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Yang YX, Kang Y, Ge XY, Yuan SL, Li XY, Liu HY. A Mysterious Asian Firefly Genus, Oculogryphus Jeng, Engel & Yang (Coleoptera, Lampyridae): The First Complete Mitochondrial Genome and Its Phylogenetic Implications. INSECTS 2024; 15:464. [PMID: 39057197 PMCID: PMC11277304 DOI: 10.3390/insects15070464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024]
Abstract
The firefly genus Oculogryphus Jeng, Engel & Yang, 2007 is a rare-species group endemic to Asia. Since its establishment, its position has been controversial but never rigorously tested. To address this perplexing issue, we are the first to present the complete mitochondrial sequence of Oculogryphus, using the material of O. chenghoiyanae Yiu & Jeng, 2018 determined through a comprehensive morphological identification. Our analyses demonstrate that its mitogenome exhibits similar characteristics to that of Stenocladius, including a rearranged gene order between trnC and trnW, and a long intergenic spacer (702 bp) between the two rearranged genes, within which six remnants (29 bp) of trnW were identified. Further, we incorporated this sequence into phylogenetic analyses of Lampyridae based on different molecular markers and datasets using ML and BI analyses. The results consistently place Oculogryphus within the same clade as Stenocladius in all topologies, and the gene rearrangement is a synapomorphy for this clade. It suggests that Oculogryphus should be classified together with Stenocladius in the subfamily Ototretinae at the moment. This study provides molecular evidence confirming the close relationship between Oculogryphus and Stenocladius and discovers a new phylogenetic marker helpful in clarifying the monophyly of Ototretinae, which also sheds a new light on firefly evolution.
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Affiliation(s)
- Yu-Xia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China
| | - Ya Kang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
| | - Xue-Ying Ge
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
| | - Shuai-Long Yuan
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hao-Yu Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China
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Wang Z, Xu X, Zheng Y, Xu Z, Li Y, Chen H. Analysis of the Overlength Main Noncoding Region in Metacarcinus magister (Decapoda: Brachyura) and a Phylogenetic Study of the Cancroidea Species. Genes (Basel) 2024; 15:437. [PMID: 38674372 PMCID: PMC11049931 DOI: 10.3390/genes15040437] [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: 01/26/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide important information regarding the molecular evolution and phylogenetic relationships of marine invertebrates, especially in Brachyura. Only one Cancroidea species of mitogenomes has been sequenced before; in this research, the mitogenomic characteristics of Metacarcinus magister (Cancridae: Cancroidea) are newly studied. The length of the M. magister mitogenome was 48,820 bp, and it contained the typical 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. We performed a series of analyses on the characteristics of the mNCR of M. magister. The phylogenetics, life circumstances, and selective pressures were all analyzed to explain the formation of this length, which revealed the length of the M. magister mitogenome to be approximately three times greater than the normal length of Brachyuran mitogenomes. Phylogenetic analyses based on a dataset of 215 Decapodan mitogenomes indicated that all Eriphioidea crabs were clustered together as a group. Moreover, the rearrangement mechanism of the Cancroidea species was predicted to provide stronger evidence for the phylogenetic analysis. In general, the results obtained in this study will contribute to a better understanding of the cause of the unusual length of the M. magister mitogenome and provide new insights into the phylogeny of Brachyura.
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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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Xu T, Bravo H, van der Meij SE. Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae). PeerJ 2023; 11:e16217. [PMID: 37868050 PMCID: PMC10586294 DOI: 10.7717/peerj.16217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/11/2023] [Indexed: 10/24/2023] Open
Abstract
Background Thoracotremata belong to the large group of "true" crabs (infraorder Brachyura), and they exhibit a wide range of physiological and morphological adaptations to living in terrestrial, freshwater and marine habitats. Moreover, the clade comprises various symbiotic taxa (Aphanodactylidae, Cryptochiridae, Pinnotheridae, some Varunidae) that are specialised in living with invertebrate hosts, but the evolutionary history of these symbiotic crabs is still partially unresolved. Methods Here we assembled and characterised the complete mitochondrial genomes (hereafter mitogenomes) of three gall crab species (Cryptochiridae): Kroppcarcinus siderastreicola, Opecarcinus hypostegus and Troglocarcinus corallicola. A phylogenetic tree of the Thoracotremata was reconstructed using 13 protein-coding genes and two ribosomal RNA genes retrieved from three new gall crab mitogenomes and a further 72 available thoracotreme mitogenomes. Furthermore, we applied a comparative analysis to characterise mitochondrial gene order arrangement, and performed a selection analysis to test for selective pressure of the protein-coding genes in symbiotic Cryptochiridae, Pinnotheridae, and Varunidae (Asthenognathus inaequipes and Tritodynamia horvathi). Results The results of the phylogenetic reconstruction confirm the monophyly of Cryptochiridae, which clustered separately from the Pinnotheridae. The latter clustered at the base of the tree with robust branch values. The symbiotic varunids A. inaequipes and T. horvathi clustered together in a clade with free-living Varunidae species, highlighting that symbiosis in the Thoracotremata evolved independently on multiple occasions. Different gene orders were detected in symbionts and free-living species when compared with the ancestral brachyuran gene order. Lastly, the selective pressure analysis detected two positively selected sites in the nad6 gene of Cryptochiridae, but the evidence for positive selection in Pinnotheridae and A. inaequipes and T. horvathi was weak. Adaptive evolution of mitochondrial protein-coding genes is perhaps related to the presumably higher energetic demands of a symbiotic lifestyle.
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Affiliation(s)
- Tao Xu
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Henrique Bravo
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Sancia E.T. van der Meij
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Marine Biodiversity Group, Naturalis Biodiversity Center, Leiden, Netherlands
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Wang Z, Zheng Y, Zhao X, Xu X, Xu Z, Cui C. Molecular Phylogeny and Evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences. BIOLOGY 2023; 12:974. [PMID: 37508404 PMCID: PMC10376310 DOI: 10.3390/biology12070974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
Tuerkayana is of particular interest because it has been separated, in recent years, from Cardisoma and Discoplax but studies of its taxonomic status, especially from a whole mitochondrial genome perspective, have been lacking. In this study, the mitogenomes of four species (Tuerkayana magnum, Tuerkayana rotundum, Tuerkayana hirtipes, and Tuerkayana celeste) of Tuerkayana are sequenced and contrasted with other species in Brachyura for the first time. The phylogenetic tree of Brachyura, which includes 206 crab species (189 species of Brachyuran and 17 Anomura species) with a complete mitogenome, was constructed to evaluate the phylogenetic position of Tuerkayana and Gecarcinidae within Brachyuran, and explore the monophyly of Gecarcinidae. Furthermore, two single gene trees based on cox1 and 16SrRNA separately within interspecies of Gecarcinidae were reconstructed, providing molecular evidence for Tuerkayana and further clarifying the division of genera in Gecarcinidae. Based on the mitogenome dataset of 206 crabs, the branch-site model was utilized to explore selective pressure in individual codons with CodeML. The strong selective pressure shown in nad6 indicates that it may have played a significant role in the evolution of Gecarcinidae.
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Affiliation(s)
- Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
| | - Yuqing Zheng
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
| | - Xinyue Zhao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
| | - Xinyi Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200000, China
| | - Zhiwen Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
| | - Chong Cui
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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Xu H, Liu X, Wang P, Li H, Wu SA. Phylogenetic Implications of Mitogenomic Sequences and Gene Rearrangements of Scale Insects (Hemiptera, Coccoidea). INSECTS 2023; 14:257. [PMID: 36975942 PMCID: PMC10051623 DOI: 10.3390/insects14030257] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Coccoidea (scale insects) are important plant parasites with high diversity of species. However, the phylogenetic relationship within Coccoidea has not been fully determined. In this study, we sequenced mitogenomes of six species belonging to five coccoid families. With the addition of three previously published mitogenomes, a total of 12 coccoid species were adopted for the phylogenetic reconstruction based on the maximum likelihood and Bayesian inference. The monophyly of Coccoidea was recovered and Aclerdidae and Coccidae were recovered as the sister group, successively sister to Cerococcidae, Kerriidae, and Eriococcidae. In addition, there were gene rearrangements occurring in all mitogenomes of coccoid species studied here. The novel gene rearrangement ND6-trnP and trnI-ND2-trnY supported the monophyly of Coccoidea and the sister relationship of Aclerdidae and Coccidae. This implies that data from the mitogenome can provide new insight for clarifying the deeper level of phylogenetic relationship within Coccoidea.
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Affiliation(s)
- Han Xu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Xiaochen Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Pei Wang
- Key Laboratory of Molluscan Quarantine and Identification of GACC, Fuzhou Customs District, Fuzhou 350001, China
| | - Hu Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - San-an Wu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
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Wang Z, Xu X, Zheng Y, Wang J, Yu Q, Liu B. Taxonomic status and phylogenetic relationship of Anomura (Crustacea: Decapoda) based on mitochondrial sequences and gene order rearrangements. Gene X 2022; 851:147042. [DOI: 10.1016/j.gene.2022.147042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/26/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022] Open
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Pang X, Han C, Guo B, Liu K, Lin X, Lu X. The First Complete Mitochondrial Genome of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) and Phylogenetic Relationships within Infraorder Brachyura. Genes (Basel) 2022; 13:genes13071127. [PMID: 35885910 PMCID: PMC9323885 DOI: 10.3390/genes13071127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022] Open
Abstract
Characterizing the complete mitochondrial genome (mitogenome) of an organism is useful for genomic studies in taxonomy and evolution. The mitogenomic characteristics of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) have never been studied. The present study decodes the first mitogenome of E. crenata by high-throughput sequencing (HTS). The length of the mitogenome is 15,597 bp, and it contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL), and 22 transfer RNA genes. There are 14 and 23 genes observed on the heavy and light strands, respectively. E. crenata possesses a trnH-cac translocation, with the trnH-cac shifted between trnE-gaa and trnF-ttc instead of the usual location between nad5 and nad4 in decapods. Phylogenetic analyses based on the current dataset of 33 Brachyuran mitogenomes indicate that E. crenata. is closely related to Ashtoret lunaris of Matutidae. The similar codon usage and rearrangements in the two species provide evidence for their close phylogenetic relationship. Positive selection analysis showed that one residue located in cox1 was identified as a positively selected site with high BEB value (>95%), indicating that this gene was under positive selection pressure. This study is the first complete mitogenome record for the family Goneplacidae, and the results obtained may improve the understanding of the phylogeny of Goneplacidae in Brachyura.
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Affiliation(s)
- Xiaoke Pang
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; (X.P.); (C.H.)
| | - Chenglong Han
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; (X.P.); (C.H.)
| | - Biao Guo
- Tianjin Fisheries Research Institute, Tianjin 300457, China; (B.G.); (K.L.)
| | - Kefeng Liu
- Tianjin Fisheries Research Institute, Tianjin 300457, China; (B.G.); (K.L.)
| | - Xiaolong Lin
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Correspondence: (X.L.); (X.L.)
| | - Xueqiang Lu
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; (X.P.); (C.H.)
- Correspondence: (X.L.); (X.L.)
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Bojko J, Burgess AL, Allain TW, Ross EP, Pharo D, Kreuze JF, Behringer DC. Pathology and genetic connectedness of the mangrove crab (Aratus pisonii) – a foundation for understanding mangrove disease ecology. ANIMAL DISEASES 2022. [DOI: 10.1186/s44149-022-00039-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractMangrove forests are productive ecosystems, acting as a sink for CO2, a habitat for a diverse array of terrestrial and marine species, and as a natural barrier to coastline erosion. The species that reside within mangrove ecosystems have important roles to play, including litter decomposition and the recycling of nutrients. Crustacea are important detritivores in such ecosystems and understanding their limitations (i.e. disease) is an important endeavour when considering the larger ecological services provided.Histology and metagenomics were used to identify viral (Nudiviridae, Alphaflexiviridae), bacterial (Paracoccus sp., 'Candidatus Gracilibacteria sp.’, and Pseudoalteromonas sp.), protozoan, fungal, and metazoan diversity that compose the symbiome of the mangrove crab, Aratus pisonii. The symbiotic groups were observed at varying prevalence under histology: nudivirus (6.5%), putative gut epithelial virus (3.2%), ciliated protozoa (35.5%), gonad fungus (3.2%), gill ectoparasitic metazoan (6.5%). Metagenomic analysis of one specimen exhibiting a nudivirus infection provided the complete host mitochondrial genome (15,642 bp), nudivirus genome (108,981 bp), and the genome of a Cassava common mosaic virus isolate (6387 bp). Our phylogenetic analyses group the novel nudivirus with the Gammanudivirus and protein similarity searches indicate that Carcinus maenas nudivrius is the most similar to the new isolate. The mitochondrial genome were used to mine short fragments used in population genetic studies to gauge an idea of diversity in this host species across the USA, Caribbean, and central and southern America.This study report several new symbionts based on their pathology, taxonomy, and genomics (where available) and discuss what effect they may have on the crab population. The role of mangrove crabs from a OneHealth perspective were explored, since their pathobiome includes cassava-infecting viruses. Finally, given that this species is abundant in mangrove forests and now boasts a well-described pathogen profile, we posit that A. pisonii is a valuable model system for understanding mangrove disease ecology.
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Liu D, Basso A, Babbucci M, Patarnello T, Negrisolo E. Macrostructural Evolution of the Mitogenome of Butterflies (Lepidoptera, Papilionoidea). INSECTS 2022; 13:insects13040358. [PMID: 35447800 PMCID: PMC9031222 DOI: 10.3390/insects13040358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Papilionoidea is a superfamily of Lepidoptera encompassing about 19,000 species. In the present work, we study the evolution of the structure of the mitogenome of these lepidopterans. The mechanisms generating the eight arrangements known for Papilionoidea were investigated analysing the movements of different mitochondrial genes. Five newly sequenced/assembled mitogenomes were included in our analysis involving more than 600 genomes. We provide new findings that help to understand the evolution of the gene orders MIQGO, IMQGO, 2S1GO, ES1GO and S1NGO in different butterflies. We demonstrate that the evolution of the 2S1GO in Lycaenidae followed a complicated pathway with multiple events of duplication and loss of trnS1 and changes in anticodon. We describe two new gene orders 2FFGO and 4QGO for Ampittia subvittatus (Hesperiidae) and Bhutanitis thaidina (Papilionidae). Abstract The mitogenome of the species belonging to the Papilionodea (Lepidoptera) is a double stranded circular molecule containing the 37 genes shared by Metazoa. Eight mitochondrial gene orders are known in the Papilionoidea. MIQGO is the plesiomorphic gene order for this superfamily, while other mitochondrial arrangements have a very limited distribution. 2S1GO gene order is an exception and is present in several Lycaenidae and one species of Hesperiidae. We studied the macrostructural changes generating the gene orders of butterflies by analysing a large data set (611 taxa) containing 5 new mitochondrial sequences/assemblies and 87 de novo annotated mitogenomes. Our analysis supports a possible origin of the intergenic spacer trnQ-nad2, characterising MIQGO, from trnM. We showed that the homoplasious gene order IMQGO, shared by butterflies, species of ants, beetles and aphids, evolved through different transformational pathways. We identify a complicated evolutionary scenario for 2S1GO in Lycaenidae, characterised by multiple events of duplication/loss and change in anticodon of trnS1. We show that the gene orders ES1GO and S1NGO originated through a tandem duplication random loss mechanism. We describe two novel gene orders. Ampittia subvittatus (Hesperiidae) exhibits the gene order 2FFGO, characterised by two copies of trnF, one located in the canonical position and a second placed in the opposite strand between trnR and trnN. Bhutanitis thaidina (Papilionidae) exhibits the gene order 4QGO, characterised by the quadruplication of trnQ.
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Affiliation(s)
- Di Liu
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (D.L.); (M.B.); (T.P.)
| | - Andrea Basso
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35020 Legnaro, Italy;
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (D.L.); (M.B.); (T.P.)
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (D.L.); (M.B.); (T.P.)
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (D.L.); (M.B.); (T.P.)
- Correspondence:
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Castellucci F, Luchetti A, Mantovani B. Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera. Sci Rep 2022; 12:4931. [PMID: 35322086 PMCID: PMC8942981 DOI: 10.1038/s41598-022-08873-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 03/08/2022] [Indexed: 11/20/2022] Open
Abstract
The class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy and brine shrimps) is sister to all other branchiopods, and the Notostraca (tadpole shrimps) results as sister group to Diplostraca, which includes Laevicaudata + Spinicaudata (clam shrimps) and Cladoceromorpha (water fleas + Cyclestherida). In the present analysis, thanks to an increased taxon sampling, a complex picture emerges. Most of the analyzed mitogenomes show the Pancrustacea gene order while in several other taxa they are found rearranged. These rearrangements, though, occur unevenly among taxa, most of them being found in Cladocera, and their taxonomic distribution does not agree with the phylogeny. Our data also seems to suggest the possibility of potentially homoplastic, alternative gene order within Daphniidae.
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Affiliation(s)
- Filippo Castellucci
- Department of Biological, Geological and Environmental Sciences-University of Bologna, via Selmi 3, 40126, Bologna, Italy.,Zoology Section, Natural History Museum of Denmark-University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences-University of Bologna, via Selmi 3, 40126, Bologna, Italy.
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences-University of Bologna, via Selmi 3, 40126, Bologna, Italy
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Lü J, Xia L, Liu X, Ma Y, Li J, Ye Y, Guo B. The mitochondrial genome of Grapsus albolineatus (Decapoda: Brachyura: Grapsidae) and phylogenetic associations in Brachyura. Sci Rep 2022; 12:2104. [PMID: 35136145 PMCID: PMC8826855 DOI: 10.1038/s41598-022-06080-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/11/2022] [Indexed: 11/09/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and evolutionary traits. In this study, we determined the complete mitochondrial DNA sequence of the herbivorous crab Grapsus albolineatus. It is a typical metazoan mitochondrial genome. The total size is 15,583 bp, contains the entire set of 37 genes, and has an AT-rich region. Then, 23 of the 37 genes were encoded by the heavy (+) strand while 14 are encoded by the light (−) strand. Compared with the pan-crustacean ground pattern, two tRNA genes (tRNA-His and tRNA-Gln) were rearranged and the tandem duplication/random loss model was used to explain the observed gene rearrangements. The phylogenetic results showed that all Grapsidae crabs clustered together as a group. Furthermore, the monophyly of each family was well supported, with the exception of Menippidae. In general, the results obtained in this study will contribute to the better understanding of gene rearrangements in Grapsidae crab mitogenomes and provide new insights into the phylogeny of Brachyura.
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Affiliation(s)
- Jiayin Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Liping Xia
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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13
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Ge XY, Liu T, Kang Y, Liu HY, Yang YX. First complete mitochondrial genomes of Ototretinae (Coleoptera, Lampyridae) with evolutionary insights into the gene rearrangement. Genomics 2022; 114:110305. [DOI: 10.1016/j.ygeno.2022.110305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 01/09/2022] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
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14
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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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15
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Lau NS, Sam KK, Ahmad AB, Siti KA, Ahmad Zafir AW, Shu-Chien AC. Gene Arrangement and Adaptive Evolution in the Mitochondrial Genomes of Terrestrial Sesarmid Crabs Geosesarma faustum and Geosesarma penangensis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.778570] [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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16
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Hartmann T, Bannach M, Middendorf M. Sorting Signed Permutations by Inverse Tandem Duplication Random Losses. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2177-2188. [PMID: 31095495 DOI: 10.1109/tcbb.2019.2917198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gene order evolution of unichromosomal genomes, for example mitochondrial genomes, has been modelled mostly by four major types of genome rearrangements: inversions, transpositions, inverse transpositions, and tandem duplication random losses. Generalizing models that include all those rearrangements while admitting computational tractability are rare. In this paper, we study such a rearrangement model, namely the inverse tandem duplication random loss (iTDRL) model, where an iTDRL duplicates and inverts a continuous segment of a gene order followed by the random loss of one of the redundant copies of each gene. The iTDRL rearrangement has currently been proposed by several authors suggesting it to be a possible mechanisms of mitochondrial gene order evolution. We initiate the algorithmic study of this new model of genome rearrangement by proving that a shortest rearrangement scenario that transforms one given gene order into another given gene order can be obtained in quasilinear time. Furthermore, we show that the length of such a scenario, i.e., the minimum number of iTDRLs in the transformation, can be computed in linear time.
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17
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Papetti C, Babbucci M, Dettai A, Basso A, Lucassen M, Harms L, Bonillo C, Heindler FM, Patarnello T, Negrisolo E. Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish. Genome Biol Evol 2021; 13:6133229. [PMID: 33570582 PMCID: PMC7936035 DOI: 10.1093/gbe/evab017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.
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Affiliation(s)
- Chiara Papetti
- Department of Biology, University of Padova, Padova 35121,Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma 00196, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Agnes Dettai
- Institut de Systematique, Evolution, Biodiversité (ISYEB) Muséum national d'Histoire naturelle-CNRS-Sorbonne Université-EPHE, MNHN, Paris 75005, France
| | - Andrea Basso
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Magnus Lucassen
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany
| | - Lars Harms
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany.,Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg (HIFMB), Ammerlsity of Oldenburg (HIFMOldenburg 26129, Germany
| | - Celine Bonillo
- Service de Systématique Moléculaire, UMS2700 Acquisition et Analyse de Données (2AD), MNHN, Paris 75005, France
| | | | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy.,CRIBI Interdepartmental Research Centre for Innovative Biotechnologies, University of Padova, viale G. Colombo 3, Padova 35121, Italy
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18
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Zhang J, Miao G, Hu S, Sun Q, Ding H, Ji Z, Guo P, Yan S, Wang C, Kan X, Nie L. Quantification and evolution of mitochondrial genome rearrangement in Amphibians. BMC Ecol Evol 2021; 21:19. [PMID: 33563214 PMCID: PMC7871395 DOI: 10.1186/s12862-021-01755-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution. RESULTS Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation. CONCLUSION It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.
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Affiliation(s)
- Jifeng Zhang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China.
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
- Anhui Key Laboratory of Low Temperature Co-Fired Materials, Huainan Normal University, Huainan, 232001, People's Republic of China.
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Health and Safety, Ministry of Education, Huainan, 232001, People's Republic of China.
- Anhui Shanhe Pharmaceutical Excipients Co., Ltd., Huainan, 232001, People's Republic of China.
| | - Guopen Miao
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Shunjie Hu
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Qi Sun
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Hengwu Ding
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China
| | - Zhicheng Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Pen Guo
- Life Science and Food Engineering College, Yibin University, Yibin, Sichuan, 644000, People's Republic of China
| | - Shoubao Yan
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Chengrun Wang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Xianzhao Kan
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
| | - Liuwang Nie
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
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19
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Huang L, Zhong S, Liu Y, Huang G, Chen X. The complete mitochondrial genome of Matuta victor (Decapoda: Matutidae) from Beibu Bay. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:241-242. [PMID: 33537455 PMCID: PMC7832593 DOI: 10.1080/23802359.2020.1861999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The true crabs (Brachyura) including Calappidea are one of the most diverse groups of Decapod crustaceans However, despite their great diversity and commercial importance, phylogenetic and classification relationships within Calappidea are still complicated and controversial. In this study, we report the first complete mitochondrial genome of Matuta victos. The mitogenome has 17,782 base pairs (70.1% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and two ribosomal RNAs), plus a putative control region. This study will provide useful molecular resources for clarifying evolutionary and phylogenetic confusion within Calappidea.
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Affiliation(s)
- Lianghua Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Shengping Zhong
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China.,Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd, Beihai, China
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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20
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Xu X, Wang Q, Wu Q, Xu J, Wang J, Wang Z. The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura. Biochem Genet 2021; 59:617-636. [PMID: 33415669 DOI: 10.1007/s10528-020-10025-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (- 0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.
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Affiliation(s)
- Xinyi Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Qi Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Qiong Wu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Jiayan Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Jie Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China.
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21
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Insights into the evolution of Brachyura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Int J Biol Macromol 2021; 170:717-727. [PMID: 33412200 DOI: 10.1016/j.ijbiomac.2020.12.210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/29/2020] [Accepted: 12/29/2020] [Indexed: 11/23/2022]
Abstract
Brachyura is one of the most species rich and highly derived groups among extant crustaceans, with over 7250 known species. However, brachyuran phylogeny remains controversial and requires further study. Here, we combined 103 brachyuran mitogenomes from GenBank with 10 new mitogenomes to describe gene rearrangement patterns and explore the internal phylogenetic relationships of Brachyura. Most of the 10 novel mitogenomes had the typical 37 genes, except that of Longpotamon depressum, which lacked trnQ. We discovered 15 gene rearrangement patterns among Brachyura and preliminarily determined their rearrangement mechanisms with the help of CREx. We identified seven putative ancestral family gene orders among the 15 rearrangement patterns and expounded systematically upon the mechanisms of their rearrangement. In our phylogenetic analysis, Raninoida shared a sister relationship with an eubrachyuran clade ((Heterotremata [Potamoidea] + Thoracotremata) + Heterotremata) at maximum nodal support rather than Dromiacea, which did not support monophyly of Podotremata. In addition, Potamoidea (Parathelphusidae + Potamidae) retained a close relationship with Thoracotremata rather than their marine relatives in Heterotremata. Our study provides important information for the evolution of Brachyura by using the large taxon sampling currently available for systematic rearrangement and phylogenetic analyses.
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22
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Arribas P, Andújar C, Moraza ML, Linard B, Emerson BC, Vogler AP. Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari. Mol Biol Evol 2020; 37:683-694. [PMID: 31670799 DOI: 10.1093/molbev/msz255] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - María Lourdes Moraza
- Departamento de Biología Ambiental, Universidad de Navarra, Facultad de Ciencias, Pamplona, Spain
| | - Benjamin Linard
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,LIRMM, Université de Montpellier, CNRS, Montpellier, France.,ISEM, Université de Montpellier, CNRS, IRD, EPHE, CIRAD, INRAP, Montpellier, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
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23
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Li YT, Xin ZZ, Tang YY, Yang TT, Tang BP, Sun Y, Zhang DZ, Zhou CL, Liu QN, Yu XM. Comparative Mitochondrial Genome Analyses of Sesarmid and Other Brachyuran Crabs Reveal Gene Rearrangements and Phylogeny. Front Genet 2020; 11:536640. [PMID: 33240311 PMCID: PMC7667018 DOI: 10.3389/fgene.2020.536640] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/28/2020] [Indexed: 01/26/2023] Open
Abstract
Mitochondrial genomes (mitogenomes) are important for understanding molecular evolution and phylogenetic relationships. The complete mitogenome of Perisesarma bidens was determined, which is 15,641 bp in length. The A + T content of P. bidens mitogenome was 74.81%. The AT skew was slightly negative (-0.021). The 22 tRNAs ranged from 65 to 73 bp and were highly A + T biased. All tRNA genes had typical cloverleaf structures, except for the trnS1 gene, which lacked a dihydrouridine (DHU) arm. The gene order within the P. bidens mitogenome was identical to the pancrustacean ground pattern, except for the translocation of the trnH. Additionally, the gene order of trnI-trnQ-trnM in pancrustacean ground pattern became trnQ-trnI-trnM in P. bidens. Phylogenetic analyses supported the inclusion of P. bidens in Sesarmidae and the promotion of Sesarminae to Sesarmidae. The results will help us to better understand the status and evolutionary history of Grapsoidea crabs.
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Affiliation(s)
- Yue-Tian Li
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
- College of Life Sciences, Nankai University, Tianjin, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, China
| | - Ying-Yu Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, China
| | - Ting-Ting Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Yue Sun
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Xiao-Min Yu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
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24
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Zhang Y, Gong L, Lu X, Jiang L, Liu B, Liu L, Lü Z, Li P, Zhang X. Gene rearrangements in the mitochondrial genome of Chiromantes eulimene (Brachyura: Sesarmidae) and phylogenetic implications for Brachyura. Int J Biol Macromol 2020; 162:704-714. [DOI: 10.1016/j.ijbiomac.2020.06.196] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 11/25/2022]
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Kobayashi G, Itoh H, Fukuda H, Kojima S. The complete mitochondrial genome of the sand bubbler crab Scopimera globosa and its phylogenetic position. Genomics 2020; 113:831-839. [PMID: 33091547 DOI: 10.1016/j.ygeno.2020.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/29/2020] [Accepted: 10/16/2020] [Indexed: 01/19/2023]
Abstract
The mitochondrial genome has become commonly used for the molecular phylogenetic analysis of animals. Most phylogenetic studies on brachyurans using mitogenome sequences have indicated the paraphyly of superfamilies Grapsoidea and Ocypodoidea but taxon sampling remains limited. The phylogenetic position of Scopimera has been tested in several previous studies using nuclear and/or mitochondrial DNA sequences, but the phylogenetic relationship within the family remains to be resolved. We newly sequenced the complete mitochondrial genome of the sand bubbler crab Scopimera globosa (Ocypodoidea: Dotillidae). Scopimera globosa was clustered with Ilyoplax despite the morphological similarity between Scopimera and Dotilla. The mitochondrial gene order of S. globosa was unique, whereas that of other genera in the family was the same. These results suggest that phylogenetic analysis based on mitogenome sequences and gene order comparison would provide a more robust phylogeny of Dotillidae.
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Affiliation(s)
- Genki Kobayashi
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan.
| | - Hajime Itoh
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Hideki Fukuda
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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Kim YH, Kim KR, Park JY, Sung MS, Yun BH, Jeon A, Kim MS, Bang IC. The complete mitochondrial genome of Chionoecetes japonicus (Crustacea: Decapoda: Majoidea). Mitochondrial DNA B Resour 2020; 5:3524-3526. [PMID: 33458227 PMCID: PMC7782079 DOI: 10.1080/23802359.2020.1827061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The complete mitochondrial genome of Chionoecetes japonicus was sequenced using a specimen collected offshore in the East Sea. The genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (D-loop), with a total length of 16,060 bp. The overall nucleotide composition was 34.91% A, 17.29% C, 10.93% G, and 36.87% T, with 71.78% A + T. In the phylogenetic tree was constructed using maximum-likelihood and Bayesian inference analyses, C. japonicus and C. japonicus pacificus formed a genetic clade that was sister to C. opilio.
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Affiliation(s)
- Yong Hwi Kim
- Department of Life Science and Biotechnology, Soonchunhyang University, Asan, Republic of Korea
| | - Kang-Rae Kim
- Department of Life Science and Biotechnology, Soonchunhyang University, Asan, Republic of Korea
| | - Jong Yeon Park
- Department of Life Science and Biotechnology, Soonchunhyang University, Asan, Republic of Korea
| | - Mu Sung Sung
- Department of Life Science and Biotechnology, Soonchunhyang University, Asan, Republic of Korea
| | - Bong Han Yun
- Department of Life Science and Biotechnology, Soonchunhyang University, Asan, Republic of Korea
- Department of Biology, Soonchunhyang University, Asan, Republic of Korea
| | - Ahhyeon Jeon
- Department of Life Science and Biotechnology, Soonchunhyang University, Asan, Republic of Korea
| | - Moo-Sang Kim
- Department of Bioinformatics, MOAGEN, Daejeon, Republic of Korea
| | - In-Chul Bang
- Department of Life Science and Biotechnology, Soonchunhyang University, Asan, Republic of Korea
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Jeong JH, Ryu S, Kim W. The complete mitogenome of the Chionoecetes opilio (Crustacea: Decapoda: Oregoniidae) and its unique characteristics. Mitochondrial DNA B Resour 2020; 5:2550-2552. [PMID: 33457859 PMCID: PMC7782958 DOI: 10.1080/23802359.2020.1780974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The complete mitochondrial genome of Chionoecetes opilio is a 16,067 bp long, circular molecule which contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). Its gene contents and organization are generally similar to other majoid mitogenomes. However, the mitogenome shows unique characteristics; long terminal amino acids, loss or addition of 3 PCGs, a 1216 bp long putative D-loop region, and peculiar secondary structures of 5 tRNAs. The concatenated amino acid sequences of 13 PCGs were used to analyze the phylogenetic tree, which well supported the monophyly of brachyuran clades of Majoidea, Heterotremata, Thoracotremata, and Eubrachyura.
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Affiliation(s)
- Jin-Hyeop Jeong
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Seongho Ryu
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan, Korea
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul, Korea
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Lu X, Gong L, Zhang Y, Chen J, Liu L, Jiang L, Lü Z, Liu B, Tong G, Wei X. The complete mitochondrial genome of Calappa bilineata: The first representative from the family Calappidae and its phylogenetic position within Brachyura. Genomics 2020; 112:2516-2523. [PMID: 32045669 DOI: 10.1016/j.ygeno.2020.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/08/2020] [Accepted: 02/07/2020] [Indexed: 12/15/2022]
Abstract
In this study, we determined the complete mitogenome sequence of Calappa bilineata, which is the first mitogenome of Calappidae up to now. The total length is 15,606 bp and includes 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and one control region. The genome composition is highly A + T biased (68.7%), and exhibits a negative AT-skew (-0.010) and GC-skew (-0.267). As with other invertebrate mitogenomes, the PCGs start with the standard ATN and stop with the standard TAN codons or incomplete T. Phylogenetic analysis showed that C. bilineata was most closely related to Matuta planipes (Matutidae), and these two species formed a sister clade, constituting a Calappoidea group and forming a sister clade with part of Eriphioidea. The existence of the polyphyletic families raised doubts over the traditional classification system. These results will help to better understand the features of the C. bilineata mitogenome and lay foundation for further evolutionary relationships within Brachyura.
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Affiliation(s)
- Xinting Lu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China; Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China.
| | - Ying Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Jian Chen
- Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Lihua Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Guixiang Tong
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fishery Sciences, Nanning, Guangxi 530021, China
| | - Xinxian Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fishery Sciences, Nanning, Guangxi 530021, China.
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Phylogenetic implications of mitogenome rearrangements in East Asian potamiscine freshwater crabs (Brachyura: Potamidae). Mol Phylogenet Evol 2020; 143:106669. [DOI: 10.1016/j.ympev.2019.106669] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 11/18/2022]
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Characterization of the complete mitochondrial genome of Uca lacteus and comparison with other Brachyuran crabs. Genomics 2020; 112:10-19. [DOI: 10.1016/j.ygeno.2019.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/13/2019] [Accepted: 06/03/2019] [Indexed: 01/15/2023]
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Wang Q, Tang D, Guo H, Wang J, Xu X, Wang Z. Comparative mitochondrial genomic analysis of Macrophthalmus pacificus and insights into the phylogeny of the Ocypodoidea & Grapsoidea. Genomics 2020; 112:82-91. [DOI: 10.1016/j.ygeno.2019.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 01/24/2023]
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Froufe E, Bolotov I, Aldridge DC, Bogan AE, Breton S, Gan HM, Kovitvadhi U, Kovitvadhi S, Riccardi N, Secci-Petretto G, Sousa R, Teixeira A, Varandas S, Zanatta D, Zieritz A, Fonseca MM, Lopes-Lima M. Mesozoic mitogenome rearrangements and freshwater mussel (Bivalvia: Unionoidea) macroevolution. Heredity (Edinb) 2020; 124:182-196. [PMID: 31201385 PMCID: PMC6906506 DOI: 10.1038/s41437-019-0242-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 11/08/2022] Open
Abstract
Using a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female mitogenome (i.e., gene orders MF1 and UF1). Our results suggest that this macroevolutionary jump was completed within a relatively short time interval (95% HPD 201-226 Ma) that coincided with the Triassic-Jurassic mass extinction. Both gene orders have persisted within these clades for ~200 Ma. The monophyly of the so-called "problematic" Gonideinae taxa was supported by all the inferred phylogenies in this study using, for the first time, the M- and F-type mitogenomes either singly or combined. Within Gonideinae, two additional splits in the gene order (UF1 to UF2, UF2 to UF3) occurred in the Mesozoic and have persisted for ~150 and ~100 Ma, respectively. Finally, the mitogenomic results suggest ancient connections between freshwater basins of East Asia and Europe near the Cretaceous-Paleogene boundary, probably via a continuous paleo-river system or along the Tethys coastal line, which are well supported by at least three independent but almost synchronous divergence events.
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Affiliation(s)
- Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal.
| | - Ivan Bolotov
- IBIGER - Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk, 163000, Russian Federation
- Northern Arctic Federal University, Severnaya Dvina Emb. 17, Arkhangelsk, 163000, Russian Federation
| | - David C Aldridge
- Department of Zoology, University of Cambridge, The David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK
| | - Arthur E Bogan
- North Carolina State Museum of Natural Sciences, 11 West Jones St., Raleigh, NC, 27601, USA
| | - Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, H2V 2S9, Canada
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3220, VIC, Australia
| | - Uthaiwan Kovitvadhi
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Satit Kovitvadhi
- Department of Agriculture, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok, 10600, Thailand
| | | | - Giulia Secci-Petretto
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal
| | - Ronaldo Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
| | - Amilcar Teixeira
- CIMO/ESA/IPB - Mountain Research Centre, School of Agriculture, Polytechnic Institute of Bragança, Campus de Santa Apolónia, Apartado 1172, Bragança, 5301-854, Portugal
| | - Simone Varandas
- CITAB/UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, Vila Real, 5000-801, Portugal
| | - David Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Biosciences Bldg. 2408, Mount Pleasant, MI, 48859, USA
| | - Alexandra Zieritz
- School of Environmental and Geographical Sciences, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, 43500, Malaysia
| | - Miguel M Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal
| | - Manuel Lopes-Lima
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, 4450-208, Portugal
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, Vairão, Porto, 4485-661, Portugal
- SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, c/o The David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, UK
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Yang M, He Y, Liu H. The complete mitochondrial genome of rubble crab Daldorfia horrida (Linnaeus, 1758) using next-generation sequencing. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3320-3321. [PMID: 33365974 PMCID: PMC7707263 DOI: 10.1080/23802359.2019.1673255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome of the rubble carb Daldorfia horrida was determined using Illumina next-generation sequencing. The circular mitogenome is 15,737 bp, with 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and one control region. The base composition is significantly biased (A, G, T, and C was 35.5%, 10.2%, 34.9%, and 19.4%, respectively) with A + T contents of 70.4%. Five microsatellites were identified in the mitogenome located in ND1, ND4, 16S genes and D-loop region. Phylogenetic tree showed that D. horrida is first clustered with Pseudocarcinus gigas and Myomenippe fornasinii, which revealed that Parthenopoidea has a close affinity with Eriphioidea in Heterotremata.
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Affiliation(s)
- Mingqiu Yang
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Yugui He
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Hongtao Liu
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
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Wang Q, Wang Z, Tang D, Xu X, Tao Y, Ji C, Wang Z. Characterization and comparison of the mitochondrial genomes from two Alpheidae species and insights into the phylogeny of Caridea. Genomics 2019; 112:65-70. [PMID: 31437541 DOI: 10.1016/j.ygeno.2019.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/01/2019] [Accepted: 08/18/2019] [Indexed: 11/18/2022]
Abstract
The mitochondrial genome (mitogenome) has been widely used in phylogenetics and molecular evolution as a parameter, due to its simple genetic structure, high evolutionary rate, and compositional heterogeneity properties. Alpheidae is a large and highly diverse family of the Caridea infraorder, currently containing about 600 species dispersed all over the world. However, only a few shrimps in Alpheidae have their complete mitogenome annotated in GenBank. In our study, the entire mitogenomes of two shrimps from Alpheidae were determined, Alpheus randalli and Alpheus bellulus. The mitogenomes of both shrimps share the complete set of 37 mitochondrial genes found in other Alpheidae species. In A. randalli the AT-skew is slightly positive and GC-skew is negative, whereas in A. bellulus the AT-skew is negative and GC-skew is slightly positive. Furthermore, the secondary structures of trnS1 in the two shrimps are partially missing, and another three tRNAs formed the typical cloverleaf shaped secondary structures. Also, the trnS1 of A. randalli has an unusual anticodon stem with some unpaired nucleotides. Comparative genomic analysis suggests that the mitochondrial gene order of Alpheus genus exhibits a different gene rearrangement compared with that of Caridea. Most species in Alpheus share the same gene order, except for A. lobidens, which has an additional pseudogenomic trnQ (trnQ*). Compared with the mitochondrial gene order of Caridea the Alpheus trnE underwent both translocation and inversion, which were caused by a recombination event. Bayesian inferences (BI) and Maximum Likelihood (ML) phylogenetic analyses of 105 species amino acid datasets resulted in a well-supported topology, whereas four families in Caridea are monophyletic and can be divided into two major clades. Moreover, we demonstrated the phylogenetic relationships of six infraorders in Decapoda (Dendrobranchiata, (Caridea, (Stenopodidea, (Achelata, (Polychelida, Astacidea))))). This study used the large taxon sampling available to date for phylomitogenomic analysis. The results provide a theoretical basis for further research on the evolution of the Decapoda order, specifically Caridea infraorder.
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Affiliation(s)
- Qi Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Ziqian Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Dan Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Xinyi Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Yitao Tao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Chenyao Ji
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China.
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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Gan HM, Linton SM, Austin CM. Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes. Mar Genomics 2019; 45:64-71. [DOI: 10.1016/j.margen.2019.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 01/01/2023]
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Luchetti A, Forni G, Skaist AM, Wheelan SJ, Mantovani B. Mitochondrial genome diversity and evolution in Branchiopoda (Crustacea). ZOOLOGICAL LETTERS 2019; 5:15. [PMID: 31149346 PMCID: PMC6537178 DOI: 10.1186/s40851-019-0131-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/19/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The crustacean class Branchiopoda includes fairy shrimps, clam shrimps, tadpole shrimps, and water fleas. Branchiopods, which are well known for their great variety of reproductive strategies, date back to the Cambrian and extant taxa can be mainly found in freshwater habitats, also including ephemeral ponds. Mitochondrial genomes of the notostracan taxa Lepidurus apus lubbocki (Italy), L. arcticus (Iceland) and Triops cancriformis (an Italian and a Spanish population) are here characterized for the first time and analyzed together with available branchiopod mitogenomes. RESULTS Overall, branchiopod mitogenomes share the basic structure congruent with the ancestral Pancrustacea model. On the other hand, rearrangements involving tRNAs and the control region are observed among analyzed taxa. Remarkably, an unassigned region in the L. apus lubbocki mitogenome showed a chimeric structure, likely resulting from a non-homologous recombination event between the two flanking trnC and trnY genes. Notably, Anostraca and Onychocaudata mitogenomes showed increased GC content compared to both Notostraca and the common ancestor, and a significantly higher substitution rate, which does not correlate with selective pressures, as suggested by dN/dS values. CONCLUSIONS Branchiopod mitogenomes appear rather well-conserved, although gene rearrangements have occurred. For the first time, it is reported a putative non-homologous recombination event involving a mitogenome, which produced a pseudogenic tRNA sequence. In addition, in line with data in the literature, we explain the higher substitution rate of Anostraca and Onychocaudata with the inferred GC substitution bias that occurred during their evolution.
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Affiliation(s)
- Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bolgna, Italy
| | - Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bolgna, Italy
| | - Alyza M. Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Sarah J. Wheelan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bolgna, Italy
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Kim HS, Kim KY, Lee SH, Hong SS, Cho IY, Yi CH, Kim IH, Yoon M, Kim MS. The complete mitochondrial genome of Pseudohelice subquadrata (Dana, 1851) (Crustacea: Decapoda: Varunidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1536491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Hye Seon Kim
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Keun-Yong Kim
- Department of Genetic Analysis, AquaGenTech Co., Ltd, Busan, Republic of Korea
| | - Sang-Hui Lee
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Soon-Sang Hong
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - In-Young Cho
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Chang Ho Yi
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Il Hun Kim
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Moongeun Yoon
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Min-Seop Kim
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
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39
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Guinot D, Ng NK, Moreno PAR. Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838). ZOOSYSTEMA 2018. [DOI: 10.5252/zoosystema2018v40a26] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Danièle Guinot
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, case postale 53, 57 rue Cuvier, F-75231 Paris cedex 05 (France)
| | - Ngan Kee Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Republic of Singapore)
| | - Paula A. Rodríguez Moreno
- Direction générale déléguée aux Collections, Muséum national d'Histoire naturelle, case postale 30, 57 rue Cuvier, F-75231 Paris cedex 05 (France)
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40
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ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Mol Phylogenet Evol 2018; 127:320-331. [DOI: 10.1016/j.ympev.2018.05.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/03/2018] [Accepted: 05/13/2018] [Indexed: 01/08/2023]
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41
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Kienbaum K, Vehof J, Becker C, Scholtz G. The reproductive system of Limnopilos naiyanetri indicates a thoracotreme affiliation of Hymenosomatidae (Decapoda, Eubrachyura). ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:513-520. [PMID: 29966700 DOI: 10.1016/j.asd.2018.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
The eubrachyuran Hymenosomatoidea is widely distributed in tropical and subtropical regions ranging from marine to freshwater habitats. Even though the biology of this taxon has been studied to some extent, its phylogenetic relationships are not resolved. Based on different morphological characters, some authors suggested a close affinity of hymenosomatid crabs to heterotremes. However, many of these characters are ambiguous, and the few molecular studies did not provide convincing solutions either. To address this issue, we studied the reproductive system of the hymenosomatid freshwater species Limnopilos naiyanetri Chuang and Ng, 1991 using histology and scanning electron microscopy. The females show the characteristic organization of the paired eubrachyuran reproductive system. Additionally, a bursa (an accessory sperm storing cuticle cavity) is present. The male copulatory system is characterized by paired long first and short second gonopods, and a pair of sternal gonopores equipped with a penis. Both, the female and male reproductive organs reveal a number of similarities to thoracotreme crabs. The seminal receptacle is lined by a very thin cuticle and by a mono-layered glandular epithelium. The male gonopods and the sternal genital opening also resemble the thoracotreme condition. Thus, our results indicate that Hymenosomatidae are most likely part of the Thoracotremata.
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Affiliation(s)
- Katja Kienbaum
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany.
| | - Juliane Vehof
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany.
| | - Carola Becker
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany.
| | - Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany; Cluster of Excellence, "Image Knowledge Gestaltung", Humboldt-Universität zu Berlin, Sophienstr. 22a, 10178 Berlin, Germany.
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42
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Guo Z, Jiang Z, Han L, Ding Y, Hou X. Characterisation of the complete mitochondrial genome of the black-footed abalone Haliotis iris. NEW ZEALAND JOURNAL OF ZOOLOGY 2018. [DOI: 10.1080/03014223.2018.1495655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Zhansheng Guo
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
| | - Zhaoyang Jiang
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
| | - Leng Han
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
| | - Yi Ding
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
| | - Xuguang Hou
- Marine College, Shandong University at Weihai, Weihai, People’s Republic of China
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Characterization of four new mitogenomes from Ocypodoidea & Grapsoidea, and phylomitogenomic insights into thoracotreme evolution. Gene 2018; 675:27-35. [PMID: 29960073 DOI: 10.1016/j.gene.2018.06.088] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/01/2018] [Accepted: 06/25/2018] [Indexed: 11/24/2022]
Abstract
Four new complete mitochondrial genomes (mitogenomes) from the two superfamilies Ocypodoidea and Grapsoidea were sequenced, which represented Uca (Gelasimus) borealis (Ocypodidae: Ucinae), Dotilla wichmani (Dotillidae), Metopograpsus quadridentatus (Grapsidae: Grapsinae), and Gaetice depressus (Varunidae: Gaeticinae). All of the mitogenomes shared the complete set of 37 mitochondrial genes. Mitogenome lengths were 15,659, 15,600, 15,517, and 16,288 bp, respectively, with A + T contents of 69.41%, 68.46%, 70.30%, and 72.96%, respectively. Comparative genomic analyses suggested that they exhibited different genomic rearrangements. In particular, G. depressus shared a major rearrangement pattern present in Eriocheir crabs, while the remainder shared the brachyuran ground genomic rearrangement patterns. Phylomitogenomic inferences provided new evidence for the strongly supported nesting of Thoracotremata within Heterotremata clades. A close phylogenetic relationship was observed between Varunidae and Macrophthalmidae crabs, and between Dotillidae and Grapsidae crabs, which was consistent with mitochondrial genomic rearrangement similarities. Altogether, these results suggest the presence of reciprocal paraphyly for Ocypodoidea and Grapsoidea.
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44
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The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites. Sci Rep 2018; 8:7558. [PMID: 29765106 PMCID: PMC5954100 DOI: 10.1038/s41598-018-25981-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 05/02/2018] [Indexed: 01/06/2023] Open
Abstract
Bilaterian mitochondrial (mt) genomes are circular molecules that typically contain 37 genes. To date, only a single complete mitogenome sequence is available for the species-rich sarcoptiform mite order Oribatida. We sequenced the mitogenome of Paraleius leontonychus, another species of this suborder. It is 14,186 bp long and contains 35 genes, including only 20 tRNAs, lacking tRNAGly and tRNATyr. Re-annotation of the mitogenome of Steganacarus magnus increased the number of mt tRNAs for this species to 12. As typical for acariform mites, many tRNAs are highly truncated in both oribatid species. The total number of tRNAs and the number of tRNAs with a complete cloverleaf-like structure in P. leontonychus, however, clearly exceeds the numbers previously reported for Sarcoptiformes. This indicates, contrary to what has been previously assumed, that reduction of tRNAs is not a general characteristic for sarcoptiform mites. Compared to other Sarcoptiformes, the two oribatid species have the least rearranged mt genome with respect to the pattern observed in Limulus polyphemus, a basal arachnid species. Phylogenetic analysis of the newly sequenced mt genome and previously published data on other acariform mites confirms paraphyly of the Oribatida and an origin of the Astigmata within the Oribatida.
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45
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Chen L, Chen PY, Xue XF, Hua HQ, Li YX, Zhang F, Wei SJ. Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). Sci Rep 2018; 8:7034. [PMID: 29728615 PMCID: PMC5935716 DOI: 10.1038/s41598-018-25338-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/20/2018] [Indexed: 12/01/2022] Open
Abstract
Animal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma. Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.
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Affiliation(s)
- Long Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng-Yan Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,Department of Entomology, South China Agricultural University, Guangzhou, 510640, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hai-Qing Hua
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan-Xi Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Fan Zhang
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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46
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Vehof J, Scholtz G, Becker C. Paradorippe granulata - A crab with external fertilization and a novel type of sperm storage organ challenges prevalent ideas on the evolution of reproduction in Eubrachyura (Crustacea: Brachyura: Dorippidae). ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:82-90. [PMID: 29221680 DOI: 10.1016/j.asd.2017.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/16/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
Two fundamentally different sperm storage organs occur in Brachyura. The probably paraphyletic podotremes show intersegmental spermathecae, which are distant from oviducts and coxal gonopores. Hence, fertilization is external. In contrast to this, the seminal receptacles of Eubrachyura are directly connected with the ovaries. Thus, at least initial fertilization is internal. This pattern has been interpreted as an apomorphy of Eubrachyura. To test this hypothesis, we studied the morphology of the reproductive organs of Paradorippe granulata, a representative of the putatively early diverging eubrachyuran lineage Dorippoidea. Applying histology, 3D-reconstructions and micro-computed-tomography we revealed a novel type of sperm storage organ. Female P.granulata lack the characteristic eubrachyuran seminal receptacle. Instead sperm is stored in four cuticle-lined bursae, two on each side of the paired oviducts. The elaborate bulbous male gonopod with several terminal processes is adapted to transferring sperm into the female twin bursae. Since oviducts and twin bursae are not directly connected, spermatozoa and oocytes mix when gametes pass through the sternal vulva. Thus, fertilization in P.granulata is external. Our finding of a eubrachyuran crab that lacks seminal receptacles and exhibits external fertilization calls prevailing concepts on the evolution of sperm storage in Eubrachyura into question.
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Affiliation(s)
- Juliane Vehof
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany.
| | - Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany; Cluster of Excellence Image Knowledge Gestaltung, Sophienstr. 22a, 10099 Berlin, Germany
| | - Carola Becker
- Cluster of Excellence Image Knowledge Gestaltung, Sophienstr. 22a, 10099 Berlin, Germany
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47
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Tang BP, Liu Y, Xin ZZ, Zhang DZ, Wang ZF, Zhu XY, Wang Y, Zhang HB, Zhou CL, Chai XY, Liu QN. Characterisation of the complete mitochondrial genome of Helice wuana (Grapsoidea: Varunidae) and comparison with other Brachyuran crabs. Genomics 2017; 110:S0888-7543(17)30099-X. [PMID: 28982639 DOI: 10.1016/j.ygeno.2017.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 11/28/2022]
Abstract
The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterised the mitogenome of the crab Helice wuana to better understand its molecular evolution and phylogeny. The 16,359bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The genome composition is highly A+T biased 68.42%, and exhibits a negative AT-skew (-0.036) and GC-skew (-0.269) among Brachyura crabs. Gene rearrangements were detected, as was tandem duplication followed by random loss, which explains the translocation of mitochondrial genes. Phylogenetic analysis showed that H. wuana and H. tientsinensis clustered on one branch with high nodal support values. These results confirm that the placement of H. wuana within the Varunidae family of Thoracotrematan crabs. This study will provided a better understanding for gene rearrangements and crab evolution in the further.
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Affiliation(s)
- Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Zheng-Fei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Ying Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China.
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