scholarly journals Chromosomal Characterization of Tripidium arundinaceum Revealed by Oligo-FISH

2021 ◽  
Vol 22 (16) ◽  
pp. 8539
Author(s):  
Fan Yu ◽  
Jin Chai ◽  
Xueting Li ◽  
Zehuai Yu ◽  
Ruiting Yang ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Cytogenetic Study ◽  
Economic Value ◽  
5S Rdna ◽  
Chromosome Markers ◽  
Sugarcane Varieties ◽  
35S Rdna ◽  
Sequential Fish ◽  
Painting Probes

Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum. Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum, even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum. Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding.

Characterization of genome in tetraploid StY species of Elymus (Triticeae: Poaceae) using sequential FISH and GISH

Genome ◽  
2017 ◽  
Vol 60 (8) ◽  
pp. 679-685 ◽  
Author(s):  
Ruijuan Liu ◽  
Richard R.-C. Wang ◽  
Feng Yu ◽  
Xingwang Lu ◽  
Quanwen Dou
Keyword(s):  
In Situ Hybridization ◽  
5S Rdna ◽  
Type I ◽  
Genomic Variations ◽  
26S Rdna ◽  
Close Relationship ◽  
Species Type ◽  
Sequential Fish

Genomes of ten species of Elymus, either presumed or known as tetraploid StY, were characterized using fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH). These tetraploid species could be grouped into three categories. Type I included StY genome reported species—Roegneria pendulina, R. nutans, R. glaberrima, R. ciliaris, and Elymus nevskii, and StY genome presumed species—R. sinica, R. breviglumis, and R. dura, whose genome could be separated into two sets based on different GISH intensities. Type I genome constitution was deemed as putative StY. The St genome were mainly characterized with intense hybridization with pAs1, fewer AAG sites, and linked distribution of 5S rDNA and 18S-26S rDNA, while the Y genome with less intense hybridization with pAs1, more varied AAG sites, and isolated distribution of 5S rDNA and 18S-26S rDNA. Nevertheless, further genomic variations were detected among the different StY species. Type II included E. alashanicus, whose genome could be easily separated based on GISH pattern. FISH and GISH patterns suggested that E. alashanicus comprised a modified St genome and an unknown genome. Type III included E. longearistatus, whose genome could not be separated by GISH and was designated as StlYl. Notably, a close relationship between Sl and Yl genomes was observed.

Parental origin and genome evolution of several Eurasian hexaploid species of Chenopodium (Chenopodiaceae)

Phytotaxa ◽  
2019 ◽  
Vol 392 (3) ◽  
pp. 163 ◽  
Author(s):  
BOZENA KOLANO ◽  
JAMIE McCANN ◽  
MAJA OSKĘDRA ◽  
MARCELINA CHRAPEK ◽  
MAGDALENA ROJEK ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
5S Rdna ◽  
The Other ◽  
Parental Origin ◽  
B Genome ◽  
Rdna Loci ◽  
History Of ◽  
35S Rdna

Hybridization and polyploidization appear to be ubiquitous in the evolution of Chenopodium s.s., but the origin and the evolutionary history of the polyploid chenopods is still poorly understood. Phylogenetic analyses of DNA sequences of nrITS, four plastid regions, and 5S rDNA spacer region (NTS) of five Eurasian hexaploid chenopods (2n = 6x = 54), C. album, C. giganteum, C. pedunculare C. formosanum and C. opulifolium, and their diploid and tetraploid relatives as well as genomic in situ hybridization (GISH) indicate their allohexaploid origin. The origin of all the analyzed hexaploids have been inferred to have involved B-genome diploid. The identity of the other parent/parents is more elusive. In the case of C. album, C. giganteum and C. pedunculare the second maternal parent seems to be similar to extant C. strictum or C. striatiforme or Asian diploids (e.g. C. acuminatum). In genomes of allohexaploid C. album, C. giganteum and C. pedunculare half of the rDNA were located in the chromosomes of B-subgenome. The remaining rDNA loci were placed in chromosomes originating from the other parent/parents. Although 35S rDNA loci inherited from two parental species seems to be present in these hexaploids, only one ribotype of nrITS was detected.

scholarly journals Molecular cytogenetic study of Eranthis (Ranunculaceae)

2021 ◽  
Vol 20 (1) ◽  
pp. 305-308
Author(s):  
E. Yu. Mitrenina ◽  
A. S. Erst ◽  
E. D. Badaeva ◽  
S. S. Alekseeva ◽  
G. N. Artemov
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Ribosomal Dna ◽  
Cytogenetic Study ◽  
5S Rdna ◽  
45S Rdna ◽  
5.8S Rdna ◽  
Molecular Cytogenetic ◽  
Specific Hybridization

45S and 5S ribosomal DNA were originally localized on chromosomes of five species of winter aconits,namely, Eranthis cilicica, E. hyemalis (section Eranthis), E. pinnatifida, E. stellata и E. tanhoensis (section Shibateranthis).Fluorescence in situ hybridization was performed with oligonucleotide DNA probes Oligo-pTa71-2 and Oligo-5S rDNAof wheat that are complementary to 45S and 5S ribosomal DNA. In addition, oligonucleotide DNA probe (Oligo-5.8SrDNA-Ran, 50 b) for localization of 45S rDNA was designed and tested. This probe is based on the 5.8S rDNA sequencesof some species of fam. Ranunculaceae taken from GenBank. A specific hybridization of the Oligo-5S rDNA and Oligo5.8S rDNA-Ran probes with the chromosomes of Eranthis was shown. The use of the Oligo-pTa71-2 probe did not localizeclusters of 45S rDNA on chromosomes of studied species.

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

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.

A gene with sequence similarity to Drosophila engrailed is expressed during the development of the neural tube and vertebrae in the mouse

Development ◽  
1988 ◽  
Vol 104 (2) ◽  
pp. 305-316 ◽  
Author(s):  
D. Davidson ◽  
E. Graham ◽  
C. Sime ◽  
R. Hill
Keyword(s):  
In Situ Hybridization ◽  
Neural Tube ◽  
Mouse Embryo ◽  
Sequence Similarity ◽  
Anterior Part ◽  
Limb Bud ◽  
Tissue Type ◽  
Restricted Domains ◽  
Restricted Region

The mouse genes En-1 and En-2 display sequence similarity, in and around the homeobox region, to the engrailed family in Drosophila. This paper describes their pattern of expression in the 12.5-day mouse embryo as determined by in situ hybridization. En-2 is expressed in a subset of cells expressing En-1. Both genes are expressed in the developing midbrain and its junction with the hindbrain. In addition, En-1 is expressed in the floor of the hindbrain, a restricted ventrolateral segment of the neural tube throughout the trunk and anterior part of the tail, the dermatome of tail somites, the centrum and costal processes in developing vertebrae, a restricted region of facial mesenchyme and the limb-bud ectoderm. Supplementary studies of 9.5-day and 10.5-day embryos showed that the same pattern of expression pertained in the neural tube, but that expression in the somites is at first confined to the dermatome and later found at a low level in restricted sclerotomal regions. Both genes are expressed in restricted domains which do not cross tissue-type boundaries. In several instances, however, boundaries of expression lie within morphologically undifferentiated tissue. These results suggest that En-1 and En-2 may be involved in the establishment or maintenance of the spatial integrity of specific domains within developing tissues.

Chromosome Banding in Amphibia. XXXV. Highly Mobile Nucleolus Organizing Regions in Craugastor fitzingeri (Anura, Craugastoridae)

2017 ◽  
Vol 152 (4) ◽  
pp. 180-193 ◽  
Author(s):  
Michael Schmid ◽  
Claus Steinlein ◽  
Wolfgang Feichtinger ◽  
Indrajit Nanda
Keyword(s):  
Chromosome Banding ◽  
Cytogenetic Study ◽  
Variable Number ◽  
28S Rdna ◽  
Fish Analysis ◽  
Intraindividual Variation ◽  
Length Polymorphisms ◽  
Somatic Tissues

A 7-year cytogenetic study on the leaf litter frog Craugastor fitzingeri from Costa Rica and Panama revealed the existence of highly mobile nucleolus organizing regions (NORs) in their genomes. Silver (Ag)-staining of the active NORs demonstrated an exceptional interindividual pattern of NOR distribution at the telomeres of the chromosomes. All individuals examined showed a different and specific NOR location in their karyotypes. Furthermore, intraindividual variation in the NOR sites was found. This observation suggested the existence of mobile NORs in C. fitzingeri. Confirmation of this phenomenon was possible by systematic FISH analysis using an 18S + 28S rDNA probe. The extremely variable number and position of the NORs in C. fitzingeri is best explained by highly mobile NORs that move freely between the telomeres of the chromosomes. These transpositions must occur preferentially in premeiotic, meiotic, or postmeiotic stages, but also at a lower incidence in the somatic tissues of the animals. It is hypothesized that transposable (mobile) elements are closely linked to the NORs or are inserted into the major 18S + 28S rDNA spacers of C. fitzingeri. When such transposable elements spread by transpositions, they can carry with them complete or partial NORs. The present study provides detailed information on various differential chromosome banding techniques, in situ hybridization experiments, chromosomal hypermethylation patterns, determination of the genome size, and analyses of restriction fragment length polymorphisms of the DNA.

scholarly journals Interindividual size heteromorphism of NOR and chromosomal location of 5S rRNA genes in Iheringichthys labrosus

2007 ◽  
Vol 50 (1) ◽  
pp. 141-146 ◽  
Author(s):  
Rafael Augusto de Carvalho ◽  
Ana Lúcia Dias
Keyword(s):  
Chromosomal Location ◽  
5S Rdna ◽  
Rrna Genes ◽  
Telomeric Region ◽  
Fluorescent Staining ◽  
Homologous Chromosomes ◽  
Rdna Probe ◽  
5S Rrna Genes ◽  
Iheringichthys Labrosus

Twenty-five specimens of Iheringichthys labrosus from the Capivara Reservoir were analysed cytogenetically. AgNORs were detected in a pair of ST chromosomes, in the telomeric region of the long arm. Some individuals showed size heteromorphism of this region between homologous chromosomes. Treatment with CMA3 displayed GC-rich regions corresponding to the AgNOR pair, plus other fluorescent staining. In situ hybridization by fluorescence (FISH) with the 18S rDNA probe showed only one pair of stained chromosomes, confirming the heteromorphism observed with AgNO3 and CMA3 in some individuals. The 5S rDNA probe revealed telomeric staining on the long arm of a pair of chromosomes of the ST-A group, probably different from the NOR pair.

scholarly journals The hormone neuroparsin seems essential in Lepidoptera but not in domesticated silkworms

2019 ◽  
Author(s):  
Jan A. Veenstra
Keyword(s):  
Bombyx Mori ◽  
Genome Assembly ◽  
Galleria Mellonella ◽  
Sequence Similarity ◽  
Neuroendocrine Cells ◽  
Primary Sequence ◽  
Genome Assemblies ◽  
Limited Sequence ◽  
Wax Moth

AbstractThe primary sequence of the Arthropod neurohormone neuroparsin is so variable that so far no orthologs from moths and butterflies have been characterized, even though classical neurosecretory stains identify cells that are homologous to those producing this hormone in other insect species. Here Lepidopteran cDNAs showing limited sequence similarity to other insect neuroparsins are described. That these cDNAs do indeed code for authentic neuroparsins was confirmed by in situ hybridization in the wax moth, Galleria mellonella, which labeled the neuroparsin neuroendocrine cells. Although in virtually all genome assemblies from Lepidoptera a neuroparsin gene could be identified, the genome assembly from the silkworm, Bombyx mori, has a neuroparsin gene containing a 16 nucleotide deletion that renders this gene nonfunctional. Although only a small number of all silkworm strains carry this deletion, it suggests that the domestication of the silkworm has rendered the function of this neurohormone dispensable.

scholarly journals DISTRIBUTION AND SURVIVAL OF MEGAPODIUS REINWARDT FOR ECOTOURISM CONTRIBUTING ON MOYO ISLAND

2018 ◽  
Vol 18 (2) ◽  
Author(s):  
Muhammad Yamin ◽  
Khaeruddin Khaeruddin
Keyword(s):  
Population Distribution ◽  
Economic Value ◽  
Bird Species ◽  
Research Data ◽  
Primary Forest ◽  
Ecological Role ◽  
Active Nest ◽  
In Captivity ◽  
Distribution Mapping

Abstract: Megapodius reinwardt is one of the protected bird species in Indonesia. The protection toward megapodius reinwardt because of limited distribution, high economic value, has an important ecological role, has a unique, difficult breeding in captivity, the population is drastically shrinking and getting scarce.Based on this condition, the purpose of this research is to know population distribution mapping, active nest study, disturber population in order to support the atraction tourism and conservation of Megapodius reinwardt at Moyo island. Survey and observation are used to collect research data. The distributionofMegapodius reinwardt is spread around Moyo Island. The nest is located in the forest and it build by heap of soil with high 150 centimeters until 175 centimeters and diameters up to 825 cm. The location of Megapodius reinwardtnests are mostly in secundary forest than primary forest and savana at 25 m above sea level. The r-product moment correlation coefficient (r = 0,484) conclude that, Varanus sp, Sus barbatus, Prinodon linsang, Haliastur indus, Microhierax fringillarius, and human as predators are not significant to influence the nests and population of Megapodius reinwardtdecrease. So the existence of Megapodius reinwardtmanagement is needed according to in-situ cencervation on Moyo Island forEcotourism Contributing Keywords:   Ecotourism, distribution, Megapodius, survival.

scholarly journals Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active

2018 ◽  
Author(s):  
Estelle Couradeau ◽  
Joelle Sasse ◽  
Danielle Goudeau ◽  
Nandita Nath ◽  
Terry C. Hazen ◽  
...  
Keyword(s):  
Soil Microbes ◽  
Sequence Similarity ◽  
Large Fraction ◽  
Amplicon Sequencing ◽  
Bulk Soil ◽  
Soil Microbiome ◽  
Active Fraction ◽  
Soil Microbial Diversity ◽  
Oak Ridge

AbstractThe ability to link soil microbial diversity to soil processes requires technologies that differentiate active subpopulations of microbes from so-called relic DNA and dormant cells. Measures of microbial activity based on various techniques including DNA labelling have suggested that most cells in soils are inactive, a fact that has been difficult to reconcile with observed high levels of bulk soil activities. We hypothesized that measures of in situ DNA synthesis may be missing the soil microbes that are metabolically active but not replicating, and we therefore applied BONCAT (Bioorthogonal Non Canonical Amino Acid Tagging) i.e. a proxy for activity that does not rely on cell division, to measure translationally active cells in soils. We compared the active population of two soil depths from Oak Ridge (TN) incubated under the same conditions for up to seven days. Depending on the soil, a maximum of 25 – 70% of the cells were active, accounting for 3-4 million cells per gram of soil type, which is an order of magnitude higher than previous estimates. The BONCAT positive cell fraction was recovered by fluorescence activated cell sorting (FACS) and identified by 16S rDNA amplicon sequencing. The diversity of the active fraction was a selected subset of the bulk soil community. Excitingly, some of the same members of the community were recruited at both depths independently from their abundance rank. On average, 86% of sequence reads recovered from the active community shared >97% sequence similarity with cultured isolates from the field site. Our observations are in line with a recent report that, of the few taxa that are both abundant and ubiquitous in soil, 45% are also cultured – and indeed some of these ubiquitous microorganisms were found to be translationally active. The use of BONCAT on soil microbiomes provides evidence that a large portion of the soil microbes can be active simultaneously. We conclude that BONCAT coupled to FACS and sequencing is effective for interrogating the active fraction of soil microbiomes in situ and provides new perspectives to link metabolic capacity to overall soil ecological traits and processes.

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