Evolutionary Dynamics of rDNA Clusters in Chromosomes of Five Clam Species Belonging to the Family Veneridae (Mollusca, Bivalvia)

BioMed Research International ◽

10.1155/2014/754012 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 11

Author(s):

Concepción Pérez-García ◽

Ninoska S. Hurtado ◽

Paloma Morán ◽

Juan J. Pasantes

Keyword(s):

Phylogenetic Trees ◽

Evolutionary Dynamics ◽

5S Rdna ◽

Gene Clusters ◽

Ruditapes Philippinarum ◽

Ruditapes Decussatus ◽

Rdna Cluster ◽

Single Chromosome ◽

Molecular Phylogenetic ◽

Chromosomal Changes

The chromosomal changes accompanying bivalve evolution are an area about which few reports have been published. To improve our understanding on chromosome evolution in Veneridae, ribosomal RNA gene clusters were mapped by fluorescentin situhybridization (FISH) to chromosomes of five species of venerid clams (Venerupis corrugata,Ruditapes philippinarum,Ruditapes decussatus,Dosinia exoleta, andVenus verrucosa). The results were anchored to the most comprehensive molecular phylogenetic tree currently available for Veneridae. While a single major rDNA cluster was found in each of the five species, the number of 5S rDNA clusters showed high interspecies variation. Major rDNA was either subterminal to the short arms or intercalary to the long arms of metacentric or submetacentric chromosomes, whereas minor rDNA signals showed higher variability. Major and minor rDNAs map to different chromosome pairs in all species, but inR. decussatusone of the minor rDNA gene clusters and the major rDNA cluster were located in the same position on a single chromosome pair. This interspersion of both sequences was confirmed by fiber FISH. Telomeric signals appeared at both ends of every chromosome in all species. FISH mapping data are discussed in relation to the molecular phylogenetic trees currently available for Veneridae.

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Molecular Cytogenetics in Digenean Parasites: Linked and Unlinked Major and 5S rDNAs, B Chromosomes and Karyotype Diversification

Cytogenetic and Genome Research ◽

10.1159/000442504 ◽

2015 ◽

Vol 147 (2-3) ◽

pp. 195-207 ◽

Cited By ~ 4

Author(s):

Daniel García-Souto ◽

Juan J. Pasantes

Keyword(s):

Molecular Cytogenetics ◽

5S Rdna ◽

B Chromosomes ◽

Ruditapes Decussatus ◽

Metazoan Parasites ◽

Single Chromosome ◽

Telomeric Sequences ◽

Digenetic Trematodes ◽

Parorchis Acanthus ◽

Morphological Differences

Digenetic trematodes are the largest group of internal metazoan parasites, but their chromosomes are poorly studied. Although chromosome numbers and/or karyotypes are known for about 300 of the 18,000 described species, molecular cytogenetic knowledge is mostly limited to the mapping of telomeric sequences and/or of major rDNA clusters in 9 species. In this work we mapped major and 5S rDNA clusters and telomeric sequences in chromosomes of Bucephalus minimus, B. australis, Prosorhynchoides carvajali (Bucephaloidea), Monascus filiformis (Gymnophalloidea), Parorchis acanthus (Echinostomatoidea), Cryptocotyle lingua (Opisthorchioidea), Cercaria longicaudata, Monorchis parvus (Monorchioidea), Diphterostomum brusinae, and Bacciger bacciger (Microphalloidea). Whilst single major and minor rDNA clusters were mapped to different chromosome pairs in B. minimus and P. acanthus, overlapping signals were detected on a single chromosome pair in the remaining taxa. FISH experiments using major rDNA and telomeric probes clearly demonstrated the presence of highly stretched NORs in most of the digenean taxa analyzed. B chromosomes were detected in the B. bacciger samples hosted by Ruditapes decussatus. Although the cercariae specimens obtained from Donax trunculus, Tellina tenuis, and R. decussatus were in agreement with B. bacciger, their karyotypes showed striking morphological differences in agreement with the proposed assignation of these cercariae to different species of the genus Bacciger. Results are discussed in comparison with previous data on digenean chromosomes.

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Prokaryotic Phylogenies Inferred from Whole-Genome Sequence and Annotation Data

BioMed Research International ◽

10.1155/2013/409062 ◽

2013 ◽

Vol 2013 ◽

pp. 1-15 ◽

Cited By ~ 2

Author(s):

Wei Du ◽

Zhongbo Cao ◽

Yan Wang ◽

Ying Sun ◽

Enrico Blanzieri ◽

...

Keyword(s):

Phylogenetic Trees ◽

Sequence Similarity ◽

Genomic Structure ◽

Evolutionary Relationship ◽

Orthologous Gene ◽

Gene Clusters ◽

Whole Genome Sequence ◽

Whole Genome ◽

Orthologous Genes ◽

Single Chromosome

Phylogenetic trees are used to represent the evolutionary relationship among various groups of species. In this paper, a novel method for inferring prokaryotic phylogenies using multiple genomic information is proposed. The method is called CGCPhy and based on the distance matrix of orthologous gene clusters between whole-genome pairs. CGCPhy comprises four main steps. First, orthologous genes are determined by sequence similarity, genomic function, and genomic structure information. Second, genes involving potential HGT events are eliminated, since such genes are considered to be the highly conserved genes across different species and the genes located on fragments with abnormal genome barcode. Third, we calculate the distance of the orthologous gene clusters between each genome pair in terms of the number of orthologous genes in conserved clusters. Finally, the neighbor-joining method is employed to construct phylogenetic trees across different species. CGCPhy has been examined on different datasets from 617 complete single-chromosome prokaryotic genomes and achieved applicative accuracies on different species sets in agreement with Bergey's taxonomy in quartet topologies. Simulation results show that CGCPhy achieves high average accuracy and has a low standard deviation on different datasets, so it has an applicative potential for phylogenetic analysis.

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Cytogenetic characterization of the invasive mussel species Xenostrobus securis Lmk. (Bivalvia: Mytilidae)

Genome ◽

10.1139/g11-040 ◽

2011 ◽

Vol 54 (9) ◽

pp. 771-778 ◽

Cited By ~ 14

Author(s):

Concepción Pérez-García ◽

Paloma Morán ◽

Juan J. Pasantes

Keyword(s):

5S Rdna ◽

Gene Clusters ◽

Linker Histone ◽

Histone Gene ◽

Core Histone ◽

Histone Genes ◽

Single Chromosome ◽

Telomeric Sequences ◽

Xenostrobus Securis ◽

Dapi Fluorescence

The chromosomes of the invasive black-pigmy mussel (Xenostrobus securis (Lmk. 1819)) were analyzed by means of 4’,6-diamidino-2-phenylindole (DAPI) / propidium iodide (PI) and chromomycin A3 (CMA) / DAPI fluorescence staining and fluorescent in situ hybridization using major rDNA, 5S rDNA, core histone genes, linker histone genes, and telomeric sequences as probes. The diploid chromosome number in this species is 2n = 30. The karyotype is composed of seven metacentric, one meta/submetacentric, and seven submetacentric chromosome pairs. Telomeric sequences appear at both ends of every single chromosome. Major rDNA clusters appear near the centromeres on chromosome pairs 1 and 3 and are associated with bright CMA fluorescence and dull DAPI fluorescence. This species shows five 5S rDNA clusters close to the centromeres on four chromosome pairs (2, 5, 6, and 8). Three of the four core histone gene clusters map to centromeric positions on chromosome pairs 7, 10, and 13. The fourth core histone gene cluster occupies a terminal position on chromosome pair 8, also bearing a 5S rDNA cluster. The two linker histone gene clusters are close to the centromeres on chromosome pairs 12 and 14. Therefore, the use of these probes allows the unequivocal identification of 11 of the 15 chromosome pairs that compose the karyotype of X. securis.

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Larval cryopreservation as new management tool for threatened clam fisheries

Scientific Reports ◽

10.1038/s41598-021-94197-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

P. Heres ◽

J. Troncoso ◽

E. Paredes

Keyword(s):

Shell Growth ◽

Natural Populations ◽

Ruditapes Philippinarum ◽

Management Tool ◽

Equilibration Time ◽

Ruditapes Decussatus ◽

Larval Stages ◽

Long Term Storage ◽

Declining Species ◽

Conservation Of Endangered Species

AbstractCryopreservation is the only reliable method for long-term storage of biological material that guarantees genetic stability. This technique can be extremely useful for the conservation of endangered species and restock natural populations for declining species. Many factors have negatively affected the populations of high economical value shellfish in Spain and, as a result, many are declining or threatened nowadays. This study was focused on early-life stages of Venerupis corrugata, Ruditapes decussatus and Ruditapes philippinarum to develop successful protocols to enhance the conservation effort and sustainable shellfishery resources. Firstly, common cryoprotecting agents (CPAs) were tested to select the suitable permeable CPA attending to toxicity. Cryopreservation success using different combinations of CPA solutions, increasing equilibrium times and larval stages was evaluated attending to survival and shell growth at 2 days post-thawing. Older clam development stages were more tolerant to CPA toxicity, being ethylene-glycol (EG) and Propylene-glycol (PG) the least toxic CPAs. CPA solution containing EG yielded the highest post-thawing survival rate and the increase of equilibration time was not beneficial for clam larvae. Cryopreservation of trochophores yielded around 50% survivorship, whereas over 80% of cryopreserved D-larvae were able to recover after thawing.

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Molecular Phylogenetic Diversity and Biological Characterization of Diaporthe Species Associated with Leaf Spots of Camellia sinensis in Taiwan

Plants ◽

10.3390/plants10071434 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1434

Author(s):

Hiran A. Ariyawansa ◽

Ichen Tsai ◽

Jian-Yuan Wang ◽

Patchareeya Withee ◽

Medsaii Tanjira ◽

...

Keyword(s):

Camellia Sinensis ◽

Leaf Spot ◽

Phylogenetic Trees ◽

Fungal Infections ◽

Elongation Factor ◽

Fungal Species ◽

Tea Leaves ◽

Phenotypic Characters ◽

Leaf Spots ◽

Molecular Phylogenetic

Camellia sinensis is one of the major crops grown in Taiwan and has been widely cultivated around the island. Tea leaves are prone to various fungal infections, and leaf spot is considered one of the major diseases in Taiwan tea fields. As part of a survey on fungal species causing leaf spots on tea leaves in Taiwan, 19 fungal strains morphologically similar to the genus Diaporthe were collected. ITS (internal transcribed spacer), tef1-α (translation elongation factor 1-α), tub2 (beta-tubulin), and cal (calmodulin) gene regions were used to construct phylogenetic trees and determine the evolutionary relationships among the collected strains. In total, six Diaporthe species, including one new species, Diaporthe hsinchuensis, were identified as linked with leaf spot of C. sinensis in Taiwan based on both phenotypic characters and phylogeny. These species were further characterized in terms of their pathogenicity, temperature, and pH requirements under laboratory conditions. Diaporthe tulliensis, D. passiflorae, and D. perseae were isolated from C. sinensis for the first time. Furthermore, pathogenicity tests revealed that, with wound inoculation, only D. hongkongensis was pathogenic on tea leaves. This investigation delivers the first assessment of Diaporthe taxa related to leaf spots on tea in Taiwan.

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Effects of the diploidisation process upon the 5S and 35S rDNA sequences in the allopolyploid species of the Dilatata group of Paspalum (Poaceae, Paniceae)

Australian Journal of Botany ◽

10.1071/bt18236 ◽

2019 ◽

Vol 67 (7) ◽

pp. 521

Author(s):

Magdalena Vaio ◽

Cristina Mazzella ◽

Marcelo Guerra ◽

Pablo Speranza

Keyword(s):

Evolutionary Dynamics ◽

In Situ Hybridisation ◽

5S Rdna ◽

Its Region ◽

Variable Number ◽

Rrna Genes ◽

Fluorescence In Situ Hybridisation ◽

Rdna Sites ◽

35S Rdna ◽

Genome Restructuring

The Dilatata group of Paspalum includes species and biotypes native to temperate South America. Among them, five sexual allotetraploids (x = 10) share the same IIJJ genome formula: P. urvillei Steud, P. dasypleurum Kunze ex Desv., P. dilatatum subsp. flavescens Roseng., B.R. Arrill. & Izag., and two biotypes P. dilatatum Vacaria and P. dilatatum Virasoro. Previous studies suggested P. intermedium Munro ex Morong & Britton and P. juergensii Hack. or related species as their putative progenitors and donors of the I and J genome, respectively, and pointed to a narrow genetic base for their maternal origin. It has not yet been established whether the various members of the Dilatata group are the result of a single or of multiple allopolyploid formations. Here, we aimed to study the evolutionary dynamics of rRNA genes after allopolyploidisation in the Dilatata group of Paspalum and shed some light into the genome restructuring of the tetraploid taxa with the same genome formula. We used double target fluorescence in situ hybridisation of 35S and 5S rDNA probes and sequenced the nrDNA internal transcribed spacer (ITS) region. A variable number of loci at the chromosome ends were observed for the 35S rDNA, from 2 to 6, suggesting gain and loss of sites. For the 5S rDNA, only one centromeric pair of signals was observed, indicating a remarkable loss after polyploidisation. All ITS sequences generated were near identical to the one found for P. intermedium. Although sequences showed a directional homogeneisation towards the putative paternal progenitor in all tetraploid species, the observed differences in the number and loss of rDNA sites suggest independent ongoing diploidisation processes in all taxa and genome restructuring following polyploidy.

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Reproductive cycle of the Manila clam (Ruditapes philippinarum): an intensively harvested invasive species in the Tagus Estuary (Portugal)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315417001382 ◽

2017 ◽

Vol 98 (7) ◽

pp. 1645-1657 ◽

Cited By ~ 5

Author(s):

Paula Moura ◽

Paulo Vasconcelos ◽

Fábio Pereira ◽

Paula Chainho ◽

José Lino Costa ◽

...

Keyword(s):

Invasive Species ◽

Reproductive Cycle ◽

Sexual Maturity ◽

Ruditapes Philippinarum ◽

Manila Clam ◽

Tagus Estuary ◽

Gonad Maturation ◽

Oocyte Diameter ◽

Ruditapes Decussatus ◽

Spawning Period

The present study aimed to describe the reproductive cycle and estimate the size at sexual maturity of the Manila clam (Ruditapes philippinarum) in the Tagus Estuary (Portugal). Specimens were collected monthly from September 2013 to December 2015 during fishing surveys using bivalve dredges. The gametogenic cycle was described in detail using gonad histology and monitored throughout the study period by the monthly variation in the frequency of gonad maturation stages, mean gonadal index and mean oocyte diameter. This invasive population of R. philippinarum displayed synchronous gonadal development between sexes, with ripening occurring mainly in April and May followed by an extensive spawning period until November–December. Individuals reached the size at first sexual maturity at 29.4 mm in shell length (i.e. before 1 year old). Furthermore, the reproductive strategy, dynamics and potential were compared between the invasive R. philippinarum and the native congeneric carpet shell clam (Ruditapes decussatus). Overall, the data gathered in this study constitutes valuable baseline information to propose conservation strategies and implement management measures to minimize the harmful impacts caused by this invasive species on local ecosystems and native biodiversity, particularly over populations of autochthonous bivalves.

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Comparative study of gonadal development of Ruditapes philippinarum (Adams and Reeve) and Ruditapes decussatus (L.) (Mollusca: Bivalvia): Influence of temperature

Scientia Marina ◽

10.3989/scimar.2007.71n3471 ◽

2007 ◽

Vol 71 (3) ◽

pp. 471-484 ◽

Cited By ~ 39

Author(s):

Marina Delgado ◽

Alejandro Pérez-Camacho

Keyword(s):

Comparative Study ◽

Gonadal Development ◽

Ruditapes Philippinarum ◽

Ruditapes Decussatus ◽

Influence Of Temperature

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Can the Cambrian explosion be inferred through molecular phylogeny?

Development ◽

10.1242/dev.1994.supplement.15 ◽

1994 ◽

Vol 1994 (Supplement) ◽

pp. 15-25

Author(s):

Hervé Philippe ◽

Anne Chenuil ◽

André Adoutte

Keyword(s):

Phylogenetic Trees ◽

18S Rrna ◽

Phylogenetic Reconstruction ◽

Cambrian Explosion ◽

Bootstrap Support ◽

Time Interval ◽

Short Time Interval ◽

Data Set ◽

Molecular Phylogenetic ◽

Animal Phyla

Most of the major invertebrate phyla appear in the fossil record during a relatively short time interval, not exceeding 20 million years (Myr), 540-520 Myr ago. This rapid diversification is known as the `Cambrian explosion'. In the present paper, we ask whether molecular phylogenetic reconstruction provides confirmation for such an evolutionary burst. The expectation is that the molecular phylogenetic trees should take the form of a large unresolved multifurcation of the various animal lineages. Complete 18S rRNA sequences of 69 extant representatives of 15 animal phyla were obtained from data banks. After eliminating a major source of artefact leading to lack of resolution in phylogenetic trees (mutational saturation of sequences), we indeed observe that the major lines of triploblast coelomates (arthropods, molluscs, echinoderms, chordates...) are very poorly resolved i.e. the nodes defining the various clades are not supported by high bootstrap values. Using a previously developed procedure consisting of calculating bootstrap proportions of each node of the tree as a function of increasing amount of nucleotides (Lecointre, G., Philippe, H. Le, H. L. V. and Le Guyader, H. (1994) Mol. Phyl. Evol., in press) we obtain a more informative indication of the robustness of each node. In addition, this procedure allows us to estimate the number of additional nucleotides that would be required to resolve confidently the currently uncertain nodes; this number turns out to be extremely high and experimentally unfeasible. We then take this approach one step further: using parameters derived from the above analysis, assuming a molecular clock and using palaeontological dates for calibration, we establish a relationship between the number of sites contained in a given data set and the time interval that this data set can confidently resolve (with 95% bootstrap support). Under these assumptions, the presently available 18S rRNA database cannot confidently resolve cladogenetic events separated by less than about 40 Myr. Thus, at the present time, the potential resolution by the palaeontological approach is higher than that by the molecular one.

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