural Resources, Ningde Marine Center, Ningde, 352000, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Meng
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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Fan F, Pei L, Jiang L, Ye Y, Liu Y, Liu B. Gene Rearrangements in the Mitochondrial Genome of Gonatopsis borealis and Onychoteuthis compacta Reveal Their Phylogenetic Implications for Oegopsida. Biochem Genet 2024:10.1007/s10528-024-10707-7. [PMID: 38466493 DOI: 10.1007/s10528-024-10707-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/16/2024] [Indexed: 03/13/2024]
Abstract
The complete mitochondrial genome provides crucial information for comprehending gene rearrangement, molecular evolution, and phylogenetic analysis. Here, we have determined the complete mitogenome sequence of Gonatopsis borealis and Onychoteuthis compacta for the first time. Their genome sizes were 20,148 bp and 20,491 bp, respectively, including 18 protein-coding genes, COI-COIII, ATP6, and ATP8 are duplicated, 23 transfer RNA genes, and 2 ribosomal RNA (rRNA) genes (12S and 16S rRNA). Specifically, the overall A+T content is 70.69% and 72.67%. It shows a significant AT bias. The whole mitogenomes indicate positive AT skew (0.070 and 0.062). Furthermore, the gene order has been rearranged within Oegopsida. The tandem duplication random loss model was determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis was performed, and the result tree was found to be consistent with the morphological identification classification. Estimation of divergence time for 35 species showed that the main differentiation of Oegopsida occurred in 140.70 Mya. These results will help to better understand the gene rearrangements and evolution of G. borealis and O. compacta and lay a foundation for further phylogeny genetic studies of Oegopsida.
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Affiliation(s)
- Fan Fan
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Liyi Pei
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Yingying Ye
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yifan Liu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Bilin Liu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
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Sterling-Montealegre RA, Prada CF. Variability and evolution of gene order rearrangement in mitochondrial genomes of arthropods (except Hexapoda). Gene 2024; 892:147906. [PMID: 37844850 DOI: 10.1016/j.gene.2023.147906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
In the species-rich Phylum Arthropoda, the mitochondrial genome is relatively well conserved both in terms of number and order of genes. However, specific clades have a 'typical' gene order that differs from the putative arthropod ancestral arrangement. The aim of this work was to compare the rate of mitochondrial gene rearrangements at inter- and intra-taxonomic levels in the Arthropoda and to postulate the most parsimonious ancestral orders representing the four major arthropod lineages. For this purpose, we performed a comparative genomic analysis of arthropod mitochondrial genomes available in the NCBI database. Using a combination of bioinformatics methods that examined mitochondrial gene rearrangements in 464 species of arthropods from three subphyla (Chelicerata, Myriapoda, and Crustacea [except Hexapoda, previously analyzed]), we observed differences in the rate of rearrangement within major lineages. A higher rate of mitochondrial genome rearrangement was observed in Crustacea and Chelicerata compared to Myriapoda. Likewise, early branching clades exhibit less variability in mitochondrial genome order than late branching clades, within each subphylum. We identified 'hot regions' in the mitochondrial genome of each studied subphylum, and postulated the most likely ancestral gene order in each subphylum and taxonomic order. Our work provides new evidence on the evolutionary dynamics of mitochondrial genome gene order in arthropods and new mitochondrial genome architectures in different taxonomic divisions within each major lineage of arthropods.
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Affiliation(s)
| | - Carlos Fernando Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia.
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11
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Yahyaolu Z, Doan CT, Uluar O, Karaka MY, Iplak B. Mitogenome of Xya pfaendleri (Orthoptera: Caelifera): Its comparative description and phylogenetic position within Tridactylidea. Zootaxa 2023; 5369:576-584. [PMID: 38220698 DOI: 10.11646/zootaxa.5369.4.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Indexed: 01/16/2024]
Abstract
We report the comparative examination of the complete mitochondrial genome of the pygmy mole cricket Xya pfaendleri (Orthoptera: Caelifera: Tridactylidae). The mitogenome consists of 13 protein-coding regions, 22 tRNAs, two rRNAs, and one control region, following the gene order of the ancestral pancrustacean mitogenome. The length of the mitogenome in Xya pfaendleri is 15352 bp. The start and stop codons of the protein-coding genes exhibit the general pattern observed in orthopterans. The data indicate that the pattern of gene overlapping/intergenic sequences exhibits a significant phylogenetic signal. A phylogenetic tree inferred using 12 mitogenomes (seven belonging to Tridactylidea, three to Acrididea, and two to Ensifera) confirms the sister group relationship of Acrididea and Tridactylidea. The relationship among the families of Tridactylidea is Cylindrachetidae + (Ripipterygidae + Tridactylidae). The mitogenome sequences of Xya and Tridactylus constitute a single clade, sharing a last common ancestor 94 million years ago, and rendering the first genus paraphyletic. The present preliminary data suggest that we still have much to learn about the evolution and diversity of Tridactylidea.
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Affiliation(s)
- Zgl Yahyaolu
- Department of Biology; Faculty of Science; Akdeniz University; Antalya; Turkey.
| | - Ceren Tutku Doan
- Department of Biology; Faculty of Art & Science; Gaziantep University; Gaziantep; Turkey.
| | - Onur Uluar
- Department of Biology; Faculty of Science; Akdeniz University; Antalya; Turkey.
| | - Merref Y Karaka
- Department of Biology; Faculty of Art & Science; Hatay Mustafa Kemal University; Hatay; Turkey.
| | - Battal Iplak
- Department of Biology; Faculty of Science; Akdeniz University; Antalya; Turkey.
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12
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Gao T, Shi Y, Xiao J. Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae). Genes (Basel) 2023; 14:2043. [PMID: 38002986 PMCID: PMC10671150 DOI: 10.3390/genes14112043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.
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Affiliation(s)
- Tianxiang Gao
- School of Fishery, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Yijia Shi
- Fisheries College, Jimei University, Xiamen 361021, China;
| | - Jiaguang Xiao
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
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13
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Jakovlić I, Zou H, Ye T, Zhang H, Liu X, Xiang CY, Wang GT, Zhang D. Mitogenomic evolutionary rates in bilateria are influenced by parasitic lifestyle and locomotory capacity. Nat Commun 2023; 14:6307. [PMID: 37813879 PMCID: PMC10562372 DOI: 10.1038/s41467-023-42095-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023] Open
Abstract
The evidence that parasitic animals exhibit elevated mitogenomic evolutionary rates is inconsistent and limited to Arthropoda. Similarly, the evidence that mitogenomic evolution is faster in species with low locomotory capacity is limited to a handful of animal lineages. We hypothesised that these two variables are associated and that locomotory capacity is a major underlying factor driving the elevated rates in parasites. Here, we study the evolutionary rates of mitogenomes of 10,906 bilaterian species classified according to their locomotory capacity and parasitic/free-living life history. In Bilateria, evolutionary rates were by far the highest in endoparasites, much lower in ectoparasites with reduced locomotory capacity and free-living lineages with low locomotory capacity, followed by parasitoids, ectoparasites with high locomotory capacity, and finally micropredatory and free-living lineages. The life history categorisation (parasitism) explained ≈45%, locomotory capacity categorisation explained ≈39%, and together they explained ≈56% of the total variability in evolutionary rates of mitochondrial protein-coding genes in Bilateria. Our findings suggest that these two variables play major roles in calibrating the mitogenomic molecular clock in bilaterian animals.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Tong Ye
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hong Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Xiang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Chuan-Yu Xiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Dong Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, 850000, Lhasa, China.
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14
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Guo S, Chen J, Song N. Phylogenomic analysis of Syrphoidea (Diptera: Syrphidae, Pipunculidae) based on the expanded mitogenomic data. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-13. [PMID: 36597178 DOI: 10.1002/arch.21998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 09/27/2023]
Abstract
The mitochondrial genome has become the most widely used genomic resource in resolving the insect phylogenetic relationships. In this study, we assess the interrelationships among the syrphid and pipunculid members of Syrphoidea using mitochondrial genome sequences of 152 taxa, 9 of which are newly reported and three are assembled from the existing transcriptome data. The Pipunculidae was found to be deeply nested members of Schizophora, which resulted in a nonmonophyletic Syrphoidea. In the monophyletic Syrphidae, unequivocal robust support was found for Microdontinae as the sister group of all other Syrphidae. The subfamily Eristalinae was nonmonophyletic. The Pipizinae was recovered as the sister group to the Syrphinae, albeit with strong support. As a whole, our results are concord with previously established hypotheses on Syrphoidea from the genome scale data. The mitochondrial genomes were successful in producing a robustly supported phylogenetic framework for the Syrphoidea.
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Affiliation(s)
- Shibao Guo
- Department of Plant Protection, College of Agronomy,Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Junhua Chen
- Department of Plant Protection, College of Agronomy,Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Nan Song
- Department of Entomology, College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
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15
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Li F, Zhang Y, Zhong T, Heng X, Ao T, Gu Z, Wang A, Liu C, Yang Y. The Complete Mitochondrial Genomes of Two Rock Scallops (Bivalvia: Spondylidae) Indicate Extensive Gene Rearrangements and Adaptive Evolution Compared with Pectinidae. Int J Mol Sci 2023; 24:13844. [PMID: 37762147 PMCID: PMC10531248 DOI: 10.3390/ijms241813844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Different from the diverse family Pectinidae, the Spondylidae is a small group with a single genus that shares the sedentary life habit of cementing themselves to the substrate. However, little information related to the genetic diversity of Spondylidae has been reported. In the present study, the complete mitochondrial genomes of Spondylus versicolor and S. spinosus were sequenced and compared with those of pectinids. The mtDNA of S. versicolor and S. spinosus show similar patterns with respect to genome size, AT content, AT skew, GC skew, and codon usage, and their mitogenomic sizes are longer than most pectinid species. The mtDNA of S. spinosus is 27,566 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes, while an additional tRNA-Met was found in the mtDNA of S. versicolor, which is 28,600 bp in length. The monophylies of Spondylidae and Pectinidae were well supported, but the internal relationships within Pectinidae remain unresolved due to the paraphyly of the genus Mimachlamy and the controversial position of the tribe Aequipectinini. The gene orders of S. versicolor and S. spinosus are almost identical but differ greatly from species of the Pectinidae, indicating extensive gene rearrangements compared with Pectinidae. Positive selection analysis revealed evidence of adaptive evolution in the branch of Spondylidae. The present study could provide important information with which to understand the evolutionary progress of the diverse and economically significant marine bivalve Pectinoidea.
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Affiliation(s)
- Fengping Li
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Yu Zhang
- Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Tao Zhong
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
| | - Xin Heng
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Tiancheng Ao
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
| | - Zhifeng Gu
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Aimin Wang
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Chunsheng Liu
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Yi Yang
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
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16
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Struck TH, Golombek A, Hoesel C, Dimitrov D, Elgetany AH. Mitochondrial Genome Evolution in Annelida-A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution. Syst Biol 2023; 72:925-945. [PMID: 37083277 PMCID: PMC10405356 DOI: 10.1093/sysbio/syad023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/22/2023] Open
Abstract
The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA, and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene order variability including, among others, increased substitution rates, base composition differences, structure of noncoding regions, parasitism, living in extreme habitats, short generation times, and biomineralization. However, these analyses were neither done systematically nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits, and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best-predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, variability of the gene order does not predict if a taxon is difficult to place in molecular phylogenetic reconstructions using sequence data or not. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why the canonical views do not always fit to the observed patterns without making some adjustments. [Annelida; compositional biases; ecology; gene order; life history; macroevolution; mitochondrial genomes; substitution rates.].
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Affiliation(s)
- Torsten H Struck
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
- Centre of Molecular Biodiversity Research, Zoological Research Museum Alexander KoenigBonn 53113, Germany
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Anja Golombek
- Centre of Molecular Biodiversity Research, Zoological Research Museum Alexander KoenigBonn 53113, Germany
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Christoph Hoesel
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
| | - Asmaa Haris Elgetany
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
- Zoology Department, Faculty of Science, Damietta University, New Damietta, Central zone, 34517, Egypt
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17
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Zhao T, Song N, Lin X, Zhang Y. Complete mitochondrial genomes of the slugs Deroceraslaeve (Agriolimacidae) and Ambigolimaxvalentianus (Limacidae) provide insights into the phylogeny of Stylommatophora (Mollusca, Gastropoda). Zookeys 2023; 1173:43-59. [PMID: 37560262 PMCID: PMC10407649 DOI: 10.3897/zookeys.1173.102786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023] Open
Abstract
In this study, we sequenced two complete mitogenomes from Deroceraslaeve and Ambigolimaxvalentianus. The mitogenome of Ambigolimaxvalentianus represented the first such data from the family Limacidae. The lengths of the mitogenomes of Deroceraslaeve and Ambigolimaxvalentianus were 14,773 bp and 15,195 bp, respectively. The entire set of 37 mitochondrial genes were identified for both mitogenomes. Compared with the mitogenome of Achatinafulica, the trnP_trnA tRNA cluster was rearranged in both Deroceraslaeve and Ambigolimaxvalentianus. The secondary structures of tRNA and rRNA genes for the two species were predicted. Phylogenetic analyses based on amino acid sequences supported (1) monophyly of Stylommatophora, (2) division of Stylommatophora into the 'achatinoid' clade (i.e., the suborder Achatinina) and the 'non-achatinoid' clade (i.e., the suborder Helicina), (3) placement of the Orthurethra in the 'non-achatinoid' clade, and (4) monophyly of each of the superfamilies Helicoidea, Urocoptoidea, Succineoidea, Arionoidea, Pupilloidea and Limacoidea. The exemplars of Helicidae, Philomycidae and Achatinellidae displayed many more mitochondrial gene rearrangements than other species of Stylommatophora.
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Affiliation(s)
- Te Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Xingyu Lin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
| | - Yang Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Agricultural UniversityZhengzhouChina
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18
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Lin X, Song N. The First Complete Mitochondrial Genome of the Genus Pachycondyla (Formicidae, Ponerinae) and Insights into the Phylogeny of Ants. Genes (Basel) 2023; 14:1528. [PMID: 37628580 PMCID: PMC10454067 DOI: 10.3390/genes14081528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Ants are the standout group among eusocial insects in terms of their exceptional species richness and ecological dominance. The phylogenetic relationships among the group remain elusive. Mitochondrial genome sequences, as a kind of molecular marker, have been widely utilized in the phylogenetic analysis of insects. However, the number of ant mitogenomes published is still very limited. In this study, we utilized next-generation sequencing to determine the complete mitogenome of Pachycondyla annamita (Formicidae, Ponerinae). This is the first mitogenome from the genus Pachycondyla. Two gene rearrangements were identified in the mitogenome, the transposition of trnQ and trnM and the transposition of trnV and rrnS. The secondary structures of tRNAs were predicted. The tRNA genes trnR and trnS1 lacked the dihydrouridine (DHU) arm, and the trnE lacked the TΨC (T) arm. Phylogenetic analyses of the mitochondrial protein-coding genes under maximum likelihood (ML) and Bayesian inference (BI) criteria resulted in conflicting hypotheses. BI analysis using amino acid data with the site-heterogeneous mixture model produced a tree topology congruent with previous studies. The Formicidae was subdivided into two main clades, namely the "poneroid" clade and the "formicoid" clade. A sister group relationship between Myrmicinae and Formicinae was recovered within the "formicoid" clade.
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Affiliation(s)
| | - Nan Song
- Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China;
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19
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Nikolaeva OV, Beregova AM, Efeykin BD, Miroliubova TS, Zhuravlev AY, Ivantsov AY, Mikhailov KV, Spiridonov SE, Aleoshin VV. Expression of Hairpin-Enriched Mitochondrial DNA in Two Hairworm Species (Nematomorpha). Int J Mol Sci 2023; 24:11411. [PMID: 37511167 PMCID: PMC10380579 DOI: 10.3390/ijms241411411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Nematomorpha (hairworms) is a phylum of parasitic ecdysozoans, best known for infecting arthropods and guiding their hosts toward water, where the parasite can complete its life cycle. Over 350 species of nematomorphs have been described, yet molecular data for the group remain scarce. The few available mitochondrial genomes of nematomorphs are enriched with long inverted repeats, which are embedded in the coding sequences of their genes-a remarkably unusual feature exclusive to this phylum. Here, we obtain and annotate the repeats in the mitochondrial genome of another nematomorph species-Parachordodes pustulosus. Using genomic and transcriptomic libraries, we investigate the impact of inverted repeats on the read coverage of the mitochondrial genome. Pronounced drops in the read coverage coincide with regions containing long inverted repeats, denoting the 'blind spots' of short-fragment sequencing libraries. Phylogenetic inference with the novel data reveals multiple disagreements between the traditional system of Nematomorpha and molecular data, rendering several genera paraphyletic, including Parachordodes.
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Affiliation(s)
- Olga V. Nikolaeva
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 40, Moscow 119991, Russia
| | - Aleksandra M. Beregova
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 40, Moscow 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 73, Moscow 119991, Russia
| | - Boris D. Efeykin
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskiy Ave., 33, Moscow 119071, Russia (S.E.S.)
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Per., 19, Bld. 1, Moscow 127051, Russia
| | - Tatiana S. Miroliubova
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskiy Ave., 33, Moscow 119071, Russia (S.E.S.)
| | - Andrey Yu. Zhuravlev
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 12, Moscow 119991, Russia
| | - Andrey Yu. Ivantsov
- Borissiak Palaeontological Institute, Russian Academy of Sciences, Profsoyuznaya Str., 123, Moscow 117647, Russia
| | - Kirill V. Mikhailov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 40, Moscow 119991, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Per., 19, Bld. 1, Moscow 127051, Russia
| | - Sergei E. Spiridonov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskiy Ave., 33, Moscow 119071, Russia (S.E.S.)
| | - Vladimir V. Aleoshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 40, Moscow 119991, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Per., 19, Bld. 1, Moscow 127051, Russia
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20
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Fiedler L, Bernt M, Middendorf M, Stadler PF. Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs. BMC Bioinformatics 2023; 24:235. [PMID: 37277700 DOI: 10.1186/s12859-023-05371-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Identifying the locations of gene breakpoints between species of different taxonomic groups can provide useful insights into the underlying evolutionary processes. Given the exact locations of their genes, the breakpoints can be computed without much effort. However, often, existing gene annotations are erroneous, or only nucleotide sequences are available. Especially in mitochondrial genomes, high variations in gene orders are usually accompanied by a high degree of sequence inconsistencies. This makes accurately locating breakpoints in mitogenomic nucleotide sequences a challenging task. RESULTS This contribution presents a novel method for detecting gene breakpoints in the nucleotide sequences of complete mitochondrial genomes, taking into account possible high substitution rates. The method is implemented in the software package DeBBI. DeBBI allows to analyze transposition- and inversion-based breakpoints independently and uses a parallel program design, allowing to make use of modern multi-processor systems. Extensive tests on synthetic data sets, covering a broad range of sequence dissimilarities and different numbers of introduced breakpoints, demonstrate DeBBI 's ability to produce accurate results. Case studies using species of various taxonomic groups further show DeBBI 's applicability to real-life data. While (some) multiple sequence alignment tools can also be used for the task at hand, we demonstrate that especially gene breaks between short, poorly conserved tRNA genes can be detected more frequently with the proposed approach. CONCLUSION The proposed method constructs a position-annotated de-Bruijn graph of the input sequences. Using a heuristic algorithm, this graph is searched for particular structures, called bulges, which may be associated with the breakpoint locations. Despite the large size of these structures, the algorithm only requires a small number of graph traversal steps.
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Affiliation(s)
- Lisa Fiedler
- Department of Computer Science, University Leipzig, Augustusplatz 10-11, 04109, Leipzig, Germany.
| | - Matthias Bernt
- Helmholtz Centre for Environmental Research -UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Martin Middendorf
- Department of Computer Science, University Leipzig, Augustusplatz 10-11, 04109, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04109, Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090, Vienna, Austria
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Ciudad Universitaria, 111321, Bogotá, D.C., Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA
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Hao CL, Wei NW, Liu YJ, Shi CX, Arken K, Yue C. Mitochondrial phylogenomics provides conclusive evidence that the family Ancyrocephalidae is deeply paraphyletic. Parasit Vectors 2023; 16:83. [PMID: 36859280 PMCID: PMC9979435 DOI: 10.1186/s13071-023-05692-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Unresolved taxonomic classification and paraphyly pervade the flatworm class Monogenea: the class itself may be paraphyletic and split into Polyopisthocotylea and Monopisthocotylea; there are some indications that the monopisthocotylean order Dactylogyridea may also be paraphyletic; single-gene markers and some morphological traits indicate that the family Ancyrocephalidae is paraphyletic and intertwined with the family Dactylogyridae. METHODS To attempt to study the relationships of Ancyrocephalidae and Monopisthocotylea using a phylogenetic marker with high resolution, we sequenced mitochondrial genomes of two fish ectoparasites from the family Dactylogyridae: Dactylogyrus simplex and Dactylogyrus tuba. We conducted phylogenetic analyses using three datasets and three methods. Datasets were ITS1 (nuclear) and nucleotide and amino acid sequences of almost complete mitogenomes of almost all available Monopisthocotylea mitogenomes. Methods were maximum likelihood (IQ-TREE), Bayesian inference (MrBayes) and CAT-GTR (PhyloBayes). RESULTS Both mitogenomes exhibited the ancestral gene order for Neodermata, and both were compact, with few and small intergenic regions and many and large overlaps. Gene sequences were remarkably divergent for nominally congeneric species, with only trnI exhibiting an identity value > 80%. Both mitogenomes had exceptionally low A + T base content and AT skews. We found evidence of pervasive compositional heterogeneity in the dataset and indications that base composition biases cause phylogenetic artefacts. All six mitogenomic analyses produced unique topologies, but all nine analyses produced topologies that rendered Ancyrocephalidae deeply paraphyletic. Mitogenomic data consistently resolved the order Capsalidea as nested within the Dactylogyridea. CONCLUSIONS The analyses indicate that taxonomic revisions are needed for multiple Polyopisthocotylea lineages, from genera to orders. In combination with previous findings, these results offer conclusive evidence that Ancyrocephalidae is a paraphyletic taxon. The most parsimonious solution to resolve this is to create a catch-all Dactylogyridae sensu lato clade comprising the current Ancyrocephalidae, Ancylodiscoididae, Pseudodactylogyridae and Dactylogyridae families, but the revision needs to be confirmed by another marker with a sufficient resolution.
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Affiliation(s)
- Cui-Lan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Nian-Wen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Yan-Jun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Cai-Xia Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Kadirden Arken
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China.
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22
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Shtolz N, Mishmar D. The metazoan landscape of mitochondrial DNA gene order and content is shaped by selection and affects mitochondrial transcription. Commun Biol 2023; 6:93. [PMID: 36690686 PMCID: PMC9871016 DOI: 10.1038/s42003-023-04471-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Mitochondrial DNA (mtDNA) harbors essential genes in most metazoans, yet the regulatory impact of the multiple evolutionary mtDNA rearrangements has been overlooked. Here, by analyzing mtDNAs from ~8000 metazoans we found high gene content conservation (especially of protein and rRNA genes), and codon preferences for mtDNA-encoded tRNAs across most metazoans. In contrast, mtDNA gene order (MGO) was selectively constrained within but not between phyla, yet certain gene stretches (ATP8-ATP6, ND4-ND4L) were highly conserved across metazoans. Since certain metazoans with different MGOs diverge in mtDNA transcription, we hypothesized that evolutionary mtDNA rearrangements affected mtDNA transcriptional patterns. As a first step to test this hypothesis, we analyzed available RNA-seq data from 53 metazoans. Since polycistron mtDNA transcripts constitute a small fraction of the steady-state RNA, we enriched for polycistronic boundaries by calculating RNA-seq read densities across junctions between gene couples encoded either by the same strand (SSJ) or by different strands (DSJ). We found that organisms whose mtDNA is organized in alternating reverse-strand/forward-strand gene blocks (mostly arthropods), displayed significantly reduced DSJ read counts, in contrast to organisms whose mtDNA genes are preferentially encoded by one strand (all chordates). Our findings suggest that mtDNA rearrangements are selectively constrained and likely impact mtDNA regulation.
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Affiliation(s)
- Noam Shtolz
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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23
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Guo S, Lin X, Song N. Mitochondrial phylogenomics reveals deep relationships of scarab beetles (Coleoptera, Scarabaeidae). PLoS One 2022; 17:e0278820. [PMID: 36512580 PMCID: PMC9746968 DOI: 10.1371/journal.pone.0278820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022] Open
Abstract
In this study, we newly sequenced the complete mitochondrial genomes (mitogenomes) of two phytophagous scarab beetles, and investigated the deep level relationships within Scarabaeidae combined with other published beetle mitogenome sequences. The complete mitogenomes of Dicronocephalus adamsi Pascoe (Cetoniinae) and Amphimallon sp. (Melolonthinae) are 15,563 bp and 17,433 bp in size, respectively. Both mitogenomes have the typical set of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) and an A+T-rich region, with the same gene arrangement found in the majority of beetles. The secondary structures for ribosomal RNA genes (rrnL and rrnS) were inferred by comparative analysis method. Results from phylogenetic analyses provide support for major lineages and current classification of Scarabaeidae. Amino acid data recovered Scarabaeidae as monophyletic. The Scarabaeidae was split into two clades. One clade contained the subfamilies Scarabaeinae and Aphodiinae. The other major clade contained the subfamilies Dynastinae, Rutelinae, Cetoniinae, Melolonthinae and Sericini. The monophyly of Scarabaeinae, Aphodiinae, Dynastinae, Cetoniinae and Sericini were strongly supported. The Scarabaeinae was the sister group of Aphodiinae. The Cetoniinae was sister to the Dynastinae + Rutelinae clade. The Melolonthinae was a non-monophyletic group. The removal of fast-evolving sites from nucleotide dataset using a pattern sorting method (OV-sorting) supported the family Scarabaeidae as a monophyletic group. At the tribe level, the Onthophagini was non-monophyletic with respect to Oniticellini. Ateuchini was sister to a large clade comprising the tribes Onthophagini, Oniticellini and Onitini. Eurysternini was a sister group of the Phanaeini + Ateuchini clade.
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Affiliation(s)
- Shibao Guo
- Xinyang Agriculture and Forestry University, Xinyang, Henan, China
- * E-mail: (SG); (NS)
| | - Xingyu Lin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
- * E-mail: (SG); (NS)
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24
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Tian L, Yang W, Si C, Guo X, Zhang B. Complete Mitogenome Analysis of Five Leafhopper Species of Idiocerini (Hemiptera: Cicadellidae). Genes (Basel) 2022; 13:2000. [PMID: 36360236 PMCID: PMC9690763 DOI: 10.3390/genes13112000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 10/03/2023] Open
Abstract
Insect mitochondrial genomes (mitogenomes) are of great interest in exploring molecular evolution, phylogenetics, and biogeography. So far, only 12 mitogenomes of the leafhopper tribe Idiocerini have been released in GenBank, although the tribe comprises 488 known species including some agricultural, forestry, and horticultural pests. In order to compare and analyze the mitochondrial genome structure of Idiocerini and even the selective pressure of 13 protein-coding genes (PCGs) of the family Cicadellidae, the complete mitogenomes of five species including Nabicerus dentimus, Sahlbergotettix salicicola, Podulmorinus opacus, Podulmorinus consimilis, and a new species of a new genus were determined by next-generation sequencing. The size of the newly determined mitogenomes ranged from 14,733 bp to 15,044 bp, comprising the standard set of 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a long non-coding control region (CR). The extent of purifying selection presented different pictures in the tribe and the family. The less pronounced genes (0.5 < dN/dS < 1) were nad5 and nad4l in Idiocerin, whereas in the family Cicadellidae including the sequences of Idiocerin, nad1-nad6 and cox1 genes were less pronounced. The codon encoding leucine was the most common in all species, and the codon encoding serine 1 was the most common in all species except for P. opacus. Interestingly, in P. opacus, another of the most common codons is that encoding serine 2. Among the 17 examined species of the Idiocerini, 14 species contained the tandem repeats, and 11 species of them contained the motif "TTATA". These findings will promote research on the structure and evolution of the mitochondrial genome and highlight the need for more mitogenomes in Cicadellidae.
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Affiliation(s)
- Lili Tian
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxin Yang
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
| | - Chengyan Si
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bin Zhang
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
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25
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Gao JW, Yuan XP, Wu H, Xiang CY, Xie M, Song R, Chen ZY, Wu YA, Ou DS. Mitochondrial phylogenomics of Acanthocephala: nucleotide alignments produce long-branch attraction artefacts. Parasit Vectors 2022; 15:376. [PMID: 36261865 PMCID: PMC9583589 DOI: 10.1186/s13071-022-05488-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Classification of the Acanthocephala, a clade of obligate endoparasites, remains unresolved because of insufficiently strong resolution of morphological characters and scarcity of molecular data with a sufficient resolution. Mitochondrial genomes may be a suitable candidate, but they are available for a small number of species and their suitability for the task has not been tested thoroughly. METHODS Herein, we sequenced the first mitogenome for the large family Rhadinorhynchidae: Micracanthorhynchina dakusuiensis. These are also the first molecular data generated for this entire genus. We conducted a series of phylogenetic analyses using concatenated nucleotides (NUC) and amino acids (AAs) of all 12 protein-coding genes, three different algorithms, and the entire available acanthocephalan mitogenomic dataset. RESULTS We found evidence for strong compositional heterogeneity in the dataset, and Micracanthorhynchina dakusuiensis exhibited a disproportionately long branch in all analyses. This caused a long-branch attraction artefact (LBA) of M. dakusuiensis resolved at the base of the Echinorhynchida clade when the NUC dataset was used in combination with standard phylogenetic algorithms, maximum likelihood (ML) and Bayesian inference (BI). Both the use of the AA dataset (BI-AAs and ML-AAs) and the CAT-GTR model designed for suppression of LBA (CAT-GTR-AAs and CAT-GTR-NUC) at least partially attenuated this LBA artefact. The results support Illiosentidae as the basal radiation of Echinorhynchida and Rhadinorhynchidae forming a clade with Echinorhynchidae and Pomporhynchidae. The questions of the monophyly of Rhadinorhynchidae and its sister lineage remain unresolved. The order Echinorhynchida was paraphyletic in all of our analyses. CONCLUSIONS Future studies should take care to attenuate compositional heterogeneity-driven LBA artefacts when applying mitogenomic data to resolve the phylogeny of Acanthocephala.
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Affiliation(s)
- Jin-Wei Gao
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Xi-Ping Yuan
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Hao Wu
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Chuan-Yu Xiang
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Min Xie
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Rui Song
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China.
| | - Zhong-Yuan Chen
- Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan, China
| | - Yuan-An Wu
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
| | - Dong-Sheng Ou
- Hunan Fisheries Science Institute, 728 Shuanghe Rd, Kaifu District, Changsha, 410153, Hunan, China
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26
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Inverted base composition skews and discontinuous mitochondrial genome architecture evolution in the Enoplea (Nematoda). BMC Genomics 2022; 23:376. [PMID: 35585506 PMCID: PMC9115964 DOI: 10.1186/s12864-022-08607-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/25/2022] [Indexed: 11/26/2022] Open
Abstract
Background Within the class Enoplea, the earliest-branching lineages in the phylum Nematoda, the relatively highly conserved ancestral mitochondrial architecture of Trichinellida is in stark contrast to the rapidly evolving architecture of Dorylaimida and Mermithida. To better understand the evolution of mitogenomic architecture in this lineage, we sequenced the mitogenome of a fish parasite Pseudocapillaria tomentosa (Trichinellida: Capillariidae) and compared it to all available enoplean mitogenomes. Results P. tomentosa exhibited highly reduced noncoding regions (the largest was 98 bp), and a unique base composition among the Enoplea. We attributed the latter to the inverted GC skew (0.08) in comparison to the ancestral skew in Trichinellidae (-0.43 to -0.37). Capillariidae, Trichuridae and Longidoridae (Dorylaimida) generally exhibited low negative or low positive skews (-0.1 to 0.1), whereas Mermithidae exhibited fully inverted low skews (0 to 0.05). This is indicative of inversions in the strand replication order or otherwise disrupted replication mechanism in the lineages with reduced/inverted skews. Among the Trichinellida, Trichinellidae and Trichuridae have almost perfectly conserved architecture, whereas Capillariidae exhibit multiple rearrangements of tRNA genes. In contrast, Mermithidae (Mermithida) and Longidoridae (Dorylaimida) exhibit almost no similarity to the ancestral architecture. Conclusions Longidoridae exhibited more rearranged mitogenomic architecture than the hypervariable Mermithidae. Similar to the Chromadorea, the evolution of mitochondrial architecture in enoplean nematodes exhibits a strong discontinuity: lineages possessing a mostly conserved architecture over tens of millions of years are interspersed with lineages exhibiting architectural hypervariability. As Longidoridae also have some of the smallest metazoan mitochondrial genomes, they contradict the prediction that compact mitogenomes should be structurally stable. Lineages exhibiting inverted skews appear to represent the intermediate phase between the Trichinellidae (ancestral) and fully derived skews in Chromadorean mitogenomes (GC skews = 0.18 to 0.64). Multiple lines of evidence (CAT-GTR analysis in our study, a majority of previous mitogenomic results, and skew disruption scenarios) support the Dorylaimia split into two sister-clades: Dorylaimida + Mermithida and Trichinellida. However, skew inversions produce strong base composition biases, which can hamper phylogenetic and other evolutionary studies, so enoplean mitogenomes have to be used with utmost care in evolutionary studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08607-4.
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27
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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies. Sci Rep 2022; 12:7028. [PMID: 35487927 PMCID: PMC9054809 DOI: 10.1038/s41598-022-10547-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/21/2022] [Indexed: 11/08/2022] Open
Abstract
Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.
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28
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Baeza JA, García-De León FJ. Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis. BMC Genomics 2022; 23:320. [PMID: 35459089 PMCID: PMC9027416 DOI: 10.1186/s12864-022-08482-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/18/2022] [Indexed: 12/28/2022] Open
Abstract
Background Whole mitochondrial genomes are quickly becoming markers of choice for the exploration of within-species genealogical and among-species phylogenetic relationships. Most often, ‘primer walking’ or ‘long PCR’ strategies plus Sanger sequencing or low-pass whole genome sequencing using Illumina short reads are used for the assembling of mitochondrial chromosomes. In this study, we first confirmed that mitochondrial genomes can be sequenced from long reads using nanopore sequencing data exclusively. Next, we examined the accuracy of the long-reads assembled mitochondrial chromosomes when comparing them to a ‘gold’ standard reference mitochondrial chromosome assembled using Illumina short-reads sequencing. Results Using a specialized bioinformatics tool, we first produced a short-reads mitochondrial genome assembly for the silky shark C. falciformis with an average base coverage of 9.8x. The complete mitochondrial genome of C. falciformis was 16,705 bp in length and 934 bp shorter than a previously assembled genome (17,639 bp in length) that used bioinformatics tools not specialized for the assembly of mitochondrial chromosomes. Next, low-pass whole genome sequencing using a MinION ONT pocket-sized platform plus customized de-novo and reference-based workflows assembled and circularized a highly accurate mitochondrial genome in the silky shark Carcharhinus falciformis. Indels at the flanks of homopolymer regions explained most of the dissimilarities observed between the ‘gold’ standard reference mitochondrial genome (assembled using Illumina short reads) and each of the long-reads mitochondrial genome assemblies. Although not completely accurate, mitophylogenomics and barcoding analyses (using entire mitogenomes and the D-Loop/Control Region, respectively) suggest that long-reads assembled mitochondrial genomes are reliable for identifying a sequenced individual, such as C. falciformis, and separating the same individual from others belonging to closely related congeneric species. Conclusions This study confirms that mitochondrial genomes can be sequenced from long-reads nanopore sequencing data exclusively. With further development, nanopore technology can be used to quickly test in situ mislabeling in the shark fin fishing industry and thus, improve surveillance protocols, law enforcement, and the regulation of this fishery. This study will also assist with the transferring of high-throughput sequencing technology to middle- and low-income countries so that international scientists can explore population genomics in sharks using inclusive research strategies. Lastly, we recommend assembling mitochondrial genomes using specialized assemblers instead of other assemblers developed for bacterial and/or nuclear genomes.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281, Coquimbo, Chile.
| | - F J García-De León
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Baja California Sur, Mexico
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29
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Cejp B, Ravara A, Aguado MT. First mitochondrial genomes of Chrysopetalidae (Annelida) from shallow-water and deep-sea chemosynthetic environments. Gene 2022; 815:146159. [PMID: 34995739 DOI: 10.1016/j.gene.2021.146159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023]
Abstract
Among Annelida, Chrysopetalidae is an ecologically and morphologically diverse group, which includes shallow-water, deep-sea, free-living, and symbiotic species. Here, the four first mitochondrial genomes of this group are presented and described. One of the free-living shallow-water species Chrysopetalum debile (Chrysopetalinae), one of the yet undescribed free-living deep-sea species Boudemos sp., and those of the two deep-sea bivalve endosymbionts Craseoschema thyasiricola and Iheyomytilidicola lauensis (Calamyzinae). An updated phylogeny of Chrysopetalidae is performed, which supports previous phylogenetic hypotheses within Chrysopetalinae and indicates a complex ecological evolution within Calamyzinae. Additionally, analyses of natural selection pressure in the four mitochondrial genomes and additional genes from the two shallow-water species Bhawania goodei and Arichlidon gathofi were performed. Relaxed selection pressure in the mitochondrion of deep-sea and symbiotic species was found, with many sites under selection identified in the COX3 gene of deep-sea species.
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Affiliation(s)
- Benjamin Cejp
- Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, 37073, Germany.
| | - Ascensão Ravara
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
| | - M Teresa Aguado
- Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, 37073, Germany.
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López-Estrada EK, Sanmartín I, Uribe JE, Abalde S, Jiménez-Ruiz Y, García-París M. Mitogenomics and hidden-trait models reveal the role of phoresy and host shifts in the diversification of parasitoid blister beetles (Coleoptera: Meloidae). Mol Ecol 2022; 31:2453-2474. [PMID: 35146829 PMCID: PMC9305437 DOI: 10.1111/mec.16390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/28/2022]
Abstract
Changes in life history traits are often considered speciation triggers and can have dramatic effects on the evolutionary history of a lineage. Here, we examine the consequences of changes in two life history traits, host‐type and phoresy, in the hypermetamorphic blister beetles, Meloidae. Subfamilies Nemognathinae and Meloinae exhibit a complex life cycle involving multiple metamorphoses and parasitoidism. Most genera and tribes are bee‐parasitoids, and include phoretic or nonphoretic species, while two tribes feed on grasshopper eggs. These different life strategies are coupled with striking differences in species richness among clades. We generated a mitogenomic phylogeny for Nemognathinae and Meloinae, confirming the monophyly of these two clades, and used the dated phylogeny to explore the association between diversification rates and changes in host specificity and phoresy, using state‐dependent speciation and extinction (SSE) models that include the effect of hidden traits. To account for the low taxon sampling, we implemented a phylogenetic‐taxonomic approach based on birth‐death simulations, and used a Bayesian framework to integrate parameter and phylogenetic uncertainty. Results show that the ancestral hypermetamorphic Meloidae was a nonphoretic bee‐parasitoid, and that transitions towards a phoretic bee‐parasitoid and grasshopper parasitoidism occurred multiple times. Nonphoretic bee‐parasitoid lineages exhibit significantly higher relative extinction and lower diversification rates than phoretic bee‐and grasshopper‐parasitoids, but no significant differences were found between the latter two strategies. This suggests that Orthopteran host shifts and phoresy contributed jointly to the evolutionary success of the parasitoid meloidae. We also demonstrate that SSE models can be used to identify hidden traits coevolving with the focal trait in driving a lineage's diversification dynamics.
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Affiliation(s)
- E K López-Estrada
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España.,Real Jardín Botánico (RJB-CSIC). Plaza de Murillo, 2, 28014. Madrid, España
| | - I Sanmartín
- Real Jardín Botánico (RJB-CSIC). Plaza de Murillo, 2, 28014. Madrid, España
| | - J E Uribe
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España
| | - S Abalde
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España.,Centro de Estudios Avanzados de Blanes (CEAB-CSIC). Accéss, Cala Sant Francesc, 14, 17300, Blanes, España
| | - Y Jiménez-Ruiz
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España
| | - M García-París
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España
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31
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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32
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Xu T, Qi L, Kong L, Li Q. Mitogenomics reveals phylogenetic relationships of Patellogastropoda (Mollusca, Gastropoda) and dynamic gene rearrangements. ZOOL SCR 2021. [DOI: 10.1111/zsc.12524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Tao Xu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Lu Qi
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
- Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
- Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Qingdao China
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Wang Y, Hong D, Yao J, Tan H, Wang S, Li J, Luo Y, Wang D, Liu S. Comparative transcriptome preliminary reveals the molecular mechanism of the growth rate of Procambarus clarkii. REPRODUCTION AND BREEDING 2021. [DOI: 10.1016/j.repbre.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Waneka G, Svendsen JM, Havird JC, Sloan DB. Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias. Genetics 2021; 219:6346985. [PMID: 34849888 DOI: 10.1093/genetics/iyab116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/09/2021] [Indexed: 01/25/2023] Open
Abstract
Rapid mutation rates are typical of mitochondrial genomes (mtDNAs) in animals, but it is not clear why. The difficulty of obtaining measurements of mtDNA mutation that are not biased by natural selection has stymied efforts to distinguish between competing hypotheses about the causes of high mtDNA mutation rates. Several studies which have measured mtDNA mutations in nematodes have yielded small datasets with conflicting conclusions about the relative abundance of different substitution classes (i.e., the mutation spectrum). We therefore leveraged Duplex Sequencing, a high-fidelity DNA sequencing technique, to characterize de novo mtDNA mutations in Caenorhabditis elegans. This approach detected nearly an order of magnitude more mtDNA mutations than documented in any previous nematode mutation study. Despite an existing extreme AT bias in the C. elegans mtDNA (75.6% AT), we found that a significant majority of mutations increase genomic AT content. Compared to some prior studies in nematodes and other animals, the mutation spectrum reported here contains an abundance of CG→AT transversions, supporting the hypothesis that oxidative damage may be a driver of mtDNA mutations in nematodes. Furthermore, we found an excess of G→T and C→T changes on the coding DNA strand relative to the template strand, consistent with increased exposure to oxidative damage. Analysis of the distribution of mutations across the mtDNA revealed significant variation among protein-coding genes and as well as among neighboring nucleotides. This high-resolution view of mitochondrial mutations in C. elegans highlights the value of this system for understanding relationships among oxidative damage, replication error, and mtDNA mutation.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Joshua M Svendsen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
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Jakovlić I, Zou H, Chen JH, Lei HP, Wang GT, Liu J, Zhang D. Slow crabs - fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes. Mol Ecol 2021; 30:5488-5502. [PMID: 34418213 DOI: 10.1111/mec.16138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 02/05/2023]
Abstract
Base composition skews (G-C/G+C) of mitochondrial genomes are believed to be primarily driven by mutational pressure, which is positively correlated with metabolic rate. In marine animals, metabolic rate is also positively correlated with locomotory capacity. Given the central role of mitochondria in energy metabolism, we hypothesised that selection for locomotory capacity should be positively correlated with the strength of purifying selection (dN/dS), and thus be negatively correlated with the skew magnitude. Therefore, these two models assume diametrically opposite associations between the metabolic rate and skew magnitude: positive correlation in the prevailing paradigm, and negative in our working hypothesis. We examined correlations between the skew magnitude, metabolic rate, locomotory capacity, and several other variables previously associated with mitochondrial evolution on 287 crustacean mitogenomes. Weakly locomotory taxa had higher skew magnitude and ω (dN/dS) values, but not the gene order rearrangement rate. Skew and ω magnitudes were correlated. Multilevel regression analyses indicated that three competing variables, body size, gene order rearrangement rate, and effective population size, had negligible impacts on the skew magnitude. In most crustacean lineages selection for locomotory capacity appears to be the primary factor determining the skew magnitude. Contrary to the prevailing paradigm, this implies that adaptive selection outweighs nonadaptive selection (mutation pressure) in crustaceans. However, we found indications that effective population size (nonadaptive factor) may outweigh the impact of locomotory capacity in sessile crustaceans (Thecostraca). In conclusion, skew magnitude is a product of the interplay between adaptive and nonadaptive factors, the balance of which varies among lineages.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Hai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong-Peng Lei
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved. Sci Rep 2021; 11:13552. [PMID: 34193932 PMCID: PMC8245539 DOI: 10.1038/s41598-021-92994-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/18/2021] [Indexed: 12/15/2022] Open
Abstract
Contrary to the early evidence, which indicated that the mitochondrial architecture in one of the two major annelida clades, Sedentaria, is relatively conserved, a handful of relatively recent studies found evidence that some species exhibit elevated rates of mitochondrial architecture evolution. We sequenced complete mitogenomes belonging to two congeneric shell-boring Spionidae species that cause considerable economic losses in the commercial marine mollusk aquaculture: Polydora brevipalpa and Polydora websteri. The two mitogenomes exhibited very similar architecture. In comparison to other sedentarians, they exhibited some standard features, including all genes encoded on the same strand, uncommon but not unique duplicated trnM gene, as well as a number of unique features. Their comparatively large size (17,673 bp) can be attributed to four non-coding regions larger than 500 bp. We identified an unusually large (putative) overlap of 14 bases between nad2 and cox1 genes in both species. Importantly, the two species exhibited completely rearranged gene orders in comparison to all other available mitogenomes. Along with Serpulidae and Sabellidae, Polydora is the third identified sedentarian lineage that exhibits disproportionally elevated rates of mitogenomic architecture rearrangements. Selection analyses indicate that these three lineages also exhibited relaxed purifying selection pressures.
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Quek ZBR, Chang JJM, Ip YCA, Chan YKS, Huang D. Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms. Mol Biol Evol 2021; 38:981-985. [PMID: 33027524 PMCID: PMC7947835 DOI: 10.1093/molbev/msaa262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The mitochondrial genetic code is much more varied than the standard genetic code. The invertebrate mitochondrial code, for instance, comprises six initiation codons, including five alternative start codons. However, only two initiation codons are known in the echinoderm and flatworm mitochondrial code, the canonical ATG and alternative GTG. Here, we analyzed 23 Asteroidea mitogenomes, including ten newly sequenced species and unambiguously identified at least two other start codons, ATT and ATC, both of which also initiate translation of mitochondrial genes in other invertebrates. These findings underscore the diversity of the genetic code and expand upon the suite of initiation codons among echinoderms to avoid erroneous annotations. Our analyses have also uncovered the remarkable conservation of gene order among asteroids, echinoids, and holothuroids, with only an interchange between two gene positions in asteroids over ∼500 Ma of echinoderm evolution.
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Affiliation(s)
| | - Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yong Kit Samuel Chan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
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38
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Sarwar H, Zhao WT, Kibet CJ, Sitko J, Nie P. Morphological and complete mitogenomic characterisation of the acanthocephalan Polymorphus minutus infecting the duck Anas platyrhynchos. Folia Parasitol (Praha) 2021; 68. [PMID: 34152291 DOI: 10.14411/fp.2021.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/29/2021] [Indexed: 11/19/2022]
Abstract
Morphological characteristics of the acanthocephalan Polymorphus minutus (Goeze, 1782), which was collected from the duck Anas platyrhynchos Linnaeus in the Czech Republic, are described. The mitochondrial (mt) genome of P. minutus was sequenced, with a total length of 14,149 bp, comprising 36 genes including 12 protein coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA genes (rrnL and rrnS). This genome is similar to the mt genomes of other syndermatan species. All these genes were encoded on the same DNA strand and in the same orientation. The overall nucleotide composition of the P. minutus mt genome was 38.2% T, 27.3% G, 26.2% A, and 8.3% C. The amino acid sequences of 12 PCGs for mt genomes of 28 platyzoans, including P. minutus, were used for phylogenetic analysis, and the resulting topology recovers P. minutus as sister to Southwellina hispida (Van Cleave, 1925), and the two taxa form a sister clade to Centrorhynchus aluconis (Müller, 1780) and Plagiorhynchus transversus (Rudolphi, 1819), which are all species in the Palaeacanthocephala, thus supporting the monophyly of this class.
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Affiliation(s)
- Huda Sarwar
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Ting Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Caroline Jepkorir Kibet
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,School of Marine Science and Engineering, Qingdao Agriculture University, Qingdao, China
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Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation. Commun Biol 2021; 4:649. [PMID: 34059788 PMCID: PMC8166898 DOI: 10.1038/s42003-021-02160-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
The cryptic parasite Sparganum proliferum proliferates in humans and invades tissues and organs. Only scattered cases have been reported, but S. proliferum infection is always fatal. However, S. proliferum’s phylogeny and life cycle remain enigmatic. To investigate the phylogenetic relationships between S. proliferum and other cestode species, and to examine the mechanisms underlying pathogenicity, we sequenced the entire genomes of S. proliferum and a closely related non–life-threatening tapeworm Spirometra erinaceieuropaei. Additionally, we performed larvae transcriptome analyses of S. proliferum plerocercoid to identify genes involved in asexual reproduction in the host. The genome sequences confirmed that the S. proliferum has experienced a clearly distinct evolutionary history from S. erinaceieuropaei. Moreover, we found that nonordinal extracellular matrix coordination allows asexual reproduction in the host, and loss of sexual maturity in S. proliferum are responsible for its fatal pathogenicity to humans. Our high-quality reference genome sequences should be valuable for future studies of pseudophyllidean tapeworm biology and parasitism. Kikuchi et al. sequence the genome of the fatal tapeworm Sparganum proliferum and a closely related non–life-threatening tapeworm Spirometra erinaceieuropaei, and describe its genomic features suggesting the natural history and molecular mechanisms underlying pathogenicity. Their findings indicate that nonordinal extracellular matrix coordination is important for its asexual reproduction, and suggest that loss of sexual maturity contributes to the fatal pathogenicity of S. proliferum to humans.
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40
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Lehikoinen A, Pohjola P, Valkama J, Mutanen M, Pohjoismäki JLO. Promiscuous specialists: Host specificity patterns among generalist louse flies. PLoS One 2021; 16:e0247698. [PMID: 34043636 PMCID: PMC8158981 DOI: 10.1371/journal.pone.0247698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022] Open
Abstract
Ectoparasites such as louse flies (Diptera: Hippoboscidae) have tendency for host specialization, which is driven by adaptation to host biology as well as competition avoidance between parasites of the same host. However, some louse fly species, especially in genera attacking birds, show wide range of suitable hosts. In the presented study, we have surveyed the current status of bird specific louse flies in Finland to provide comprehensive host association data to analyse the ecological requirements of the generalist species. A thorough sampling of 9342 birds, representing 134 species, recovered 576 specimens of louse flies, belonging to six species: Crataerina hirundinis, C. pallida, Ornithomya avicularia, O. chloropus, O. fringillina and Ornithophila metallica. Despite some overlapping hosts, the three Ornithomya species showed a notable pattern in their host preference, which was influenced not only by the host size but also by the habitat and host breeding strategy. We also provide DNA barcodes for ten Finnish species of Hippoboscidae, which can be used as a resource for species identification as well as metabarcoding studies in the future.
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Affiliation(s)
- Aleksi Lehikoinen
- The Helsinki Lab of Ornithology, Finnish Museum of Natural History, Helsinki University, Helsinki, Finland
| | - Pekka Pohjola
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Jari Valkama
- The Helsinki Lab of Ornithology, Finnish Museum of Natural History, Helsinki University, Helsinki, Finland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
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41
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Jauss RT, Solf N, Kolora SRR, Schaffer S, Wolf R, Henle K, Fritz U, Schlegel M. Mitogenome evolution in the Lacerta viridis complex (Lacertidae, Squamata) reveals phylogeny of diverging clades. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1912205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Robin-Tobias Jauss
- Institute of Biology, Biodiversity & Evolution, University of Leipzig, Talstraße 33, Leipzig, 04103, Germany
| | - Nadiné Solf
- Institute of Biology, Biodiversity & Evolution, University of Leipzig, Talstraße 33, Leipzig, 04103, Germany
| | - Sree Rohit Raj Kolora
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Stefan Schaffer
- Institute of Biology, Molecular Evolution & Animal Systematics, University of Leipzig, Talstraße 33, Leipzig, 04103, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Ronny Wolf
- Institute of Biology, Molecular Evolution & Animal Systematics, University of Leipzig, Talstraße 33, Leipzig, 04103, Germany
| | - Klaus Henle
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Conservation Biology, UFZ – Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318, Leipzig, Germany
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Martin Schlegel
- Institute of Biology, Biodiversity & Evolution, University of Leipzig, Talstraße 33, Leipzig, 04103, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
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42
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Tang Y, Zhang X, Ma Y, Zheng X. Descriptive study of the mitogenome of the diamondback squid (
Thysanoteuthis rhombus
Troschel, 1857) and the evolution of mitogenome arrangement in oceanic squids. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan Tang
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
| | - Xiaoying Zhang
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
| | - Yuanyuan Ma
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
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43
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Kutyumov VA, Predeus AV, Starunov VV, Maltseva AL, Ostrovsky AN. Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features. Mitochondrion 2021; 59:96-104. [PMID: 33631347 DOI: 10.1016/j.mito.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022]
Abstract
Bryozoans are aquatic colonial suspension-feeders abundant in many marine and freshwater benthic communities. At the same time, the phylum is under studied on both morphological and molecular levels, and its position on the metazoan tree of life is still disputed. Bryozoa include the exclusively marine Stenolaemata, predominantly marine Gymnolaemata and exclusively freshwater Phylactolaemata. Here we report the mitochondrial genome of the phylactolaemate bryozoan Cristatella mucedo. This species has the largest (21,008 bp) of all currently known bryozoan mitogenomes, containing a typical metazoan gene compendium as well as a number of non-coding regions, three of which are longer than 1500 bp. The trnS1/trnG/nad3 region is presumably duplicated in this species. Comparative analysis of the gene order in C. mucedo and another phylactolaemate bryozoan, Pectinatella magnifica, confirmed their close relationships, and revealed a stronger similarity to mitogenomes of phoronids and other lophotrochozoan species than to marine bryozoans, indicating the ancestral nature of their gene arrangement. We suggest that the ancestral gene order underwent substantial changes in different bryozoan cladesshowing mosaic distribution of conservative gene blocks regardless of their phylogenetic position. Altogether, our results support the early divergence of Phylactolaemata from the rest of Bryozoa.
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Affiliation(s)
- Vladimir A Kutyumov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia.
| | - Alexander V Predeus
- Bioinformatics Institute, Kantemirovskaya 2A, 197342 Saint Petersburg, Russia
| | - Viktor V Starunov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Arina L Maltseva
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Andrew N Ostrovsky
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Department of Palaeontology, Faculty of Geography, Geology and Astronomy, University of Vienna, Althanstr. 14, 1090 Vienna, Austria.
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44
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Sun Y, Daffe G, Zhang Y, Pons J, Qiu JW, Kupriyanova EK. Another blow to the conserved gene order in Annelida: Evidence from mitochondrial genomes of the calcareous tubeworm genus Hydroides. Mol Phylogenet Evol 2021; 160:107124. [PMID: 33610649 DOI: 10.1016/j.ympev.2021.107124] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/15/2021] [Accepted: 02/11/2021] [Indexed: 01/07/2023]
Abstract
Mitochondrial genomes are frequently applied in phylogenetic and evolutionary studies across metazoans, yet they are still poorly represented in many groups of invertebrates, including annelids. Here, we report ten mitochondrial genomes from the annelid genus Hydroides (Serpulidae) and compare them with all available annelid mitogenomes. We detected all 13 protein coding genes in Hydroides spp., including the atp8 which was reported as a missing gene in the Christmas Tree worm Spirobranchus giganteus, another annelid of the family Serpulidae. All available mitochondrial genomes of Hydroides show a highly positive GC skew combined with a highly negative AT skew - a feature consistent with that found only in the mitogenome of S. giganteus. In addition, amino acid sequences of the 13 protein-coding genes showed a high genetic distance between the Hydroides clade and S. giganteus, suggesting a fast rate of mitochondrial sequence evolution in Serpulidae. The gene order of protein-coding genes within Hydroides exhibited extensive rearrangements at species level, and were different from the arrangement patterns of other annelids, including S. giganteus. Phylogenetic analyses based on protein-coding genes recovered Hydroides as a monophyletic group sister to Spirobranchus with a long branch, and sister to the fan worm Sabellidae. Yet the Serpulidae + Sabellidae clade was unexpectedly grouped with Sipuncula, suggesting that mitochondrial genomes alone are insufficient to resolve the phylogenetic position of Serpulidae within Annelida due to its high base substitution rates. Overall, our study revealed a high variability in the gene order arrangement of mitochondrial genomes within Serpulidae, provided evidence to question the conserved pattern of the mitochondrial gene order in Annelida and called for caution when applying mitochondrial genes to infer their phylogenetic relationships.
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Affiliation(s)
- Yanan Sun
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, 224 Waterloo Road, Hong Kong; Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia
| | - Guillemine Daffe
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; Universite de Bordeaux, CNRS, INRAE, La Rochelle Universite, UMS 2567 POREA, 33615 Pessac, France
| | - Yanjie Zhang
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, 224 Waterloo Road, Hong Kong
| | - Joan Pons
- Diversidad Animal y Microbiana, Instituto Mediterráneo de Estudios Avanzados IMEDEA (CSIC-UIB), Esporles, Balearic Islands, Spain
| | - Jian-Wen Qiu
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, 224 Waterloo Road, Hong Kong
| | - Elena K Kupriyanova
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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45
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Song N, Zhai Q, Zhang Y. Higher-level phylogenetic relationships of rove beetles (Coleoptera, Staphylinidae) inferred from mitochondrial genome sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:98-105. [PMID: 33570440 DOI: 10.1080/24701394.2021.1882444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Rove beetles (Staphylinidae) and allied families constitute a huge radiation of Coleoptera, but basal relationships in this group remain controversial. In this study, we newly sequenced eight mitogenomes of representatives of Staphylinidae by using next-generation sequencing method. Together with 99 existing mitogenomes of Staphyliniformia, (sub)family relationships were investigated with ML and Bayesian searches under various substitution models and data recoding schemes. The results consistently supported Scydmaenidae and Silphidae to be subordinate groups of Staphylinidae. Within the monophyletic Staphylinidae (including Scydmaenidae and Silphidae), the hypothesis of four major subfamily groups cannot be confirmed. Bayesian inferences under the site-heterogeneous mixture model generally supported the basal position of major clades corresponding to the Omaliine group. At the subfamily level, the monophyly of Pselaphinae, Oxytelinae, Scaphidiinae, Steninae and Staphylininae was supported. However, the subfamilies Omaliinae, Tachyporinae, Aleocharinae and Paederinae were each non-monophyletic.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Qing Zhai
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yaling Zhang
- Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
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Isokallio MA, Stewart JB. High-Throughput Detection of mtDNA Mutations Leading to tRNA Processing Errors. Methods Mol Biol 2021; 2192:117-132. [PMID: 33230770 DOI: 10.1007/978-1-0716-0834-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Some mutations in the tRNA genes of mitochondrial DNA (mtDNA) have been demonstrated to affect the processing of the mitochondrial transcriptome in human patients with mitochondrial disease. A recent analysis of mtDNA mutations in 527 human tumors revealed that approximately a quarter of the somatic mt-tRNA gene mutations lead to aberrant processing of the mitochondrial transcriptome in these tumors. Here, we describe a method, based on mtDNA mutations induced by the mtDNA mutator mouse, to map the sites that lead to transcript processing abnormalities. Mutations in the mtDNA are identified and quantified by amplicon-based mtDNA sequencing, and compared to the allelic ratios observed in matched RNASeq data. Strong deviation in the variant allele frequencies between the amplicon and RNASeq data suggests that such mutations lead to disruptions in mitochondrial transcript processing.
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Prospective enzymes for omega-3 PUFA biosynthesis found in endoparasitic classes within the phylum Platyhelminthes. J Helminthol 2020; 94:e212. [DOI: 10.1017/s0022149x20000954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
The free-living infectious stages of macroparasites, specifically, the cercariae of trematodes (flatworms), are likely to be significant (albeit underappreciated) vectors of nutritionally important polyunsaturated fatty acids (PUFA) to consumers within aquatic food webs, and other macroparasites could serve similar roles. In the context of de novo omega-3 (n-3) PUFA biosynthesis, it was thought that most animals lack the fatty acid (FA) desaturase enzymes that convert stearic acid (18:0) into ɑ-linolenic acid (ALA; 18:3n-3), the main FA precursor for n-3 long-chain PUFA. Recently, novel sequences of these enzymes were recovered from 80 species from six invertebrate phyla, with experimental confirmation of gene function in five phyla. Given this wide distribution, and the unusual attributes of flatworm genomes, we conducted an additional search for genes for de novo n-3 PUFA in the phylum Platyhelminthes. Searches with experimentally confirmed sequences from Rotifera recovered nine relevant FA desaturase sequences from eight species in four genera in the two exclusively endoparasite classes (Trematoda and Cestoda). These results could indicate adaptations of these particular parasite species, or may reflect the uneven taxonomic coverage of sequence databases. Although additional genomic data and, particularly, experimental study of gene functionality are important future validation steps, our results indicate endoparasitic platyhelminths may have enzymes for de novo n-3 PUFA biosynthesis, thereby contributing to global PUFA production, but also representing a potential target for clinical antihelmintic applications.
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Baeza JA. Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus. BMC Genomics 2020; 21:882. [PMID: 33297960 PMCID: PMC7726883 DOI: 10.1186/s12864-020-07292-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/28/2020] [Indexed: 12/11/2022] Open
Abstract
Background Whole mitogenomes or short fragments (i.e., 300–700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ‘primer walking’ or ‘long PCR’ followed by Sanger sequencing or Illumina short-read low-coverage whole genome (LC-WGS) sequencing with or without prior enrichment of mitochondrial DNA. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I first tested whether mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a ‘gold’ standard reference mitogenome retrieved from the same individual using Illumina sequencing. Third and lastly, I tested if the long-read assemblies are useful for mitophylogenomics and barcoding research. To accomplish these goals, I used the Caribbean spiny lobster Panulirus argus, an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region. Results LC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines retrieved a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not ‘perfect’, phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other related species in the same genus, family, and superorder. Conclusions This study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income countries.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Rocha-Reis DA, Pasa R, Menegidio FB, Heslop-Harrison JS, Schwarzacher T, Kavalco KF. The Complete Mitochondrial Genome of Two Armored Catfish Populations of the Genus Hypostomus (Siluriformes, Loricariidae, Hypostominae). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.579965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Léger T, Mally R, Neinhuis C, Nuss M. Refining the phylogeny of Crambidae with complete sampling of subfamilies (Lepidoptera, Pyraloidea). ZOOL SCR 2020. [DOI: 10.1111/zsc.12452] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Théo Léger
- Museum für Naturkunde – Leibniz‐Institut für Evolutions‐ und Biodiversitätsforschung Berlin Germany
| | - Richard Mally
- Faculty of Forestry and Wood Sciences Czech University of Life Sciences in Prague Praha Czech Republic
| | | | - Matthias Nuss
- Museum of Zoology Senckenberg Natural History Collections Dresden Germany
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