scholarly journals Chromosome Painting Provides Insights Into the Genome Structure and Evolution of Sugarcane

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhuang Meng ◽  
Qinnan Wang ◽  
Haris Khurshid ◽  
Ghulam Raza ◽  
Jinlei Han ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Genomic Structure ◽  
Genome Structure ◽  
Saccharum Officinarum ◽  
Chromosome 2 ◽  
Saccharum Spontaneum ◽  
High Level ◽  
Interspecific Recombination ◽  
Homoeologous Chromosomes

The genus Saccharum is composed of species with high polyploidy and highly varied chromosome numbers, laying a challenge for uncovering its genomic structure and evolution. We developed a chromosome 2 painting (CP2) probe by designing oligonucleotides covering chromosome 2 of Saccharum spontaneum (2n = 8x = 64). Fluorescence in situ hybridization (FISH) using this CP2 probe revealed six types of ploidies from twenty S. spontaneum clones, including 6x, 8x, 10x, 11x, 12x, and 13x clones. The finding of S. spontaneum clones with uneven of ploid suggested that certain S. spontaneum clones come from hybridization. It renews our knowledge that S. spontaneum is derived from autopolyploidization. Combined with a S. spontaneum-specific probe, chromosome 2-derived chromosome or fragments from either S. spontaneum or Saccharum officinarum can be identified in sugarcane modern cultivars. We revealed unexpected high level of interspecific recombination from introgressive S. spontaneum chromosomes (>50.0%) in cultivars ROC22 and ZZ1, indicating frequent chromosome exchange in cultivars. Intriguingly, we observed interspecific recombination recurring among either homoeologous or non-homoeologous chromosomes in sugarcane cultivars. These results demonstrated that chromosome painting FISH is a powerful tool in the genome dissection of sugarcane and provide new insights into the genome structure and evolution of the complex genus Saccharum.

scholarly journals Comparative genomic mapping reveals mechanisms of chromosome diversification in Rhipidomys species (Rodentia, Thomasomyini) and syntenic relationship between species of Sigmodontinae

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258474
Author(s):  
Vergiana dos Santos Paixão ◽  
Pablo Suárez ◽  
Willam Oliveira da Silva ◽  
Lena Geise ◽  
Malcolm Andrew Ferguson-Smith ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Chromosomal Rearrangements ◽  
Chromosomal Evolution ◽  
Wide Distribution ◽  
Comparative Genomic ◽  
Syntenic Block ◽  
Syntenic Relationship ◽  
Pericentric Inversions ◽  
High Level

Rhipidomys (Sigmodontinae, Thomasomyini) has 25 recognized species, with a wide distribution ranging from eastern Panama to northern Argentina. Cytogenetic data has been described for 13 species with 12 of them having 2n = 44 with a high level of autosomal fundamental number (FN) variation, ranging from 46 to 80, assigned to pericentric inversions. The species are grouped in groups with low FN (46–52) and high FN (72–80). In this work the karyotypes of Rhipidomys emiliae (2n = 44, FN = 50) and Rhipidomys mastacalis (2n = 44, FN = 74), were studied by classical cytogenetics and by fluorescence in situ hybridization using telomeric and whole chromosome probes (chromosome painting) of Hylaeamys megacephalus (HME). Chromosome painting revealed homology between 36 segments of REM and 37 of RMA. We tested the hypothesis that pericentric inversions are the predominant chromosomal rearrangements responsible for karyotypic divergence between these species, as proposed in literature. Our results show that the genomic diversification between the karyotypes of the two species resulted from translocations, centromeric repositioning and pericentric inversions. The chromosomal evolution in Rhipidomys was associated with karyotypical orthoselection. The HME probes revealed that seven syntenic probably ancestral blocks for Sigmodontinae are present in Rhipidomys. An additional syntenic block described here is suggested as part of the subfamily ancestral karyotype. We also define five synapomorphies that can be used as chromosomal signatures for Rhipidomys.

DNA Barcoding and Phylogenetic Analysis Sugarcane (Saccharum officinarum L.) Based on matK ( maturase K) Gene

2020 ◽  
Vol 840 ◽  
pp. 162-170
Author(s):  
Ganies Riza Aristya ◽  
Fauzana Putri ◽  
Rina Sri Kasiamdari ◽  
Arni Musthofa
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Level ◽  
Economic Value ◽  
Saccharum Officinarum ◽  
Saccharum Spontaneum ◽  
Dna Barcodes ◽  
Pcr Method ◽  
Hybrid Cultivar ◽  
I Gene ◽  
Sequencing Process

Sugarcane (Saccharum officinarum L.) is an agricultural commodities with a great extent of diversity and high economic value. In Indonesia, the great extent of diversity of sugarcane is evidenced by a large number of cultivars cultivated. Sugarcane diversities at the molecular level can be seen using DNA barcodes, one of which is the matK. The purpose of the study was to identify and characterize matK and reconstruct the phylogenetic tree to determine the phylogeny of 24 sugarcane cultivars Indonesia. matK was amplified using the PCR method with matK F-5’ATGATTAATTAAGAGTAAGAGGAT-3’ and matK R-5’AATGCAAAAATTCGAAGGGT-3. Results showed that the matK gene was successfully amplified as many as 1531 bp. The sequencing process was done to determine the nucleotide sequence and compared with those of the GenBank database. It showed that the samples used had a similarity of 98.87%-99.44% to that of matK in Saccharum officinarum, Saccharum hybrid cultivar and Saccharum spontaneum. Reconstruction of the phylogenetic tree showed that the samples used were located in the same clade with a zero genetic distance, while all the references from NCBI were also located in the same clade. The analysis of genetic variation indicated that it had no haplotype value.

scholarly journals Wheat, Rye, and Barley Genomes Can Associate during Meiosis in Newly Synthesized Trigeneric Hybrids

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 113
Author(s):  
María-Dolores Rey ◽  
Carmen Ramírez ◽  
Azahara C. Martín
Keyword(s):  
Chromosome Segregation ◽  
Genome Duplication ◽  
Triticum Turgidum ◽  
Aegilops Tauschii ◽  
Genomic In Situ Hybridization ◽  
Hordeum Chilense ◽  
Genomic Constitution ◽  
Chromosome Associations ◽  
High Level

Polyploidization, or whole genome duplication (WGD), has an important role in evolution and speciation. One of the biggest challenges faced by a new polyploid is meiosis, in particular, discriminating between multiple related chromosomes so that only homologs recombine to ensure regular chromosome segregation and fertility. Here, we report the production of two new hybrids formed by the genomes of species from three different genera: a hybrid between Aegilops tauschii (DD), Hordeum chilense (HchHch), and Secale cereale (RR) with the haploid genomic constitution HchDR (n = 7× = 21); and a hybrid between Triticum turgidum spp. durum (AABB), H. chilense, and S. cereale with the constitution ABHchR (n = 7× = 28). We used genomic in situ hybridization and immunolocalization of key meiotic proteins to establish the chromosome composition of the new hybrids and to study their meiotic behavior. Interestingly, there were multiple chromosome associations at metaphase I in both hybrids. A high level of crossover (CO) formation was observed in HchDR, which shows the possibility of meiotic recombination between the different genomes. We succeeded in the duplication of the ABHchR genome, and several amphiploids, AABBHchHchRR, were obtained and characterized. These results indicate that recombination between the genera of three economically important crops is possible.

scholarly journals The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jung-Hyun Kim ◽  
Vladimir N. Noskov ◽  
Aleksey Y. Ogurtsov ◽  
Ramaiah Nagaraja ◽  
Nikolai Petrov ◽  
...  
Keyword(s):  
Genomic Structure ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Chromosome 21 ◽  
Reference Sequence ◽  
Chromosome 22 ◽  
Rdna Variation ◽  
High Level ◽  
Tar Cloning

AbstractThe rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.

scholarly journals Chromosomal painting of the sandpiper (Actitis macularius) detects several fissions for the Scolopacidae family (Charadriiformes)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Melquizedec Luiz Silva Pinheiro ◽  
Cleusa Yoshiko Nagamachi ◽  
Talita Fernanda Augusto Ribas ◽  
Cristovam Guerreiro Diniz ◽  
Patricia Caroline Mary O´Brien ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Diploid Number ◽  
Chromosomal Evolution ◽  
Long Distance ◽  
Chromosomal Painting ◽  
Cytogenetic Studies ◽  
Burhinus Oedicnemus ◽  
Clear Idea ◽  
First Time

Abstract Background The Scolopacidae family (Suborder Scolopaci, Charadriiformes) is composed of sandpipers and snipes; these birds are long-distance migrants that show great diversity in their behavior and habitat use. Cytogenetic studies in the Scolopacidae family show the highest diploid numbers for order Charadriiformes. This work analyzes for the first time the karyotype of Actitis macularius by classic cytogenetics and chromosome painting. Results The species has a diploid number of 92, composed mostly of telocentric pairs. This high 2n is greater than the proposed 80 for the avian ancestral putative karyotype (a common feature among Scolopaci), suggesting that fission rearrangements have formed smaller macrochromosomes and microchromosomes. Fluorescence in situ hybridization using Burhinus oedicnemus whole chromosome probes confirmed the fissions in pairs 1, 2, 3, 4 and 6 of macrochromosomes. Conclusion Comparative analysis with other species of Charadriiformes studied by chromosome painting together with the molecular phylogenies for the order allowed us to raise hypotheses about the chromosomal evolution in suborder Scolopaci. From this, we can establish a clear idea of how chromosomal evolution occurred in this suborder.

Some observations on rock weathering, Cumberland Peninsula, Baffin Island

1979 ◽  
Vol 16 (5) ◽  
pp. 977-983 ◽  
Author(s):  
Stephen H. Waits
Keyword(s):  
Salt Crystallization ◽  
Rock Weathering ◽  
Baffin Island ◽  
Significant Modification ◽  
Bedrock Weathering ◽  
Arctic Conditions ◽  
Selective Preservation ◽  
Mechanical Weathering ◽  
High Level

A variety of bedrock weathering features—both modern and remnant—including surface grus, polygonal cracks, siliceous glaze, tors, weathering pits, and tafoni typify upland outcrops on the Cumberland Peninsula. Tor ridges are particularly prevalent and at lower elevations they show significant modification and streamlining by flowing ice. On summit areas at elevations above 750 m, however, remnant corestones are preserved in situ, suggesting selective preservation of upland surfaces. Bedrock structure and composition, topographic position, and intensity of process strongly influence tor development. Weathering pits are common on high level, open summit surfaces where weathering occurs in response to both climate and continued removal of derived debris. Pit enlargement through lateral undercutting has been favoured by accumulation of protective bottom residua, mechanical weathering, and the presence of exfoliation crusts. It is postulated that salt crystallization plays a role in outcrop microweathering under present upland arctic conditions.

scholarly journals Order and stochasticity in the folding of individual Drosophila genomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sergey V. Ulianov ◽  
Vlada V. Zakharova ◽  
Aleksandra A. Galitsyna ◽  
Pavel I. Kos ◽  
Kirill E. Polovnikov ◽  
...  
Keyword(s):  
Random Walk ◽  
High Resolution ◽  
3D Genome ◽  
Topologically Associating Domains ◽  
Chromatin Folding ◽  
A Cell ◽  
Single Nucleus ◽  
High Level ◽  
Cell To Cell Variability

AbstractMammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome.

Relationship between the membrane potential of the contractile vacuole complex and its osmoregulatory activity inParamecium multimicronucleatum

2002 ◽  
Vol 205 (20) ◽  
pp. 3261-3270 ◽  
Author(s):  
Heidi K. Grønlien ◽  
Christian Stock ◽  
Marilynn S. Aihara ◽  
Richard D. Allen ◽  
Yutaka Naitoh
Keyword(s):  
Reference Electrode ◽  
Maximum Level ◽  
The Other ◽  
Contractile Vacuole ◽  
Hypertonic Solution ◽  
Hypotonic Solution ◽  
Atpase Inhibitor ◽  
Filling Phase ◽  
High Level

SUMMARYThe electric potential of the contractile vacuole (CV) of Paramecium multimicronucleatum was measured in situ using microelectrodes,one placed in the CV and the other (reference electrode) in the cytosol of a living cell. The CV potential in a mechanically compressed cell increased in a stepwise manner to a maximal value (approximately 80 mV) early in the fluid-filling phase. This stepwise change was caused by the consecutive reattachment to the CV of the radial arms, where the electrogenic sites are located. The current generated by a single arm was approximately 1.3×10-10 A. When cells adapted to a hypotonic solution were exposed to a hypertonic solution, the rate of fluid segregation, RCVC, in the contractile vacuole complex (CVC) diminished at the same time as immunological labelling for V-ATPase disappeared from the radial arms. When the cells were re-exposed to the previous hypotonic solution, the CV potential, which had presumably dropped to near zero after the cell's exposure to the hypertonic solution, gradually returned to its maximum level. This increase in the CV potential occurred in parallel with the recovery of immunological labelling for V-ATPase in the radial arm and the resumption of RCVC or fluid segregation. Concanamycin B, a potent V-ATPase inhibitor, brought about significant decreases in both the CV potential and RCVC. We confirm that (i) the electrogenic site of the radial arm is situated in the decorated spongiome, and (ii) the V-ATPase in the decorated spongiome is electrogenic and is necessary for fluid segregation in the CVC. The CV potential remained at a constant high level(approximately 80 mV), whereas RCVC varied between cells depending on the osmolarity of the adaptation solution. Moreover, the CV potential did not change even though RCVC increased when cells adapted to one osmolarity were exposed to a lower osmolarity, implying that RCVC is not directly correlated with the number of functional V-ATPase complexes present in the CVC.

Using genomic slot blot hybridization to assess intergeneric Saccharum x Erianthus hybrids (Andropogoneae – Saccharinae)

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 428-432 ◽  
Author(s):  
P. Besse ◽  
C. L. McIntyre ◽  
D. M. Burner ◽  
C. G. de Almeida
Keyword(s):  
Genomic Dna ◽  
Blot Hybridization ◽  
Female Parent ◽  
Saccharum Officinarum ◽  
Rapid Screening ◽  
Hybridization Technique ◽  
Slot Blot ◽  
Saccharum Species ◽  
Slot Blot Hybridization

The use of genomic slot blot hybridization enabled the differentiation of hybrids from selfs in Saccharum × Erianthus intergeneric crosses in which Saccharum was used as the female parent. Based on the genomic in situ hybridization technique, slot blots of DNA from the parents and the progeny were blocked with the Saccharum parent DNA and hybridized with the labelled male Erianthus genomic DNA. This technique allowed a rapid screening for hybrids and was sensitive enough to detect a 1/20 dilution of Erianthus in Saccharum DNA, which should enable the detection of most partial hybrids. The genomic slot blot hybridization technique was shown to be potentially useful for assessing crosses involving Saccharum species with either Old World Erianthus section Ripidium or North American Erianthus (= Saccharum) species. The effectiveness of the technique was assessed on 144 progeny of a Saccharum officinarum × Erianthus arundinaceus cross, revealing that 43% of the progeny were selfs. The importance of this test as a tool to support intergeneric breeding programs is discussed.Key words: slot blot, Erianthus, genomic DNA, Saccharum, sugarcane.

scholarly journals Human neutrophilic and eosinophilic granulocytes display different levels of c-fos proto-oncogene expression: an in situ hybridization study.

1987 ◽  
Vol 35 (8) ◽  
pp. 837-842 ◽  
Author(s):  
H Kreipe ◽  
H J Radzun ◽  
K Heidorn ◽  
C Mäder ◽  
M R Parwaresch
Keyword(s):  
In Situ Hybridization ◽  
Neutrophilic Granulocytes ◽  
Blood Monocytes ◽  
In Vitro Differentiation ◽  
Monocytic Differentiation ◽  
Eosinophilic Granulocytes ◽  
Fos Expression ◽  
High Level

The cellular homologue of the retroviral oncogene v-fos has been shown to be involved in cell differentiation of hematopoietic cells. By use of the human promyelocyte cell line HL-60, several in vitro differentiation studies suggested a selective activation of c-fos during monocytic differentiation of myeloid precursor cells. In contrast to these observations, we found high levels of c-fos mRNA in purified normal human granulocytes, whereas c-fos was only faintly expressed in blood monocytes. In situ hybridization revealed that the high level of c-fos expression is restricted to neutrophilic granulocytes, whereas c-fos transcription is not detectable in eosinophilic granulocytes. These results indicate that in vitro differentiation systems can be misleading and may not reflect the in vivo situation. The high level of c-fos expression in neutrophilic granulocytes may be caused by superinduction due to the reduced capacity for protein synthesis in these cells.

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