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Marques-Neto JC, de Lima GM, Maciel CMT, Maciel BR, Abrunhosa FA, Sampaio I, Maciel CR. In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data. BMC Genomics 2023; 24:677. [PMID: 37950193 PMCID: PMC10637016 DOI: 10.1186/s12864-023-09770-y] [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: 07/18/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Macrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination "M. amazonicum complex" is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará. RESULTS Sequences were obtained from the prawn's transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91-100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial). CONCLUSIONS It was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.
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Affiliation(s)
- Jerônimo Costa Marques-Neto
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Gabriel Monteiro de Lima
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Carlos Murilo Tenório Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Bruna Ramalho Maciel
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Fernando Araujo Abrunhosa
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Carcinology, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Iracilda Sampaio
- Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Cristiana Ramalho Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
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Deng Z, Zhang X, Wolinska J, Blair D, Hu W, Yin M. Climate has contributed to population diversification of Daphnia galeata across Eurasia. Mol Ecol 2023; 32:5110-5124. [PMID: 37548328 DOI: 10.1111/mec.17094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
Climate is a fundamental abiotic factor that plays a key role in driving the evolution, distribution and population diversification of species. However, there have been few investigations of genomic signatures of adaptation to local climatic conditions in cladocerans. Here, we have provided the first high-quality chromosome-level genome assembly (~143 Mb, scaffold N50 12.6 Mb) of the waterflea, Daphnia galeata, and investigated genomic variation in 22 populations from Central Europe and Eastern China. Our ecological-niche models suggested that the historic distribution of D. galeata in Eurasia was significantly affected by Quaternary climate fluctuations. We detected pronounced genomic and morphometric divergences between European and Chinese D. galeata populations. Such divergences could be partly explained by genomic signatures of thermal adaptation to distinct climate regimes: a set of candidate single-nucleotide polymorphisms (SNPs) potentially associated with climate were detected. These SNPs were in genes significantly enriched in the Gene ontology terms "determination of adult lifespan" and "translation repressor activity", and especially, mthl5 and SOD1 involved in the IIS pathway, and EIF4EBP2 involved in the target of the rapamycin signalling pathway. Our study indicates that certain alleles might be associated with particular temperature regimes, playing a functional role in shaping the population structure of D. galeata at a large geographical scale. These results highlight the potential role of molecular variation in the response to climate variation, in the context of global climate change.
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Affiliation(s)
- Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Xiuping Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
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Hiki K, Oka K, Nakajima N, Watanabe H, Yamamoto H, Yamagishi T. The complete mitochondrial genome of water flea Ceriodaphnia dubia (Crustacea: Cladocera) NIES strain. Mitochondrial DNA B Resour 2023; 8:831-835. [PMID: 37560176 PMCID: PMC10408566 DOI: 10.1080/23802359.2023.2241663] [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: 06/09/2022] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Water flea Ceriodaphnia dubia has been widely used for risk assessments of chemicals and environmental contamination. In this study, the complete mitochondrial genome (mitogenome) of this species NIES strain was determined using short-read high throughput and long-read sequencing technologies. The mitogenome of C. dubia was 15,170 bp in length and consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs). The gene order was identical to the pattern conserved across crustaceans. The complete mitogenome of the NIES strain will serve as genetical reference in ecological risk assessments in Japan, as well as resources for future phylogenetical studies using cladocerans.
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Affiliation(s)
- Kyoshiro Hiki
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Kenta Oka
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Haruna Watanabe
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Hiroshi Yamamoto
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Takahiro Yamagishi
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
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Analysis of the complete mitogenome of Daphnia galeata from the Han River, South Korea: structure comparison and control region evolution. Funct Integr Genomics 2023; 23:65. [PMID: 36813863 DOI: 10.1007/s10142-023-00986-5] [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: 06/09/2022] [Revised: 11/30/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023]
Abstract
Daphnia galeata is an important plankton in aquatic ecosystems. As a widely distributed species, D. galeata has been found throughout the Holarctic region. Understanding the genetic diversity and evolution of D. galeata requires the accumulation of genetic information from different locations. Even though the mitochondrial genome (mitogenome) sequence of D. galeata has already been reported, little is known about the evolution of its mitochondrial control region. In this study, D. galeata samples were collected from the Han River on the Korean Peninsula and its partial nd2 gene was sequenced for haplotype network analysis. This analysis showed that four clades of D. galeata were present in the Holarctic region. Moreover, the D. galeata examined in this study belonged to clade D and was specific to South Korea. The mitogenome of D. galeata from the Han River showed similar gene content and structure compared to sequences reported from Japan. Furthermore, the structure of control region of the Han River was similar to those of Japanese clones and differed substantially from European clone. Finally, a phylogenetic analysis based on the amino acid sequences of 13 protein-coding genes (PCGs) indicated that D. galeata from the Han River formed a cluster with clones collected from Lakes Kasumigaura, Shirakaba, and Kizaki in Japan. The differences in control region structure and stem and loop structure reflect the different evolutionary directions of the mitogenomes from Asian and European clones. These findings improve our understanding of the mitogenome structure and genetic diversity of D. galeata.
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Hamza W, Hazzouri KM, Sudalaimuthuasari N, Amiri KMA, Neretina AN, Al Neyadi SES, Kotov AA. Genome Assembly of a Relict Arabian Species of Daphnia O. F. Müller (Crustacea: Cladocera) Adapted to the Desert Life. Int J Mol Sci 2023; 24:ijms24010889. [PMID: 36614331 PMCID: PMC9820869 DOI: 10.3390/ijms24010889] [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: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023] Open
Abstract
The water flea Daphnia O.F. Müller 1776 (Crustacea: Cladocera) is an important model of recent evolutionary biology. Here, we report a complete genome of Daphnia (Ctenodaphnia) arabica (Crustacea: Cladocera), recently described species endemic to deserts of the United Arab Emirates. In this study, genome analysis of D. arabica was carried out to investigate its genomic differences, complexity as well as its historical origins within the subgenus Daphnia (Ctenodaphnia). Hybrid genome assembly of D. arabica resulted in ~116 Mb of the assembled genome, with an N50 of ~1.13 Mb (BUSCO score of 99.2%). From the assembled genome, in total protein coding, 5374 tRNA and 643 rRNA genes were annotated. We found that the D. arabica complete genome differed from those of other Daphnia species deposited in the NCBI database but was close to that of D. cf. similoides. However, its divergence time estimate sets D. arabica in the Mesozoic, and our demographic analysis showed a great reduction in its genetic diversity compared to other Daphnia species. Interestingly, the population expansion in its diversity occurred during the megadrought climate around 100 Ka ago, reflecting the adaptive feature of the species to arid and drought-affected environments. Moreover, the PFAM comparative analysis highlights the presence of the important domain SOSS complex subunit C in D. arabica, which is missing in all other studied species of Daphnia. This complex consists of a few subunits (A, B, C) working together to maintain the genome stability (i.e., promoting the reparation of DNA under stress). We propose that this domain could play a role in maintaining the fitness and survival of this species in the desert environment. The present study will pave the way for future research to identify the genes that were gained or lost in this species and identify which of these were key factors to its adaptation to the harsh desert environment.
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Affiliation(s)
- Waleed Hamza
- Biology Department, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Correspondence: (W.H.); (A.A.K.)
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. A. Amiri
- Biology Department, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Anna N. Neretina
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Shamma E. S. Al Neyadi
- Biology Department, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Alexey A. Kotov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence: (W.H.); (A.A.K.)
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Kotov AA, Taylor DJ. Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance. PeerJ 2022; 10:e14113. [PMID: 36213509 PMCID: PMC9541614 DOI: 10.7717/peerj.14113] [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: 11/17/2021] [Accepted: 09/02/2022] [Indexed: 01/21/2023] Open
Abstract
The Daphnia longispina complex (Crustacea: Cladocera) contains several keystone freshwater species such as D. longispina O.F. Müller (D. rosea Sars is a junior synonym), D. galeata Sars, D. cucullata Sars, and D. dentifera Forbes. The complex is common throughout the Holarctic, but there are several geographic regions where local forms have been assigned to European species names based on a superficial morphological resemblance. Here we examine the species status of a form that was previously assigned to D. rosea from a montane bog pond on Honshu, Japan. We used two nuclear non-coding loci (nDNA), mitochondrial sequences (the ND2 protein-coding region) and morphology for evidence. The mitochondrial gene evidence supported the existence of a divergent lineage that is more closely related to D. galeata than to D. dentifera. However, morphology and the nuclear DNA data indicated a lineage that is most closely related to D. dentifera. As our evidence supported the existence of a cohesive divergent lineage, we described a new species, Daphnia japonica sp. nov. Recognition of local and subalpine diversity in this group is critical as ongoing anthropogenic disturbance has been associated with introductions, local extirpations, and hybridization.
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Affiliation(s)
- Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Derek J. Taylor
- Biological Sciences, State University of New York at Buffalo, Buffalo, NY, United States
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Kitano T, Sato H, Takahashi N, Igarashi S, Hatanaka Y, Igarashi K, Umetsu K. Complete mitochondrial genomes of three fairy shrimps from snowmelt pools in Japan. BMC ZOOL 2022; 7:11. [PMID: 37170326 PMCID: PMC10127424 DOI: 10.1186/s40850-022-00111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/27/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Fairy shrimps belong to order Anostraca, class Branchiopoda, subphylum Crustacea, and phylum Arthropoda. Three fairy shrimp species (Eubranchipus uchidai, E. asanumai, and E. hatanakai) that inhabit snowmelt pools are currently known in Japan. Whole mitochondrial genomes are useful genetic information for conducting phylogenetic analyses. Mitochondrial genome sequences for Branchiopoda members are gradually being collated.
Results
Six whole mitochondrial genomes from the three Eubranchipus species are presented here. Eubranchipus species share the anostracan pattern of gene arrangement in their mitochondrial genomes. The mitochondrial genomes of the Eubranchipus species have a higher GC content than those of other anostracans. Accelerated substitution rates in the lineage of Eubranchipus species were observed.
Conclusion
This study is the first to obtain whole mitochondrial genomes for Far Eastern Eubranchipus species. We show that the nucleotide sequences of cytochrome oxidase subunit I and the 16S ribosomal RNA of E. asanumai presented in a previous study were nuclear mitochondrial DNA segments. Higher GC contents and accelerated substitution rates are specific characteristics of the mitochondrial genomes of Far Eastern Eubranchipus. The results will be useful for further investigations of the evolution of Anostraca as well as Branchiopoda.
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Kotov AA, Garibian PG, Bekker EI, Taylor DJ, Karabanov DP. A new species group from the Daphnia curvirostris species complex (Cladocera: Anomopoda) from the eastern Palaearctic: taxonomy, phylogeny and phylogeography. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The eastern Palaearctic is a centre of diversity for freshwater cladocerans (Crustacea), but little is known about the evolution and taxonomy of this diversity. Daphnia curvirostris is a Holarctic species complex that has most of its diversity in the eastern Palaearctic. We examined the phylogeography, rates of evolution and taxonomic status for each clade of the D. curvirostris complex using morphological and genetic evidence from four genes. The cybertaxonomical and morphological evidence supported an eastern Palaearctic clade, with at least four species (described here as the Daphnia korovchinskyi sp. nov. group) having diagnostic morphological characters. We also detected convergent morphological characters in the D. curvirostris complex that provided information about species boundaries. Two of the new species (Daphnia koreana sp. nov. and Daphnia ishidai sp. nov.) are known from single ponds and are threatened by human activity. Divergence time estimates suggested an ancient origin (12–28 Mya) for the D. korovchinskyi group, but these estimates are complicated by the small number of calibration points.
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Affiliation(s)
- Alexey A Kotov
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
| | - Petr G Garibian
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
| | - Eugeniya I Bekker
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, NY, USA
| | - Dmitry P Karabanov
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
- I. D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Russia
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Lee JS, Kim DH, Choi BS, Kato Y, Watanabe H, Lee JS. Complete mitochondrial genome of the freshwater water flea Daphnia magna NIES strain (Cladocera, Daphniidae): Rearrangement of two ribosomal RNA genes. MITOCHONDRIAL DNA PART B 2020. [DOI: 10.1080/23802359.2020.1750995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Jin-Sol Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea
| | | | - Yasuhiko Kato
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea
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Zhang J, Zhou Q, Yang X, Yu P, Zhou W, Gui Y, Ouyang X, Wan Q. Characterization of the complete mitochondrial genome and phylogenetic analysis of Pelodiscus sinensis, a mutant Chinese soft-shell turtle. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-018-1007-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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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Martins Ribeiro M, Facchin S, Pereira AH, Kalapothakis E, Xu S, Han BP, Dumont HJ, Cecília Rietzler A. Mitogenome of Daphnia laevis (Cladocera, Daphniidae) from Brazil. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1545547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Marcela Martins Ribeiro
- Laboratório de Limnologia, Ecotoxicologia e Ecologia Aquática, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Susanne Facchin
- Laboratório de Biotecnologia e Marcadores Moleculares, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Adriana Heloísa Pereira
- Laboratório de Biotecnologia e Marcadores Moleculares, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Evanguedes Kalapothakis
- Laboratório de Biotecnologia e Marcadores Moleculares, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Shaolin Xu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Jinan, China
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Jinan, China
| | - Henri J. Dumont
- Department of Ecology and Institute of Hydrobiology, Jinan University, Jinan, China
- Department of Biology, University of Gent, Gent, Belgium
| | - Arnola Cecília Rietzler
- Laboratório de Limnologia, Ecotoxicologia e Ecologia Aquática, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
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13
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Jeong CB, Choi BS, Hwang DS, Choi J, Lee JS. Complete mitochondrial genome of the water flea Daphnia magna (Cladocera, Daphniidae). MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1584059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | | | - Dae-Sik Hwang
- Research Institute of Environmental Health and Safety, Bucheon, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, Seoul, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
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14
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Lu Y, Johnston PR, Dennis SR, Monaghan MT, John U, Spaak P, Wolinska J. Daphnia galeata responds to the exposure to an ichthyosporean gut parasite by down-regulation of immunity and lipid metabolism. BMC Genomics 2018; 19:932. [PMID: 30547741 PMCID: PMC6295042 DOI: 10.1186/s12864-018-5312-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Regulatory circuits of infection in the emerging experimental model system, water flea Daphnia and their microparasites, remain largely unknown. Here we provide the first molecular insights into the response of Daphnia galeata to its highly virulent and common parasite Caullerya mesnili, an ichthyosporean that infects the gut epithelium. We generated a transcriptomic dataset using RNAseq from parasite-exposed (vs. control) Daphnia, at two time points (4 and 48 h) after parasite exposure. RESULTS We found a down-regulation of metabolism and immunity-related genes, at 48 h (but not 4 h) after parasite exposure. These genes are involved in lipid metabolism and fatty acid biosynthesis, as well as microbe recognition (e.g. c-type lectins) and pathogen attack (e.g. gut chitin). CONCLUSIONS General metabolic suppression implies host energy shift from reproduction to survival, which is in agreement with the known drastic reduction in Daphnia fecundity after Caullerya infection. The down-regulation of gut chitin indicates a possible interaction between the peritrophic matrix and the evading host immune system. Our study provides the first description of host transcriptional responses in this very promising host-parasite experimental system.
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Affiliation(s)
- Yameng Lu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany. .,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany.
| | - Paul R Johnston
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany.,Freie Universität Berlin, Berlin, Germany
| | - Stuart R Dennis
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
| | - Uwe John
- Alfred Wegener Institut Helmholtz Zentrum für Polar und Meeresforschung (AWI), Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Piet Spaak
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Justyna Wolinska
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Freie Universität Berlin, Berlin, Germany
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15
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Jiang Z, Gao B, Hu M, Ding L, Lan Z, Yu M, Yu H, Cui Q, Lin J, Li M. Conserved structure and function of chemokine CXCL8 between Chinese tree shrews and humans. Gene 2018; 677:149-162. [DOI: 10.1016/j.gene.2018.07.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/23/2018] [Accepted: 07/10/2018] [Indexed: 12/11/2022]
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16
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Microsporidian genus Berwaldia (Opisthosporidia, Microsporidia), infecting daphnids (Crustacea, Branchiopoda): Biology, structure, molecular phylogeny and description of two new species. Eur J Protistol 2017; 61:1-12. [DOI: 10.1016/j.ejop.2017.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/25/2017] [Accepted: 07/28/2017] [Indexed: 11/23/2022]
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