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Fernández-Pérez J, Nantón A, Méndez J. Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae). BMC Genet 2018; 19:97. [PMID: 30367592 PMCID: PMC6204057 DOI: 10.1186/s12863-018-0684-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/11/2018] [Indexed: 01/04/2023] Open
Abstract
Background The whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and their variation were described. The phylogenetic usefulness of 5S and ITS sequences in the inference of evolutionary relationships among these wedge clams was also investigated. Results The length of the 5S repeat presented little variation among species, except D. trunculus that differed from the rest of the Donax species in 170–210 bp. The deduced coding region covered 120 bp, and showed recognizable internal control regions (ICRs) involved in the transcription. The length of non-transcribed spacer region (NTS) ranged from 157 bp to 165 bp in Donax trunculus and from 335 bp to 367 bp in the other three species. The conservation degree of transcriptional regulatory regions was analysed revealing a conserved TATA-like box in the upstream region. Regarding ITS sequences, the four Donax species showed slight size differences among clones due to the variation occurring in the ITS1 and ITS2, except Donax variegatus did not display size differences in the ITS2. The total length of the ITS sequence ranged between 814 and 1014 bp. Resulting phylogenetic trees display that the two ribosomal DNA regions provide well-resolved phylogenies where the four European Donax species form a single clade receiving high support in nodes. The topology obtained with 5S sequences was in agreement with Donax evolutionary relationships inferred from several sequences of different nature in previous studies. Conclusions This is not only a basic research work, where new data and new knowledge is provided about Donax species, but also have allowed the authentication of these wedge clams and offers future applications to provide other genetic resources. Electronic supplementary material The online version of this article (10.1186/s12863-018-0684-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain.
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
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Serb JM. Reconciling Morphological and Molecular Approaches in Developing a Phylogeny for the Pectinidae (Mollusca: Bivalvia). SCALLOPS - BIOLOGY, ECOLOGY, AQUACULTURE, AND FISHERIES 2016. [DOI: 10.1016/b978-0-444-62710-0.00001-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Kornobis E, Pálsson S. The ITS region of groundwater amphipods: length, secondary structure and phylogenetic information content in Crangonyctoids and Niphargids. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/jzs.12006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Etienne Kornobis
- Department of Life and Environmental Sciences; University of Iceland; Reykjavik Iceland
| | - Snaebjörn Pálsson
- Department of Life and Environmental Sciences; University of Iceland; Reykjavik Iceland
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Malkowsky Y, Klussmann-Kolb A. Phylogeny and spatio-temporal distribution of European Pectinidae (Mollusca: Bivalvia). SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.676572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Vizoso M, Vierna J, González-Tizón AM, Martínez-Lage A. The 5S rDNA Gene Family in Mollusks: Characterization of Transcriptional Regulatory Regions, Prediction of Secondary Structures, and Long-Term Evolution, with Special Attention to Mytilidae Mussels. J Hered 2011; 102:433-47. [DOI: 10.1093/jhered/esr046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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The analysis of rRNA sequence-structure in phylogenetics: An application to the family Pectinidae (Mollusca: Bivalvia). Mol Phylogenet Evol 2010; 56:1059-67. [DOI: 10.1016/j.ympev.2010.04.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 04/12/2010] [Accepted: 04/16/2010] [Indexed: 11/17/2022]
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7
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Vierna J, Martínez-Lage A, González-Tizón AM. Analysis of ITS1 and ITS2 sequences in Ensis razor shells: suitability as molecular markers at the population and species levels, and evolution of these ribosomal DNA spacers. Genome 2010; 53:23-34. [DOI: 10.1139/g09-080] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Internal transcribed spacer 1 and 2 (ITS1 and ITS2) sequences were analysed in Ensis razor shells (Mollusca: Bivalvia: Pharidae). We aimed to (1) test ITS1 and ITS2 as molecular markers at the population level in the successful alien E. directus (Conrad, 1843); (2) test these spacers at the species level in E. directus and three other Ensis species, E. siliqua (L., 1758), E. macha (Molina, 1782), and E. magnus (Schumacher, 1817); and (3) analyse the evolutionary processes that may be shaping Ensis ITS1 and ITS2 extant variation. In E. directus, despite the intragenomic divergence detected, ITS1 and ITS2 were informative in differentiating the geographic areas considered (Denmark and Canada) by means of both the insertion-deletion polymorphism and the nucleotide polymorphism. In this species, the 5.8S ribosomal gene (5.8S) showed scarce polymorphism. At the species level, maximum parsimony and maximum likelihood analyses revealed that ITS1 and ITS2 may be suitable to reconstruct Ensis phylogenetic relationships. Finally, the evolutionary models that best fit the long-term evolution of Ensis ITS1–5.8S–ITS2 are discussed. A mixed process of concerted evolution, birth-and-death evolution, and selection is chosen as an option that may reconcile the long-term evolution of Ensis ITS1–5.8S–ITS2 and 5S ribosomal DNA.
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Affiliation(s)
- Joaquín Vierna
- Department of Molecular and Cell Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, A Zapateira s/n, E-15071 La Coruña, Spain
| | - Andrés Martínez-Lage
- Department of Molecular and Cell Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, A Zapateira s/n, E-15071 La Coruña, Spain
| | - Ana M. González-Tizón
- Department of Molecular and Cell Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, A Zapateira s/n, E-15071 La Coruña, Spain
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Cheng HL, Xia DQ, Wu TT, Meng XP, Ji HJ, Dong ZG. Study on sequences of ribosomal DNA internal transcribed spacers of clams belonging to the Veneridae family (Mollusca: Bivalvia). ACTA ACUST UNITED AC 2009; 33:702-10. [PMID: 16939004 DOI: 10.1016/s0379-4172(06)60102-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The first and second internal transcribed spacer (ITS1 and ITS2) regions of the ribosomal DNA from four species, Meretrix meretrix L., Cyclina sinensis G., Mercenaria mercenaria L., and Protothaca jedoensis L., belonging to the family Veneridae were amplified by PCR and sequenced. The size of the ITS1 PCR amplification product ranged from 663 bp to 978 bp, with GC contents ranging from 60.78% to 64.97%. The size of the ITS1 sequence ranged from 585 bp to 900 bp, which is the largest range reported thus far in bivalve species, with GC contents ranging from 61.03% to 65.62%. The size of the ITS2 PCR amplification product ranged from 513 bp to 644 bp, with GC contents ranging from 61.29% to 62.73%. The size of the ITS2 sequence ranged from 281 bp to 412 bp, with GC contents ranging from 65.21% to 67.87%. Extensive sequence variation and obvious length polymorphisms were noted for both regions in these species, and sequence similarity of ITS2 was higher than that of ITS1 across species. The complete sequences of 5.8S ribosomal RNA gene were obtained by assembling ITS1 and ITS2 sequences, and the sequence length in all species was 157 bp. The phylogenetic tree of Veneridae clams was reconstructed using ITS2-containing partial sequences of both 5.8S and 28S ribosomal DNA as markers and the corresponding sequence information in Arctica islandica as the outgroup. Tree topologies indicated that P. jedoensis shared a close relationship with M. mercenaria and C. sinensis, a distant relationship with other species.
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Affiliation(s)
- Han-Liang Cheng
- Fisheries College, Nanjing Agricultural University, Wuxi, China
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Puslednik L, Serb JM. Molecular phylogenetics of the Pectinidae (Mollusca: Bivalvia) and effect of increased taxon sampling and outgroup selection on tree topology. Mol Phylogenet Evol 2008; 48:1178-88. [PMID: 18579415 DOI: 10.1016/j.ympev.2008.05.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 04/02/2008] [Accepted: 05/07/2008] [Indexed: 11/19/2022]
Abstract
Evolutionary relationships of the Pectinidae were examined using two mitochondrial genes (12S rRNA, 16S rRNA) and one nuclear gene (Histone H3) for 46 species. Outgroup taxa from Propeamussidae, Spondylidae and Limidae were also sequenced to examine the impact of outgroup choice on pectinid topologies. Our phylogenetic analyses resolved the Pectinidae as monophyletic, but many of the subfamilies and tribes within the family do not form monophyletic clades. The paraphyletic Aequipectinini group is the most basal member of the Pectinidae, with the Chlamydinae and Palliolinae representing the most recently derived pectinid groups. These results are in contrast with the current morphological hypothesis of Pectinidae evolution, which suggests the Chlamydinae and Pallioline are basal groups within the Pectinidae. Ingroup topology was found to be sensitive to outgroup choice and increasing taxon sampling within the Pectinidae resulted in more robust phylogenies.
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Affiliation(s)
- Louise Puslednik
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 253 Bessey Hall, Ames, IA 50011, USA
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José López-Piñón M, Freire R, Insua A, Méndez J. Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in some scallops (Bivalvia: Pectinidae). Hereditas 2008; 145:9-19. [DOI: 10.1111/j.0018-0661.2008.2034.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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José López-Piñón M, Freire R, Insua A, Méndez J. Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in some scallops (Bivalvia: Pectinidae). Hereditas 2008. [DOI: 10.1111/j.2007.0018-0661.02034x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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12
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Wang S, Bao Z, Li N, Zhang L, Hu J. Analysis of the secondary structure of ITS1 in Pectinidae: implications for phylogenetic reconstruction and structural evolution. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2007; 9:231-42. [PMID: 17286216 DOI: 10.1007/s10126-006-6113-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Revised: 10/09/2006] [Indexed: 05/13/2023]
Abstract
It is at present difficult to accurately position gaps in sequence alignment and to determine substructural homology in structure alignment when reconstructing phylogenies based on highly divergent sequences. Therefore, we have developed a new strategy for inferring phylogenies based on highly divergent sequences. In this new strategy, the whole secondary structure presented as a string in bracket notation is used as phylogenetic characters to infer phylogenetic relationships. It is no longer necessary to decompose the secondary structure into homologous substructural components. In this study, reliable phylogenetic relationships of eight species in Pectinidae were inferred from the structure alignment, but not from sequence alignment, even with the aid of structural information. The results suggest that this new strategy should be useful for inferring phylogenetic relationships based on highly divergent sequences. Moreover, the structural evolution of ITS1 in Pectinidae was also investigated. The whole ITS1 structure could be divided into four structural domains. Compensatory changes were found in all four structural domains. Structural motifs in these domains were identified further. These motifs, especially those in D2 and D3, may have important functions in the maturation of rRNAs.
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Affiliation(s)
- Shi Wang
- Laboratory of Marine Genetics and Breeding, Division of Life Science and Technology, Ocean University of China, Qingdao, 266003, People's Republic of China
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Thanwisai A, Kuvangkadilok C, Baimai V. Molecular phylogeny of black flies (Diptera: Simuliidae) from Thailand, using ITS2 rDNA. Genetica 2007; 128:177-204. [PMID: 17028950 DOI: 10.1007/s10709-005-5702-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2005] [Accepted: 12/02/2005] [Indexed: 11/26/2022]
Abstract
The sequences of the second internal transcribed spacer (ITS2) of ribosomal DNA (rDNA) were determined for 40 black fly species from Thailand, belonging to 4 subgenera of the genus Simulium, namely Gomphostilbia (12 species), Nevermannia (5 species), Montisimulium (1 species), Simulium sensu stricto (21 species), and an unknown subgenus with one species (Simulium baimaii). The length of the ITS2 ranged from 247 to 308 bp. All black fly species had high AT content, ranging from 71 to 83.8%. Intraindividual variation (clonal variation) occurred in 13 species, ranging from 0.3 to 1.1%. Large intrapopulation and interpopulation heterogeneities exist in S. feuerboni from the same and different locations in Doi Inthanon National Park, northern Thailand. Phylogenetic relationships among 40 black fly species were examined using PAUP (version 4.0b10) and MrBAYS (version 3.0B4). The topology of the trees revealed two major monophyletic clades. The subgenus Simulium and Simulium baimaii were placed in the first monophyletic clade, whereas the subgenera Nevermannia + Montisimulium were placed as the sister group to the subgenus Gomphostilbia in the second monophyletic clade. Our results suggest that S. baimaii belongs to the malyschevi-group or variegatum-group in the subgenus Simulium. The molecular phylogeny generally agrees with existing morphology-based phylogenies.
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Affiliation(s)
- Aunchalee Thanwisai
- Department of Biology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
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Odierna G, Aprea G, Barucca M, Canapa A, Capriglione T, Olmo E. Karyology of the Antarctic scallop Adamussium colbecki, with some comments on the karyological evolution of pectinids. Genetica 2006; 127:341-9. [PMID: 16850238 DOI: 10.1007/s10709-005-5366-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Accepted: 11/22/2005] [Indexed: 10/24/2022]
Abstract
Karyotype, location of the nucleolar organiser region (NOR) and heterochromatin presence and composition were studied in the Antarctic scallop Adamussium colbecki Smith, 1902. The karyotype exhibits 2n = 38 chromosomes with 11 pairs of metacentrics, 5 of submetacentrics, one subtelocentric and two telocentrics. Ag-NOR, CMA(3), DA/MM and NOR-FISH evidenced paracentromeric NORs on the short arm of 2nd pair chromosomes. Digestion with three restriction endonucleases followed by sequential staining with Giemsa, CMA(3) and DAPI evidenced on all chromosomes centromeric heterochromatin positive for both DAPI and CMA(3). In situ hybridisation analysis showed the presence of an AT-rich satellite DNA in the centromeric heterochromatin of several chromosomes. A mosaicism was detected in the germinal cell lines of one specimen, as in six of the 20 plates examined the set had 37 chromosomes with a missing pair of telocentrics and an unpaired metacentric. Comparison of the chromosome sets of all the pectinids studied to date and comparison with a phyletic tree obtained from molecular mitochondrial genes studies yielded good agreement between karyotype morphology and taxonomic classification.
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Affiliation(s)
- G Odierna
- Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, via Cinthia, I-80126, Napoli, Italy
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Insua A, López-Piñón MJ, Freire R, Méndez J. Karyotype and Chromosomal Location of 18S–28S and 5S Ribosomal DNA in the Scallops Pecten maximus and Mimachlamys varia (Bivalvia: Pectinidae). Genetica 2006; 126:291-301. [PMID: 16636923 DOI: 10.1007/s10709-005-7408-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Accepted: 05/17/2005] [Indexed: 10/24/2022]
Abstract
This work describes the karyotype and chromosomal location of the ribosomal DNA (rDNA) of Pecten maximus and Mimachlamys varia, two commercial scallop species from Europe. According to the chromosome centromeric index values found, the karyotype of P. maximus is composed of 1 metacentric, 2 metacentric-submetacentric, 1 telocentric-subtelocentric and 15 telocentric pairs, and that of M. varia of 4 metacentric, 2 subtelocentric-submetacentric, 9 subtelocentric, 3 subtelocentric-telocentric and 1 telocentric-subtelocentric pairs. In P. maximus, 18S-28S rDNA was located by FISH on a metacentric-submetacentric pair, and in M. varia on a subtelocentric-submetacentric pair using both silver staining and FISH. PCR amplification of the 5S rDNA unit yielded a single product of about 460 bp (P. maximus) and 450 bp (M. varia), that used as probe revealed a 5S rDNA site on a telocentric pair in P. maximus and a subtelocentric pair in M. varia. Two-color FISH or sequential silver staining of 5S rDNA-FISH-metaphases corroborated that the two gene families are located on different chromosomes in both species. A comparative analysis of the data allowed the inference of karyotypic relationships within scallops.
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Affiliation(s)
- Ana Insua
- Departamento de Biología Celular y Molecular, Universidade da Coruña, A Zapateira s/n, 15071, A Coruña, Spain.
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