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Ma Y, Zheng B, Li J, Meng W, Xu K, Ye Y. Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha. PLoS One 2024; 19:e0301389. [PMID: 38547307 PMCID: PMC10977763 DOI: 10.1371/journal.pone.0301389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNASer1 and tRNASer2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNAAla lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.
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Affiliation(s)
- Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Biqi Zheng
- Department of Natural Resources, Ningde Marine Center, Ningde, 352000, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Meng
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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Kong D, Gan Z, Li X. Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes. Gene 2024; 896:148054. [PMID: 38042216 DOI: 10.1016/j.gene.2023.148054] [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: 09/03/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/04/2023]
Abstract
The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment.
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Affiliation(s)
- Deming Kong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhibin Gan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xinzheng Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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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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Palmisano JN, Farrell TM, Gustafson TM, Fitak RR. The mitochondrial genome of the pentastome parasite Raillietiella orientalis Hett, 1915 (Raillietiellida; Raillietiellidae) with notes on its phylogenetic position. Mitochondrial DNA B Resour 2023; 8:756-759. [PMID: 37475776 PMCID: PMC10355681 DOI: 10.1080/23802359.2023.2224461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/07/2023] [Indexed: 07/22/2023] Open
Abstract
In this study we sequenced and annotated the complete mitochondrial genome of the invasive reptile parasite Raillietiella orientalis using Illumina DNA sequencing. The length of the mitogenome was 15,320 bp and had a GC content of 33.1%. The mitogenome contained 13 protein-coding genes, two ribosomal RNA genes, and 22 tRNA genes, the order of which was diagnostic of Pancrustacean mitogenomes. A phylogenetic tree constructed from the 13 protein-coding genes of R. orientalis and 26 other Pancrustacean mitogenomes supported the placement of R. orientalis as part of the monophyletic subclass Pentastomida within the Maxillopoda and sister to the subclass Branchiura.
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Affiliation(s)
| | | | | | - Robert R. Fitak
- Department of Biology, University of Central Florida, Orlando, FL, USA
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Kobayashi G, Itoh H, Nakajima N. Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes. Zoolog Sci 2023; 40:224-234. [PMID: 37256570 DOI: 10.2108/zs220063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/02/2023] [Indexed: 06/01/2023]
Abstract
Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.
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Affiliation(s)
- Genki Kobayashi
- Ishinomaki Senshu University, Minamisakai, Ishinomaki, Miyagi 986-8580, Japan,
| | - Hajime Itoh
- National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Nobuyoshi Nakajima
- National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
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lü J, Dong X, Li J, Ye Y, Xu K. Novel gene re-arrangement in the mitochondrial genome of Pisidiaserratifrons (Anomura, Galatheoidea, Porcellanidae) and phylogenetic associations in Anomura. Biodivers Data J 2023; 11:e96231. [PMID: 38327357 PMCID: PMC10848379 DOI: 10.3897/bdj.11.e96231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/28/2022] [Indexed: 02/25/2023] Open
Abstract
To improve the taxonomy and systematics of Porcellanidae within the evolution of Anomura, we describe the complete mitochondrial genomes (mitogenomes) sequence of Pisidiaserratifrons, which is 15,344 bp in size, contains the entire set of 37 genes and has an AT-rich region. Compared with the pancrustacean ground pattern, at least five gene clusters (or genes) are significantly different with the typical genes, involving eleven tRNA genes and four PCGs and the tandem duplication/random loss and recombination models were used to explain the observed large-scale gene re-arrangements. The phylogenetic results showed that all Porcellanidae species clustered together as a group with well nodal support. Most Anomura superfamilies were found to be monophyletic, except Paguroidea. Divergence time estimation implies that the age of Anomura is over 225 MYA, dating back to at least the late Triassic. Most of the extant superfamilies and families arose during the late Cretaceous to early Tertiary. In general, the results obtained in this study will contribute to a better understanding of gene re-arrangements in Porcellanidae mitogenomes and provide new insights into the phylogeny of Anomura.
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Affiliation(s)
- Jiayin lü
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Xiangli Dong
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Jiji Li
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Yingying Ye
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Kaida Xu
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
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Pang X, Fu W, Feng J, Guo B, Lin X, Lu X. The Complete Mitochondrial Genome of the Hermit Crab Diogenes edwardsii (Anomura: Diogenidae) and Phylogenetic Relationships within Infraorder Anomura. Genes (Basel) 2023; 14:470. [PMID: 36833397 PMCID: PMC9956181 DOI: 10.3390/genes14020470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
A complete mitochondrial genome (mitogenome) can provide important information for gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few mitogenomes of hermit crabs (superfamily Paguridae) in the infraorder Anomura have been reported. This study reports the first complete mitogenome of the hermit crab Diogenes edwardsii assembled using high-throughput sequencing. The mitogenome of Diogenes edwardsii is 19,858 bp in length and comprises 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. There are 28 and six genes observed on the heavy and light strands, respectively. The genome composition was highly A + T biased (72.16%), and exhibited a negative AT-skew (-0.110) and positive GC-skew (0.233). Phylogenetic analyses based on the nucleotide dataset of 16 Anomura species indicated that D. edwardsii was closest related to Clibanarius infraspinatus in the same family, Diogenidae. Positive selection analysis showed that two residues located in cox1 and cox2 were identified as positively selected sites with high BEB value (>95%), indicating that these two genes are under positive selection pressure. This is the first complete mitogenome of the genus Diogenes, and this finding helps us to represent a new genomic resource for hermit crab species and provide data for further evolutionary status of Diogenidae in Anomura.
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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
| | - Wenjing Fu
- 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
| | - Jianfeng Feng
- 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
| | - Biao Guo
- Department of Fishery Resources, Tianjin Fisheries Research Institute, Tianjin 300457, China
| | - 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
| | - 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
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Sun S, Xiao N, Sha Z. Mitogenomes provide insights into the phylogeny and evolution of brittle stars (Echinodermata, Ophiuroidea). ZOOL SCR 2022. [DOI: 10.1111/zsc.12576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Shao'e Sun
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- College of Biological Sciences University of Chinese Academy of Sciences Beijing China
| | - Ning Xiao
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- College of Biological Sciences University of Chinese Academy of Sciences Beijing China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology Chinese Academy of Sciences Qingdao China
- College of Biological Sciences University of Chinese Academy of Sciences Beijing China
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Höpel CG, Yeo D, Grams M, Meier R, Richter S. Mitogenomics supports the monophyly of Mysidacea and Peracarida (Malacostraca). ZOOL SCR 2022. [DOI: 10.1111/zsc.12554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Christoph G. Höpel
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften Universität Rostock Rostock Germany
| | - Darren Yeo
- Centre for Wildlife Forensics Animal and Plant Health Centre, National Parks Board Singapore Singapore
| | - Markus Grams
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften Universität Rostock Rostock Germany
| | - Rudolf Meier
- Museum für Naturkunde Leibniz‐Institut für Evolutions‐ und Biodiversitätsforschung Berlin Germany
| | - Stefan Richter
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften Universität Rostock Rostock Germany
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MANTELATTO FERNANDOL, TAMBURUS ANAF, CARVALHO-BATISTA ABNER, ROSSI NATALIA, BURANELLI RAQUELC, PANTALEÃO JOÃOA, TELES JENIFFERN, ZARA FERNANDOJ, CARVALHO FABRICIOL, BOCHINI GABRIELL, TEROSSI MARIANA, ROBLES RAFAEL, CASTILHO ANTONIOL, COSTA ROGÉRIOC. Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: V. Dendrobranchiata and Pleocyemata [Achelata, Astacidea, Axiidea, Caridea (Alpheoidea and Processoidea excluded), Gebiidea, Stenopodidea]. Zootaxa 2022; 5121:1-74. [DOI: 10.11646/zootaxa.5121.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Indexed: 11/04/2022]
Abstract
This checklist is the fifth and last compilation on the decapod crustaceans reported to São Paulo (Brazil) coastal area, resulting from long-term multidisciplinary projects, which combined morphological analyses and molecular techniques. The current research includes 75 decapod species, herein referred as shrimps/lobsters-like (shrimps, ghost-shrimps, lobsters, and related groups), reported to São Paulo coastal area. These species occur in marine, estuarine, and amphidromous habitats and are classified into 21 families as follow: Aristeidae (2 spp., 2 genera), Atyidae (4 spp., 2 genera), Axianassidae (1 sp., 1 genus), Callianassidae (1 sp., 1 genus), Callichiridae (6 spp., 4 genera), Crangonidae (1 sp., 1 genus), Glyphocrangonidae (1 sp., 1 genus), Luciferidae (2 spp., 2 genera), Nephropidae (4 spp., 2 genera), Palaemonidae (15 spp., 9 genera), Palinuridae (2 spp., 1 genus), Pandalidae (1 sp., 1 genus), Pasiphaeidae (1 sp., 1 genus), Penaeidae (10 spp., 6 genera), Sergestidae (3 spp., 3 genera), Sicyoniidae (4 spp., 1 genus), Scyllaridae (5 spp., 3 genera), Solenoceridae (4 spp., 3 genera), Stenopodidae (2 spp., 1 genus), and Upogebiidae (6 spp., 1 genus). We generated new sequences of cytochrome oxidase subunit I (barcode region) and 16S genes (51 and 54, respectively) of 54 species. Our examination concluded that 75 shrimps/lobsters-like species are reported to the São Paulo coast. We excluded Leander tenuicornis (Palaemonidae), Penaeus setiferus (Penaeidae), Philocheras gorei (Crangonidae), and Rhynchocinetes typus (Rhynchocinetidae) from this list.
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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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Kobayashi G, Itoh H, Kojima S. Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species. Sci Rep 2022; 12:4449. [PMID: 35292662 PMCID: PMC8924214 DOI: 10.1038/s41598-022-08103-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/25/2022] [Indexed: 12/05/2022] Open
Abstract
Mitogenomes are useful for inferring phylogenetic relationships between organisms. Although the mitogenomes of Annelida, one of the most morphologically and ecologically diverse metazoan groups have been well sequenced, those of several families remain unexamined. This study determined the first mitogenome from the family Travisiidae (Travisia sanrikuensis), analyzed its mitogenomic features, and reconstructed a phylogeny of Sedentaria. The monophyly of the Terebellida + Arenicolida + Travisiidae clade is supported by molecular phylogenetic analysis. The placement of Travisiidae is unclear because of the lack of mitogenomes from closely related lineages. An unexpected intron appeared within the cox1 gene of T. sanrikuensis and in the same positions of five undescribed Travisia spp. Although the introns are shorter (790–1386 bp) than other group II introns, they can be considered degenerate group II introns due to type II intron maturase open reading frames, found in two of the examined species, and motifs characteristic of group II introns. This is likely the first known case in metazoans where mitochondrial group II introns obtained by a common ancestor are conserved in several descendants. Insufficient evolutionary time for intron loss in Travisiidae, or undetermined mechanisms may have helped maintain the degenerate introns.
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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
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
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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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14
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Castejón D, Rotllant G, Alba-Tercedor J, Ribes E, Durfort M, Guerao G. Morphological and histological description of the midgut caeca in true crabs (Malacostraca: Decapoda: Brachyura): origin, development and potential role. BMC ZOOL 2022; 7:9. [PMID: 37170150 PMCID: PMC10127032 DOI: 10.1186/s40850-022-00108-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/06/2022] [Indexed: 12/31/2022] Open
Abstract
Abstract
Background
The decapods are a major group of crustaceans that includes shrimps, prawns, crayfishes, lobsters, and crabs. Several studies focused on the study of the digestive system of the decapods, constituted by the oesophagus, stomach, midgut tract, midgut gland, and hindgut. Nevertheless, in the midgut tract there are associated a set of organs called “midgut caeca”, which are among the most controversial and less studied digestive organs of this group. This work used the common spider crab Maja brachydactyla Balss, 1922 as a model to resolve the origin, development, and potential role of the midgut caeca. Such organs were studied in the larvae (zoea I, zoea II, megalopa), first juveniles, and adult phases, being employed traditional and modern techniques: dissection, micro-computed tomography (Micro-CT), and light and electron microscopical analyses (TEM and SEM).
Results
The common spider crab has a pair of anterior midgut caeca and a single posterior caecum that originate from the endoderm germ layer: they develop from the midgut tract, and their epithelium is composed by secretory cells while lacking a cuticle lining. The midgut caeca are small buds in the newly hatched larvae, enlarge linearly during the larval development, and then continue growing until became elongated and coiled blind-tubules in adults. The adult midgut caeca are internally folded to increase their inner surface. The electron microscopy observations showed that the midgut caeca are highly active organs with important macroapocrine and microapocrine secretory activity. Our results suggest that the role of the caeca might be related to the digestive enzyme secretion. The secretory activity should increase as the animal grows in size.
Conclusion
The present study resolves the embryonic origin of the midgut caeca (endoderm derived organs), development (general lengthening starting from small buds), and role (active secretory organs). The secretory activity of the midgut caeca should be incorporated in the current models of the digestive physiology in different decapod taxa.
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15
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Trevisan B, Jacob Machado D, Lahr DJG, Marques FPL. Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms). Front Genet 2022; 12:788871. [PMID: 35003223 PMCID: PMC8727539 DOI: 10.3389/fgene.2021.788871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
The recognized potential of using mitogenomics in phylogenetics and the more accessible use of high-throughput sequencing (HTS) offer an opportunity to investigate groups of neglected organisms. Here, we leveraged HTS to execute the most comprehensive documentation of mitogenomes for cestodes based on the number of terminals sequenced. We adopted modern approaches to obtain the complete mitogenome sequences of 86 specimens representing five orders of cestodes (three reported for the first time: Phyllobothriidea, “Tetraphyllidea” and Trypanorhyncha). These complete mitogenomes represent an increase of 41% of the mitogenomes available for cestodes (61–147) and an addition of 33% in the representativeness of the cestode orders. The complete mitochondrial genomes are conserved, circular, encoded in the same strand, and transcribed in the same direction, following the pattern observed previously for tapeworms. Their length varies from 13,369 to 13,795 bp, containing 36 genes in total. Except for the Trypanorhyncha specimen, the gene order of the other four cestode orders sequenced here suggests that it could be a synapomorphy for the acetabulate group (with a reversion for taenids). Our results also suggest that no single gene can tell all the evolutionary history contained in the mitogenome. Therefore, cestodes phylogenies based on a single mitochondrial marker may fail to capture their evolutionary history. We predict that such phylogenies would be improved if conducted under a total evidence framework. The characterization of the new mitochondrial genomes is the first step to provide a valuable resource for future studies on the evolutionary relationships of these groups of parasites.
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Affiliation(s)
- Bruna Trevisan
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fernando P L Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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16
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Terraneo TI, Mariappan KG, Forsman Z, Arrigoni R. Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS). Methods Mol Biol 2022; 2498:1-18. [PMID: 35727537 DOI: 10.1007/978-1-0716-2313-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mitochondrial genomes (mtgenome) represent an important source of information for addressing fundamental evolutionary, phylogeographic, systematic, and ecological questions in marine organisms. In the last two decades the advent of high-throughput next-generation sequencing (NGS) has provided an unprecedented possibility to access large amount of genomic data and, as such, there has been a rapid growth in mtgenome resources and studies. In particular, NGS strategies represent a great advantage for investigating nonmodel marine organisms for which no or limited genomic resources are available. Here, we describe a routinely used standardized protocol to obtain mtgenome of nonmodel marine organisms by NGS. The protocol is composed of five main steps, including DNA extraction, DNA fragmentation, library preparation, high-throughput sequencing, and bioinformatic analyses. Each of the first three steps is followed by size/quality and concentration validations. The advantages of the described protocol rely on the assumption that no a priori information on mtgenome of the studied organism is needed and on its versatility as researchers may choose several kits for DNA extraction and library preparation and adopt different methods for DNA fragmentation depending on their needs, experience, and suppliers.
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Affiliation(s)
- Tullia I Terraneo
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zac Forsman
- Hawaii Institute of Marine Biology, Kaneohe, HI, USA
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy.
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17
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Briscoe AG, Nichols S, Hartikainen H, Knipe H, Foster R, Green AJ, Okamura B, Bass D. High-Throughput Sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds. Mol Ecol Resour 2021; 22:1303-1318. [PMID: 34758191 DOI: 10.1111/1755-0998.13548] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Examination of faecal material has demonstrated how a broad range of organisms are distributed by bird movements. Such research has largely focused on dispersal of plant seeds by frugivores and of freshwater organisms by waterbirds. However, with few exceptions (e.g. avian influenza, Ebola virus), there is a dearth of evidence for transport of parasites and pathogens. High-throughput sequencing methods now provide a powerful means of addressing this knowledge gap by elucidating faecal contents in unprecedented detail. We collected faeces excreted by a range of migratory waterbirds in south-west Spain and pooled faecal DNA to create libraries reflective of feeding behavior. We created sets of libraries using high-throughput metagenomic and amplicon sequencing. For the latter we employed two sets of primers to broadly target the V4 region of the 18S rRNA gene (one set amplifying the region across all eukaryotes, the other excluding amplification of metazoans). Libraries revealed a wide diversity of eukaryotes, including parasites of the faecal producers themselves, parasites of food items, or those incidentally ingested. We also detected novel microbial eukaryotic taxa and found that parasite assemblage profiles were relatively distinct. Comparing the performance of the methods used supports their joint use for future studies of diversity and abundance. Because viable stages of many parasites are likely to be present in faeces, our results suggest significant levels of bird-mediated dispersal of parasites (both from avian and other hosts). Our methods revealed much hidden biodiversity, and allowed identification of the individuals who produced the faecal samples to species level, facilitating the study of interaction networks.
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Affiliation(s)
- Andrew G Briscoe
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Core Research Laboratories, Natural History Museum, London, United Kingdom
| | - Sarah Nichols
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Hanna Hartikainen
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Eawag and Institute for Integrative Biology, Eidgenössische Technische Hochschule (ETH), Zurich, Switzerland
| | - Hazel Knipe
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Rachel Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana, EBD-CSIC, 41092, Sevilla, Spain
| | - Beth Okamura
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Centre for Environment, Aquaculture and Fisheries Science (Cefas), Weymouth, UK
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18
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Hwang HS, Jung J, Baeza JA. The mitochondrial genome of Faughnia haani (Stomatopoda): novel organization of the control region and phylogenetic position of the superfamily Parasquilloidea. BMC Genomics 2021; 22:716. [PMID: 34600469 PMCID: PMC8487505 DOI: 10.1186/s12864-021-08034-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stomatopod crustaceans are aggressive marine predators featuring complex compound eyes and powerful raptorial appendages used for "smashing" or "spearing" prey and/or competitors. Among them, parasquilloids (superfamily Parasquilloidea) possess eyes with 2-3 midband rows of hexagonal ommatidia and spearing appendages. Here, we assembled and analyzed the complete mitochondrial genome of the parasquilloid Faughnia haani and explored family- and superfamily-level phylogenetic relationships within the Stomatopoda based on mitochondrial protein coding genes (PCGs). RESULTS The mitochondrial genome of F. haani is 16,089 bp in length and encodes 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region that is relatively well organized, containing 2 GA-blocks, 4 poly-T stretches, various [TA(A)]n-blocks, and 2 hairpin structures. This organized control region is likely a synapomorphic characteristic in the Stomatopoda. Comparison of the control region among superfamilies shows that parasquilloid species are more similar to gonodactyloids than to squilloids and lysiosquilloids given the presence of various poly-T stretches between the hairpin structures and [TA(A)]n-blocks. Synteny is identical to that reported for other stomatopods and corresponds to the Pancrustacea ground pattern. A maximum-likelihood phylogenetic tree based on PCGs revealed that Parasquilloidea is sister to Lysiosquilloidea and Gonodactyloidea and not to Squilloidea, contradicting previous phylogenetic studies. CONCLUSIONS The novel phylogenetic position of Parasquilloidea revealed by our study indicates that 'spearing' raptorial appendages are plesiomorphic and that the 'smashing' type is either derived (as reported in previous studies) or apomorphic. Our results raise the possibility that the spearing raptorial claw may have independently evolved twice. The superfamily Parasquilloidea exhibits a closer relationship with other stomatopod superfamilies with a different raptorial claw type and with dissimilar numbers of midband rows of hexagonal ommatidia. Additional studies focusing on the assembly of mitochondrial genomes from species belonging to different genera, families, and superfamilies within the order Stomatopoda are warranted to reach a robust conclusion regarding the evolutionary history of this iconic clade based on mitochondrial PCGs.
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Affiliation(s)
- Hee-Seung Hwang
- Research Institute of EcoScience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jongwoo Jung
- Division of EcoCreative, Ewha Womans University, Seoul, 03760, Republic of Korea. .,Department of Science Education, Ewha Womans University, Seoul, 03760, Republic of Korea.
| | - Juan Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281, Coquimbo, Chile.
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19
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Burian AN, Zhao W, Lo T, Thurtle‐Schmidt DM. Genome sequencing guide: An introductory toolbox to whole-genome analysis methods. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:815-825. [PMID: 34378845 PMCID: PMC9291972 DOI: 10.1002/bmb.21561] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/17/2021] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called "-omics," have made genetic sequencing readily available across fields in biology from applications in non-traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated, including anticipatory guides and discussion questions for active engagement in the classroom. Additionally, the Supporting Information includes a case study to apply technical and ethical concepts from the text.
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Affiliation(s)
| | - Wufan Zhao
- Department of BiologyDavidson CollegeDavidsonNorth CarolinaUSA
| | - Te‐Wen Lo
- Department of BiologyIthaca CollegeIthacaNew YorkUSA
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20
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Jakovlić I, Zou H, Chen JH, Lei HP, Wang GT, Liu J, Zhang D. Slow crabs - fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes. Mol Ecol 2021; 30:5488-5502. [PMID: 34418213 DOI: 10.1111/mec.16138] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 02/05/2023]
Abstract
Base composition skews (G-C/G+C) of mitochondrial genomes are believed to be primarily driven by mutational pressure, which is positively correlated with metabolic rate. In marine animals, metabolic rate is also positively correlated with locomotory capacity. Given the central role of mitochondria in energy metabolism, we hypothesised that selection for locomotory capacity should be positively correlated with the strength of purifying selection (dN/dS), and thus be negatively correlated with the skew magnitude. Therefore, these two models assume diametrically opposite associations between the metabolic rate and skew magnitude: positive correlation in the prevailing paradigm, and negative in our working hypothesis. We examined correlations between the skew magnitude, metabolic rate, locomotory capacity, and several other variables previously associated with mitochondrial evolution on 287 crustacean mitogenomes. Weakly locomotory taxa had higher skew magnitude and ω (dN/dS) values, but not the gene order rearrangement rate. Skew and ω magnitudes were correlated. Multilevel regression analyses indicated that three competing variables, body size, gene order rearrangement rate, and effective population size, had negligible impacts on the skew magnitude. In most crustacean lineages selection for locomotory capacity appears to be the primary factor determining the skew magnitude. Contrary to the prevailing paradigm, this implies that adaptive selection outweighs nonadaptive selection (mutation pressure) in crustaceans. However, we found indications that effective population size (nonadaptive factor) may outweigh the impact of locomotory capacity in sessile crustaceans (Thecostraca). In conclusion, skew magnitude is a product of the interplay between adaptive and nonadaptive factors, the balance of which varies among lineages.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Hai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong-Peng Lei
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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21
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Jakovlić I, Zou H, Zhao XM, Zhang J, Wang GT, Zhang D. Evolutionary History of Inversions in Directional Mutational Pressures in Crustacean Mitochondrial Genomes: Implications for Evolutionary Studies. Mol Phylogenet Evol 2021; 164:107288. [PMID: 34365015 DOI: 10.1016/j.ympev.2021.107288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 01/29/2023]
Abstract
Inversions of the origin of replication (ORI) in mitochondrial genomes produce asymmetrical mutational pressures that can cause strong base composition skews. Due to skews often being overlooked, the total number of crustacean lineages that underwent ORI events remains unknown. We analysed skews, cumulative skew plots, conserved sequence motifs, and mitochondrial architecture of all 965 available crustacean mitogenomes (699 unique species). We found indications of an ORI in 159 (22.7%) species, and mapped these to 23 ORI events: 16 identified with confidence and 7 putative (13 newly proposed, and for 5 we improved the resolution). Two ORIs occurred at or above the order level: Isopoda and Copepoda. Shifts in skew plots are not a precise tool for identifying the replication mechanism. We discuss how ORIs can produce mutational bursts in mitogenomes and show how these can interfere with various types of evolutionary studies. Phylogenetic analyses were plagued by artefactual clustering, and ORI lineages exhibited longer branches, a higher number of synonymous substitutions, higher mutational saturation, and higher compositional heterogeneity. ORI events also affected codon usage and protein properties. We discuss how this may have caused erroneous interpretation of data in previous studies that did not account for skew patterns.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xu-Mao Zhao
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Jin Zhang
- Bio-Transduction Lab, Wuhan 430075, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China.
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22
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Wang Y, Ma KY, Tsang LM, Wakabayashi K, Chan T, De Grave S, Chu KH. Confirming the systematic position of two enigmatic shrimps,
Amphionides
and Procarididae (Crustacea: Decapoda). ZOOL SCR 2021. [DOI: 10.1111/zsc.12509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yaqin Wang
- Simon F.S. Li Marine Science Laboratory School of Life Sciences The Chinese University of Hong Kong Shatin, Hong Kong China
- Shenzhen Research Institute The Chinese University of Hong Kong Shenzhen China
| | - Ka Yan Ma
- State Key Laboratory of Biocontrol School of Ecology Sun Yat‐sen University Guangzhou China
| | - Ling Ming Tsang
- Simon F.S. Li Marine Science Laboratory School of Life Sciences The Chinese University of Hong Kong Shatin, Hong Kong China
- Shenzhen Research Institute The Chinese University of Hong Kong Shenzhen China
| | - Kaori Wakabayashi
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima Japan
| | - Tin‐Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans National Taiwan Ocean University Keelung Taiwan
| | | | - Ka Hou Chu
- Simon F.S. Li Marine Science Laboratory School of Life Sciences The Chinese University of Hong Kong Shatin, Hong Kong China
- Shenzhen Research Institute The Chinese University of Hong Kong Shenzhen China
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23
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Xu SL, Han BP, Martínez A, Schwentner M, Fontaneto D, Dumont HJ, Kotov AA. Mitogenomics of Cladocera (Branchiopoda): Marked gene order rearrangements and independent predation roots. Mol Phylogenet Evol 2021; 164:107275. [PMID: 34339827 DOI: 10.1016/j.ympev.2021.107275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022]
Abstract
Cladocera (Crustacea: Branchiopoda) is a key group of invertebrates. Despite a long history of phylogenetic research, relationships within this group remain disputed. We here provide new insights based on 15 new mitochondrial genomes obtained from high-throughput sequencing (HTS) and 40 mitogenomes extracted from published HTS datasets. Together with 25 mitogenomes from GenBank, we generated a matrix of 80 mitogenomes, 44 of them belonging to Cladocera. We also obtained a matrix with 168 nuclear orthologous genes to further assess the phylogenetic result from mitogenomes based on published data and one new HTS data ofLeptodora. Maximum likelihood and Bayesian phylogenetic analyses recovered all Branchiopoda orders as monophyletic and supported a sister-group relationship between Anomopoda and Onychopoda, making the taxon Gymnomera paraphyletic and supporting an independent origin of predatory Haplopoda and Onychopoda. The nuclear phylogeny and topological tests also support Gymnomera as paraphyletic, and the nuclear phylogeny strongly supports a sister-group relationship between Ctenopoda and Haplopoda. We provide a fossil-calibrated time tree, congruent with a Carboniferous origin for Cladocera and a subsequent diversification of the crown group of Anomopoda, Onychopoda, and Ctenopoda, at least in the Triassic. Despite their long evolutionary history, non-Cladoceran Branchiopoda exhibited high mitogenome structural stability. On the other hand, 21 out of 24 gene rearrangements occurred within the relatively younger Cladocera. We found the differential base compositional skewness patterns between Daphnia s.s. and Ctenodaphnia, which might be related to the divergence between these taxa. We also provide evidence to support the recent finding that Spinicaudata possesses mitogenomes with inversed compositional skewness without gene rearrangement. Such a pattern has only been reported in Spinicaudata.
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Affiliation(s)
- Shao-Lin Xu
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Bo-Ping Han
- Jinan University, Department of Ecology, Guangzhou 510632, China.
| | - Alejandro Martínez
- National Research Council of Italy (CNR), Water Research Institute (IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
| | | | - Diego Fontaneto
- National Research Council of Italy (CNR), Water Research Institute (IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
| | - Henri J Dumont
- Jinan University, Department of Ecology, Guangzhou 510632, China; Ghent University, Department of Biology, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Alexey A Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
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24
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The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea. Sci Rep 2021; 11:14446. [PMID: 34262102 PMCID: PMC8280103 DOI: 10.1038/s41598-021-93946-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
The complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (- 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.
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Sun S, Sha Z, Xiao N. The first two complete mitogenomes of the order Apodida from deep-sea chemoautotrophic environments: New insights into the gene rearrangement, origin and evolution of the deep-sea sea cucumbers. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100839. [PMID: 33933835 DOI: 10.1016/j.cbd.2021.100839] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.
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Affiliation(s)
- Shao'e Sun
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Xiao
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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Ennis CC, Haeffner NN, Keyser CD, Leonard ST, Macdonald-Shedd AC, Savoie AM, Cronin TJ, Veldsman WP, Barden P, Chak STC, Baeza JA. Comparative mitochondrial genomics of sponge-dwelling snapping shrimps in the genus Synalpheus: Exploring differences between eusocial and non-eusocial species and insights into phylogenetic relationships in caridean shrimps. Gene 2021; 786:145624. [PMID: 33798681 DOI: 10.1016/j.gene.2021.145624] [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: 02/02/2021] [Revised: 03/18/2021] [Accepted: 03/26/2021] [Indexed: 11/29/2022]
Abstract
The genus Synalpheus is a cosmopolitan clade of marine shrimps found in most tropical regions. Species in this genus exhibit a range of social organizations, including pair-forming, communal breeding, and eusociality, the latter only known to have evolved within this genus in the marine realm. This study examines the complete mitochondrial genomes of seven species of Synalpheus and explores differences between eusocial and non-eusocial species considering that eusociality has been shown before to affect the strength of purifying selection in mitochondrial protein coding genes. The AT-rich mitochondrial genomes of Synalpheus range from 15,421 bp to 15,782 bp in length and comprise, invariably, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 648 bp to 994 bp long intergenic space is assumed to be the D-loop. Mitochondrial gene synteny is identical among the studied shrimps. No major differences occur between eusocial and non-eusocial species in nucleotide composition and codon usage profiles of PCGs and in the secondary structure of tRNA genes. Maximum likelihood phylogenetic analysis of the complete concatenated PCG complement of 90 species supports the monophyly of the genus Synalpheus and its family Alpheidae. Moreover, the monophyletic status of the caridean families Alvinocaridae, Atyidae, Thoridae, Lysmatidae, Palaemonidae, and Pandalidae within caridean shrimps are fully or highly supported by the analysis. We therefore conclude that mitochondrial genomes contain sufficient phylogenetic information to resolve relationships at high taxonomic levels within the Caridea. Our analysis of mitochondrial genomes in the genus Synalpheus contributes to the understanding of the coevolution between genomic architecture and sociality in caridean shrimps and other marine organisms.
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Affiliation(s)
- Caroline C Ennis
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Nariah N Haeffner
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Cameron D Keyser
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Shannon T Leonard
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | | | - Avery M Savoie
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Timothy J Cronin
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Werner P Veldsman
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, China
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.
| | - Solomon T C Chak
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; Department of Biological Sciences, SUNY College at Old Westbury, Old Westbury, NY 11568, USA.
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA; Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida 34949, USA; Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Wolfe JM, Luque J, Bracken-Grissom HD. How to become a crab: Phenotypic constraints on a recurring body plan. Bioessays 2021; 43:e2100020. [PMID: 33751651 DOI: 10.1002/bies.202100020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
A fundamental question in biology is whether phenotypes can be predicted by ecological or genomic rules. At least five cases of convergent evolution of the crab-like body plan (with a wide and flattened shape, and a bent abdomen) are known in decapod crustaceans, and have, for over 140 years, been known as "carcinization." The repeated loss of this body plan has been identified as "decarcinization." In reviewing the field, we offer phylogenetic strategies to include poorly known groups, and direct evidence from fossils, that will resolve the history of crab evolution and the degree of phenotypic variation within crabs. Proposed ecological advantages of the crab body are summarized into a hypothesis of phenotypic integration suggesting correlated evolution of the carapace shape and abdomen. Our premise provides fertile ground for future studies of the genomic and developmental basis, and the predictability, of the crab-like body form.
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Affiliation(s)
- Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Javier Luque
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Smithsonian Tropical Research Institute, Balboa-Ancon, Panama.,Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, USA
| | - Heather D Bracken-Grissom
- Institute of Environment and Department of Biological Sciences, Florida International University, North Miami, Florida, USA
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Katneni VK, Shekhar MS, Jangam AK, Paran BC, Selvaraj A, Krishnan K, Kaikkolante N, Prabhudas SK, Gopalapillai G, Koyadan VK. Phylogenetic relations and mitogenome-wide similarity metrics reveal monophyly of Penaeus sensu lato. Ecol Evol 2021; 11:2040-2049. [PMID: 33717440 PMCID: PMC7920775 DOI: 10.1002/ece3.7148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 11/24/2022] Open
Abstract
Splitting of the genus Penaeus sensu lato into six new genera based on morphological features alone has been controversial in penaeid shrimp taxonomy. Several studies focused on building phylogenetic relations among the genera of Penaeus sensu lato. However, they lack in utilizing full mitochondrial DNA genome of shrimp representing all the six controversial genera. For the first time, the present study targeted the testing of all the six genera of Penaeus sensu lato for phylogenetic relations utilizing complete mitochondrial genome sequence. In addition, the study reports for the first time about the complete mitochondrial DNA genome sequence of Fenneropenaeus indicus, an important candidate species in aquaculture and fisheries, and utilized it for phylogenomics. The maximum likelihood and Bayesian approaches were deployed to generate and comprehend the phylogenetic relationship among the shrimp in the suborder, Dendrobranchiata. The phylogenetic relations established with limited taxon sampling considered in the study pointed to the monophyly of Penaeus sensu lato and suggested collapsing of the new genera to a single genus. Further, trends in mitogenome-wide estimates of average amino acid identity in the order Decapoda and the genus Penaeus sensu lato supported restoration of the old genus, Penaeus, rather promoting the creation of new genera.
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Affiliation(s)
- Vinaya Kumar Katneni
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Mudagandur S. Shekhar
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Ashok Kumar Jangam
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | | | - Ashok Selvaraj
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Karthic Krishnan
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Nimisha Kaikkolante
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Sudheesh K. Prabhudas
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Gopikrishna Gopalapillai
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
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Boštjančić LL, Bonassin L, Anušić L, Lovrenčić L, Besendorfer V, Maguire I, Grandjean F, Austin CM, Greve C, Hamadou AB, Mlinarec J. The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA. Front Genet 2021; 11:611745. [PMID: 33552130 PMCID: PMC7859515 DOI: 10.3389/fgene.2020.611745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Pontastacus leptodactylus is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning P. leptodactylus have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the P. leptodactylus genome. In addition, the karyogram of P. leptodactylus (2n = 180) is presented here for the first time consisting of 75 metacentric, 14 submetacentric, and a submetacentric/metacentric heteromorphic chromosome pair. We determined the genome size to be at ~18.7 gigabase pairs. Repetitive DNA represents about 54.85% of the genome. Satellite DNA repeats are the most abundant type of repetitive DNA, making up to ~28% of the total amount of repetitive elements, followed by the Ty3/Gypsy retroelements (~15%). Our study established a surprisingly high diversity of satellite repeats in P. leptodactylus. The genome of P. leptodactylus is by far the most satellite-rich genome discovered to date with 258 satellite families described. Of the five mapped satellite DNA families on chromosomes, PlSAT3-411 co-localizes with the AT-rich DAPI positive probable (peri)centromeric heterochromatin on all chromosomes, while PlSAT14-79 co-localizes with the AT-rich DAPI positive (peri)centromeric heterochromatin on one chromosome and is also located subterminally and intercalary on some chromosomes. PlSAT1-21 is located intercalary in the vicinity of the (peri)centromeric heterochromatin on some chromosomes, while PlSAT6-70 and PlSAT7-134 are located intercalary on some P. leptodactylus chromosomes. The FISH results reveal amplification of interstitial telomeric repeats (ITRs) in P. leptodactylus. The prevalence of repetitive elements, especially the satellite DNA repeats, may have provided a driving force for the evolution of the P. leptodactylus genome.
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Affiliation(s)
| | - Lena Bonassin
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Lucija Anušić
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Leona Lovrenčić
- Division of Zoology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Ivana Maguire
- Division of Zoology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Frederic Grandjean
- Laboratoire Ecologie Biologie des Interactions-UMR CNRS 7267, University of Poitiers, Poitiers, France
| | - Christopher M. Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Alexander Ben Hamadou
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
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Reanalysis and Revision of the Complete Mitochondrial Genome of Artemia urmiana Günther, 1899 (Crustacea: Anostraca). DIVERSITY 2021. [DOI: 10.3390/d13010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In the previously published mitochondrial genome sequence of Artemia urmiana (NC_021382 [JQ975176]), the taxonomic status of the examined Artemia had not been determined, due to parthenogenetic populations coexisting with A. urmiana in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of Artemia (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. With regard to coexisting populations in Urmia Lake, and intra- and inter-specific variations in the pooled samples, NC_021382 [JQ975176] cannot be recommended as a valid sequence and any attempt to attribute it to A. urmiana or a parthenogenetic population is unreasonable. With the aid of next-generation sequencing methods, we characterized and assembled a complete mitochondrial genome of A. urmiana with defined taxonomic status. Our results reveal that in the previously published mitogenome (NC_021382 [JQ975176]), tRNA-Phe has been erroneously attributed to the heavy strand but it is encoded in the light strand. There was a major problem in the position of the ND5. It was extended over the tRNA-Phe, which is biologically incorrect. We have also identified a partial nucleotide sequence of 311 bp that was probably erroneously duplicated in the assembly of the control region of NC_021382 [JQ975176], which enlarges the control region length by 16%. This partial sequence could not be recognized in our assembled mitogenome as well as in 48 further examined specimens of A. urmiana. Although, only COX1 and 16S genes have been widely used for phylogenetic studies in Artemia, our findings reveal substantial differences in the nucleotide composition of some other genes (including ATP8, ATP6, ND3, ND6, ND1 and COX3) among Artemia species. It is suggested that these markers should be included in future phylogenetic studies.
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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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Scholtz G. Eocarcinus praecursor Withers, 1932 (Malacostraca, Decapoda, Meiura) is a stem group brachyuran. ARTHROPOD STRUCTURE & DEVELOPMENT 2020; 59:100991. [PMID: 32891896 DOI: 10.1016/j.asd.2020.100991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
Beginning with the description by Withers in 1932, Eocarcinus praecursor from the Jurassic has long been considered the oldest representative of the Brachyura. In 2010 Feldmann and Schweitzer re-investigated the specimens of E. praecursor and expressed doubts about the brachyuran nature of this species. Among other characters, the suspected existence of small chelae in the 2nd or 3rd pereopods led them to the conclusion that E. praecursor must be removed from the Brachyura and rather be seen as a representative of the Anomala. However, Anomala also do not possess chelae on the 2nd and 3rd pereopods. This contradiction and other aspects initiated a new investigation of E. praecursor. It can be shown that neither the 2nd nor the 3rd pereopods of E. praecursor are chelate. Furthermore, there are no other derived characters shared with anomalans. By contrast, there are a number of apomorphies shared with Brachyura such as the shape and articulation of the large chelae and the attachment points of the last two pereopods. However, not all apomorphies of the crown group are present yet. Thus, E. praecursor is a stem group representative, which allows statements about individual steps in the evolution of the set of characters of the crown group Brachyura.
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Affiliation(s)
- Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie/Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany.
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Chak STC, Barden P, Baeza JA. The complete mitochondrial genome of the eusocial sponge-dwelling snapping shrimp Synalpheus microneptunus. Sci Rep 2020; 10:7744. [PMID: 32385299 PMCID: PMC7210941 DOI: 10.1038/s41598-020-64269-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/13/2020] [Indexed: 01/10/2023] Open
Abstract
In the marine realm, eusociality is only known to have evolved within a clade of sponge-dwelling snapping shrimps in the genus Synalpheus. Deciphering the genomic underpinnings of eusociality in these marine shrimps has been limited by the sparse genomic resources in this genus. Here, we report, for a eusocial shrimp Synalpheus microneptunus, a complete mitochondrial genome (22X coverage) assembled from short Illumina 150 bp paired-end reads. The 15,603 bp long mitochondrial genome of S. microneptunus is AT-rich and includes 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and an 834 bp intergenic region assumed to be the D-loop. The gene order is identical to that reported for most caridean shrimps and corresponds to the presumed Pancrustacean ground pattern. All PCGs showed signs of purifying selection, with KA/KS <<1 across the whole PCGs and most sliding windows within PCGs. Maximum-likelihood and Bayesian inference phylogenetic analyses of 13 PCGs and 68 terminals supports the monophyly of the Caridea and the family Alpheidae. The complete mitochondrial genome of the eusocial shrimp Synalpheus microneptunus will contribute to a better understanding of the selective pressures and rates of molecular evolution in marine eusocial animals.
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Affiliation(s)
- Solomon T C Chak
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Tan MH, Gan HM, Lee YP, Grandjean F, Croft LJ, Austin CM. A Giant Genome for a Giant Crayfish ( Cherax quadricarinatus) With Insights Into cox1 Pseudogenes in Decapod Genomes. Front Genet 2020; 11:201. [PMID: 32211032 PMCID: PMC7069360 DOI: 10.3389/fgene.2020.00201] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/20/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Frederic Grandjean
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267 Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - Laurence J. Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Christopher M. Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
- School of Science, Monash University Malaysia, Petaling Jaya, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Malaysia
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