scholarly journals Karyotype Characterization of Nine Periwinkle Species (Gastropoda, Littorinidae)

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 517 ◽  
Author(s):  
Daniel García-Souto ◽  
Sandra Alonso-Rubido ◽  
Diana Costa ◽  
José Eirín-López ◽  
Emilio Rolán-Álvarez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Chromosome Numbers ◽  
Gene Clusters ◽  
Chromosomal Mapping ◽  
Closely Related Species ◽  
Submetacentric Chromosome ◽  
The Family ◽  
Littorina Arcana

Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Littorina arcana, L. saxatilis, and L. compressa, the flat periwinkles L. obtusata and L. fabalis, the common periwinkle L. littorea, the mangrove periwinkle Littoraria angulifera, the beaded periwinkle Cenchritis muricatus, and the small periwinkle Melarhaphe neritoides was performed. All species showed diploid chromosome numbers of 2n = 34, and karyotypes were mostly composed of metacentric and submetacentric chromosome pairs. None of the periwinkle species showed chromosomal differences between male and female specimens. The chromosomal mapping of major and minor rDNA and H3 histone gene clusters by fluorescent in situ hybridization demonstrated that the patterns of distribution of these DNA sequences were conserved among closely related species and differed among less related ones. All signals occupied separated loci on different chromosome pairs without any evidence of co-localization in any of the species.

scholarly journals Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches (Cobitis) and Their Clonal Hybrids

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 617
Author(s):  
Anatolie Marta ◽  
Dmitry Dedukh ◽  
Oldřich Bartoš ◽  
Zuzana Majtánová ◽  
Karel Janko
Keyword(s):  
Interspecific Hybridization ◽  
Dna Sequences ◽  
Species Determination ◽  
Closely Related Species ◽  
Evolutionary Force ◽  
Identification Of Species ◽  
Cytogenetic Characterization ◽  
Species Specific

Interspecific hybridization is a powerful evolutionary force. However, the investigation of hybrids requires the application of methodologies that provide efficient and indubitable identification of both parental subgenomes in hybrid individuals. Repetitive DNA, and especially the satellite DNA sequences (satDNA), can rapidly diverge even between closely related species, hence providing a useful tool for cytogenetic investigations of hybrids. Recent progress in whole-genome sequencing (WGS) offers unprecedented possibilities for the development of new tools for species determination, including identification of species-specific satDNA markers. In this study, we focused on spined loaches (Cobitis, Teleostei), a group of fishes with frequent interspecific hybridization. Using the WGS of one species, C. elongatoides, we identified seven satDNA markers, which were mapped by fluorescence in situ hybridization on mitotic and lampbrush chromosomes of C. elongatoides, C. taenia and their triploid hybrids (C. elongatoides × 2C. taenia). Two of these markers were chromosome-specific in both species, one had centromeric localization in multiple chromosomes and four had variable patterns between tested species. Our study provided a novel set of cytogenetic markers for Cobitis species and demonstrated that NGS-based development of satDNA cytogenetic markers may provide a very efficient and easy tool for the investigation of hybrid genomes, cell ploidy, and karyotype evolution.

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

scholarly journals Chromosome Mapping of Repetitive Sequences inRachycentron canadum(Perciformes: Rachycentridae): Implications for Karyotypic Evolution and Perspectives for Biotechnological Uses

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Uedson Pereira Jacobina ◽  
Marcelo de Bello Cioffi ◽  
Luiz Gustavo Rodrigues Souza ◽  
Leonardo Luiz Calado ◽  
Manoel Tavares ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Chromosome Mapping ◽  
Karyotypic Evolution ◽  
Dapi Staining ◽  
Telomeric Sequences ◽  
Replication Banding ◽  
The Family ◽  
Early Replication

The cobia,Rachycentron canadum, a species of marine fish, has been increasingly used in aquaculture worldwide. It is the only member of the family Rachycentridae (Perciformes) showing wide geographic distribution and phylogenetic patterns still not fully understood. In this study, the species was cytogenetically analyzed by different methodologies, including Ag-NOR and chromomycin A3(CMA3)/DAPI staining, C-banding, early replication banding (RGB), andin situfluorescent hybridization with probes for 18S and 5S ribosomal genes and for telomeric sequences (TTAGGG)n. The results obtained allow a detailed chromosomal characterization of the Atlantic population. The chromosome diversification found in the karyotype of the cobia is apparently related to pericentric inversions, the main mechanism associated to the karyotypic evolution of Perciformes. The differential heterochromatin replication patterns found were in part associated to functional genes. Despite maintaining conservative chromosomal characteristics in relation to the basal pattern established for Perciformes, some chromosome pairs in the analyzed population exhibit markers that may be important for cytotaxonomic, population, and biodiversity studies as well as for monitoring the species in question.

scholarly journals A Previously Uncharacterized, Nonphotosynthetic Member of the Chromatiaceae Is the Primary CO2-Fixing Constituent in a Self-Regenerating Biocathode

2014 ◽  
Vol 81 (2) ◽  
pp. 699-712 ◽  
Author(s):  
Zheng Wang ◽  
Dagmar H. Leary ◽  
Anthony P. Malanoski ◽  
Robert W. Li ◽  
W. Judson Hervey ◽  
...  
Keyword(s):  
Microbial Fuel Cells ◽  
Iron Oxidation ◽  
Extracellular Electron Transfer ◽  
Hydrogen Electrode ◽  
Content Type ◽  
Iron Oxidizing Bacteria ◽  
Distinct Cluster ◽  
The Family

ABSTRACTBiocathode extracellular electron transfer (EET) may be exploited for biotechnology applications, including microbially mediated O2reduction in microbial fuel cells and microbial electrosynthesis. However, biocathode mechanistic studies needed to improve or engineer functionality have been limited to a few select species that form sparse, homogeneous biofilms characterized by little or no growth. Attempts to cultivate isolates from biocathode environmental enrichments often fail due to a lack of some advantage provided by life in a consortium, highlighting the need to study and understand biocathode consortiain situ. Here, we present metagenomic and metaproteomic characterization of a previously described biocathode biofilm (+310 mV versus a standard hydrogen electrode [SHE]) enriched from seawater, reducing O2, and presumably fixing CO2for biomass generation. Metagenomics identified 16 distinct cluster genomes, 15 of which could be assigned at the family or genus level and whose abundance was roughly divided betweenAlpha- andGammaproteobacteria. A total of 644 proteins were identified from shotgun metaproteomics and have been deposited in the the ProteomeXchange with identifier PXD001045. Cluster genomes were used to assign the taxonomic identities of 599 proteins, withMarinobacter,Chromatiaceae, andLabrenziathe most represented. RubisCO and phosphoribulokinase, along with 9 other Calvin-Benson-Bassham cycle proteins, were identified fromChromatiaceae. In addition, proteins similar to those predicted for iron oxidation pathways of known iron-oxidizing bacteria were observed forChromatiaceae. These findings represent the first description of putative EET and CO2fixation mechanisms for a self-regenerating, self-sustaining multispecies biocathode, providing potential targets for functional engineering, as well as new insights into biocathode EET pathways using proteomics.

Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1061-1069 ◽  
Author(s):  
A. Cuadrado ◽  
N. Jouve ◽  
C. Ceoloni
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
5S Rdna ◽  
Individual Identification ◽  
Highly Repetitive Dna ◽  
The Individual

The molecular characterization of heterochromatin in six lines of rye has been performed using fluorescence in situ hybridization (FISH). The highly repetitive rye DNA sequences pSc 119.2, pSc74, and pSc34, and the probes pTa71 and pSc794 containing the 25S–5.8S–18S rDNA (NOR) and the 5S rDNA multigene families, respectively, were used. This allowed the individual identification of all seven rye chromosomes and most chromosome arms in all lines. All varieties showed similar but not identical patterns. A standard in situ hybridization map was constructed following the nomenclature system recommended for C-bands. All FISH sites observed appeared to correspond well with C-band locations, but not all C-banding sites coincided with hybridization sites of the repetitive DNA probes used. Quantitative and qualitative differences between different varieties were found for in situ hybridization response at corresponding sites. Variation between plants and even between homologous chromosomes of the same plant was found in open-pollinated lines. In inbred lines, the in situ pattern of the homologues was practically identical and no variation between plants was detected. The observed quantitative and qualitative differences are consistent with a corresponding variation for C-bands detected both within and between cultivars.Key words: fluorescence in situ hybridization, repetitive DNA, rye, Secale cereale, polymorphism.

U1 snDNA chromosomal mapping in ten spittlebug species (Cercopidade, Auchenorrhyncha, Hemiptera)

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 59-62 ◽  
Author(s):  
Allison Anjos ◽  
Andressa Paladini ◽  
Tatiane C. Mariguela ◽  
Diogo C. Cabral-de-Mello
Keyword(s):  
Evolutionary Dynamics ◽  
Chromosomal Mapping ◽  
Holocentric Chromosomes ◽  
Interstitial Position ◽  
Repetitive Dnas ◽  
Snrna Gene ◽  
Pasture Grasses ◽  
The Family ◽  
U1 Snrna

Spittlebugs, which belong to the family Cercopidae (Auchenorrhyncha, Hemiptera), form a large group of xylem-feeding insects that are best known for causing damage to plantations and pasture grasses. The holocentric chromosomes of these insects remain poorly studied in regards to the organization of different classes of repetitive DNA. To improve chromosomal maps based on repetitive DNAs and to better understand the chromosomal organization and evolutionary dynamics of multigene families in spittlebugs, we physically mapped the U1 snRNA gene with fluorescence in situ hybridization (FISH) in 10 species of Cercopidae belonging to three different genera. All the U1 snDNA clusters were autosomal and located in interstitial position. In seven species, they were restricted to one autosome per haploid genome, while three species of the genus Mahanarva showed two clusters in two different autosomes. Although it was not possible to precisely define the ancestral location of this gene, it was possible to observe the presence of at least one cluster located in a small bivalent in all karyotypes. The karyotype stability observed in Cercopidae is also observed in respect to the distribution of U1 snDNA. Our data are discussed in light of possible mechanisms for U1 snDNA conservation and compared with the available data from other species.

scholarly journals Structure and characterization of the ribosomal transcription units of small liver flukes, Opisthorchis viverrini, O. Felineus and Clonorchis sinensis

2020 ◽  
Vol 17 (3) ◽  
pp. 441-447
Author(s):  
Le Thanh Hoa ◽  
Nguyen Thi Bich Nga ◽  
Doan Thi Thanh Huong ◽  
Le Thi Kim Xuyen ◽  
Nguyen Thi Khue
Keyword(s):  
Dna Sequences ◽  
Liver Fluke ◽  
Clonorchis Sinensis ◽  
Parasitic Infection ◽  
Nucleotide Sequences ◽  
Opisthorchis Viverrini ◽  
The Family ◽  
Liver Flukes ◽  
Family Classification

Opisthorchiasis is a zoonotic parasitic infection caused by small liver fluke species, Opisthorchis viverrini,O. felineus and Clonorchis sinensis, in the family Opisthorchiidae. Vietnam has both species, of which C.sinensis is distributed in the northern and O. viverrini in the central provinces. In addition to the mitochondrialgenomes, the ribosomal DNA sequences (rDNA) of these species are highly needed to obtain for providingmolecular markers in species identification, classification, phylogeny and evolutionary studies. In this study,the near/complete nucleotide sequences of ribosomal transcription units (rTU) from O. viverrini (Vietnamesesample), O. felineus (Russian sample) and C. sinensis (Vietnamese sample) were analyzed. All rTUs for threespecies were determined, which is 7,839 bp for O. viverrini, 6,948 bp for O. felineus and 7,296 bp for C.sinensis containing structures of 18S, ITS1, 5,8S, ITS2 and 28S. The IGS region was not obtained for all threespecies. In all three species, sequence analysis revealed 2 tandem repetitive elements of 47-48 bp/each in ITS1but not in ITS2. The nucleotide sequences of 18S, ITS1, ITS2 and 28S are valuable ribosomal markers that thisstudy provides for diagnosis, identification, taxonomic classification and population genetics. In conclusion,the rTU sequences for the three species of the family Opisthorchiidae have been identified and providesmolecular markers for the use of phylogenetic analysis for species/family classification in the superfamilyOpisthorchioidea and the class Trematoda.

scholarly journals Chromosome Painting in Cultivated Bananas and Their Wild Relatives (Musa spp.) Reveals Differences in Chromosome Structure

2020 ◽  
Vol 21 (21) ◽  
pp. 7915
Author(s):  
Denisa Šimoníková ◽  
Alžběta Němečková ◽  
Jana Čížková ◽  
Allan Brown ◽  
Rony Swennen ◽  
...  
Keyword(s):  
Chromosome Structure ◽  
Diploid Species ◽  
Cross Hybridization ◽  
The Family ◽  
Structural Chromosome ◽  
Cytogenetic Characterization ◽  
Musa Species ◽  
Painting Probes

Edible banana cultivars are diploid, triploid, or tetraploid hybrids, which originated by natural cross hybridization between subspecies of diploid Musa acuminata, or between M. acuminata and diploid Musa balbisiana. The participation of two other wild diploid species Musa schizocarpa and Musa textilis was also indicated by molecular studies. The fusion of gametes with structurally different chromosome sets may give rise to progenies with structural chromosome heterozygosity and reduced fertility due to aberrant chromosome pairing and unbalanced chromosome segregation. Only a few translocations have been classified on the genomic level so far, and a comprehensive molecular cytogenetic characterization of cultivars and species of the family Musaceae is still lacking. Fluorescence in situ hybridization (FISH) with chromosome-arm-specific oligo painting probes was used for comparative karyotype analysis in a set of wild Musa species and edible banana clones. The results revealed large differences in chromosome structure, discriminating individual accessions. These results permitted the identification of putative progenitors of cultivated clones and clarified the genomic constitution and evolution of aneuploid banana clones, which seem to be common among the polyploid banana accessions. New insights into the chromosome organization and structural chromosome changes will be a valuable asset in breeding programs, particularly in the selection of appropriate parents for cross hybridization.

scholarly journals Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries

2020 ◽  
Vol 11 ◽  
Author(s):  
Neha Agrawal ◽  
Mehak Gupta ◽  
Surinder S. Banga ◽  
JS (Pat) Heslop-Harrison
Keyword(s):  
Structural Changes ◽  
Chromosomal Mapping ◽  
Structural Variations ◽  
Breeding Programs ◽  
Pak Choi ◽  
Bioinformatic Pipeline ◽  
A Genome ◽  
The Family

Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. It is difficult to distinguish Brassica chromosomes as they are small and morphologically similar. We aimed to develop a genome-sequence based cytogenetic toolkit for reproducible identification of Brassica chromosomes and their structural variations. A bioinformatic pipeline was used to extract repeat-free sequences from the whole genome assembly of B. rapa. Identified sequences were subsequently used to develop four c. 47-mer oligonucleotide libraries comprising 27,100, 11,084, 9,291, and 16,312 oligonucleotides. We selected these oligonucleotides after removing repeats from 18 identified sites (500–1,000 kb) with 1,997–5,420 oligonucleotides localized at each site in B. rapa. For one set of probes, a new method for amplification or immortalization of the library is described. oligonucleotide probes produced specific and reproducible in situ hybridization patterns for all chromosomes belonging to A, B, C, and R (Raphanus sativus) genomes. The probes were able to identify structural changes between the genomes, including translocations, fusions, and deletions. Furthermore, the probes were able to identify a structural translocation between a pak choi and turnip cultivar of B. rapa. Overall, the comparative chromosomal mapping helps understand the role of chromosome structural changes during genome evolution and speciation in the family Brassicaceae. The probes can also be used to identify chromosomes in aneuploids such as addition lines used for gene mapping, and to track transfer of chromosomes in hybridization and breeding programs.

Boeremia parva sp. nov., a novel species of the family Didymellaceae isolated from soil

Phytotaxa ◽  
2021 ◽  
Vol 518 (1) ◽  
pp. 25-35
Author(s):  
KALLOL DAS ◽  
LEONID N. TEN ◽  
JAE-HO BAN ◽  
SEUNG-YEOL LEE ◽  
HEE-YOUNG JUNG
Keyword(s):  
Dna Sequences ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
The Novel ◽  
Closely Related Species ◽  
The Family ◽  
Colony Color ◽  
Average Size ◽  
Isolated Species

Fungal strains, designated KNU-NL4 and KNU-OL2, belonging to the family Didymellaceae were isolated from a soil sample collected in Miryang, Korea. Phylogenetic analyses based on a concatenated dataset of DNA sequences of ITS regions and partial sequences of ACT, CAL, TEF1-α, and β-TUB genes showed that the isolates reside in a clade together with Boeremia species but occupy the distinct phylogenetic position. Morphologically, the novel strains produce bigger conidiomata (average size 169.8 μm) than the closely related B. rhapontica (126.59 μm) and smaller than the other close neighbor B. coffeae (187.5 μm). Both novel strains also differed from them by smaller colony size and colony color on OA and MEA. The detailed descriptions, illustrations, and discussions regarding the morphological and phylogenetic analyses of the closely related species are provided to support the novelty of the isolated species. The results of phylogenetic analysis and morphological observations indicate that strains KNU-NL4 and KNU-OL2 represent a novel species in the genus Boeremia, for which the name Boeremia parva sp. nov. is proposed.

Sign in / Sign up

Export Citation Format

Share Document