scholarly journals Genes Containing Long Introns Occupy Series of Bands and Interbands in Drosophila melanogaster Polytene Chromosomes

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 417
Author(s):  
Varvara A. Khoroshko ◽  
Galina V. Pokholkova ◽  
Victor G. Levitsky ◽  
Tatyana Yu. Zykova ◽  
Oksana V. Antonenko ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Polytene Chromosomes ◽  
Housekeeping Genes ◽  
Wide Distribution ◽  
Gene Location ◽  
Gene Arrangement ◽  
Drosophila Genome ◽  
Genetic Organization ◽  
Genome Wide ◽  
Bioinformatic Approaches

The Drosophila melanogaster polytene chromosomes are the best model for studying the genome organization during interphase. Despite of the long-term studies available on genetic organization of polytene chromosome bands and interbands, little is known regarding long gene location on chromosomes. To analyze it, we used bioinformatic approaches and characterized genome-wide distribution of introns in gene bodies and in different chromatin states, and using fluorescent in situ hybridization we juxtaposed them with the chromosome structures. Short introns up to 2 kb in length are located in the bodies of housekeeping genes (grey bands or lazurite chromatin). In the group of 70 longest genes in the Drosophila genome, 95% of total gene length accrues to introns. The mapping of the 15 long genes showed that they could occupy extended sections of polytene chromosomes containing band and interband series, with promoters located in the interband fragments (aquamarine chromatin). Introns (malachite and ruby chromatin) in polytene chromosomes form independent bands, which can contain either both introns and exons or intron material only. Thus, a novel type of the gene arrangement in polytene chromosomes was discovered; peculiarities of such genetic organization are discussed.

scholarly journals Structural variants and selective sweep foci contribute to insecticide resistance in the Drosophila melanogaster genetic reference panel

2018 ◽  
Author(s):  
Paul Battlay ◽  
Llewellyn Green ◽  
Pontus B. Leblanc ◽  
Joshua M. Schmidt ◽  
Alexandre Fournier-Level ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Selective Sweep ◽  
Association Studies ◽  
Transcript Abundance ◽  
Reference Panel ◽  
Drosophila Genome ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Number Variation

AbstractPatterns of nucleotide polymorphism within populations of Drosophila melanogaster suggest that insecticides have been the selective agents driving the strongest recent bouts of positive selection. However, there is a need to explicitly link selective sweep loci to the particular insecticide phenotypes that could plausibly account for the drastic selective responses that are observed in these non-target insects. Here, we screen the Drosophila Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a pyrethroid). Genome wide association studies map ‘survival-on-malathion’ to two of the largest sweeps in the D. melanogaster genome; Ace and Cyp6g1. Malathion survivorship also correlates with lines which have high levels of Cyp12d1 and Jheh1 and Jheh2 transcript abundance. Permethrin phenotypes map to the largest cluster of P450 genes in the Drosophila genome, however in contrast to a selective sweep driven by insecticide use, the derived state seems to be associated with susceptibility. These results underscore previous findings that highlight the importance of structural variation to insecticide phenotypes: Cyp6g1 exhibits copy number variation and transposable element insertions, Cyp12d1 is tandemly duplicated, the Jheh loci are associated with a Bari1 transposable element insertion, and a Cyp6a17 deletion is associated with susceptibility.

scholarly journals Elevated levels of expression associated with regions of the Drosophila genome that lack crossing over

2008 ◽  
Vol 4 (6) ◽  
pp. 758-761 ◽  
Author(s):  
Penelope R Haddrill ◽  
Fergal M Waldron ◽  
Brian Charlesworth
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Translational Efficiency ◽  
Crossing Over ◽  
Drosophila Genome ◽  
Deleterious Mutations ◽  
Fourth Chromosome ◽  
Genome Wide ◽  
Control Of Expression

The recombinational environment influences patterns of molecular evolution through the effects of Hill–Robertson interference. Here, we examine genome-wide patterns of gene expression with respect to recombinational environment in Drosophila melanogaster . We find that regions of the genome lacking crossing over exhibit elevated levels of expression, and this is most pronounced for genes on the entirely non-crossing over fourth chromosome. We find no evidence for differences in the patterns of gene expression between regions of high, intermediate and low crossover frequencies. These results suggest that, in the absence of crossing over, selection to maintain control of expression may be compromised, perhaps due to the accumulation of deleterious mutations in regulatory regions. Alternatively, higher gene expression may be evolving to compensate for defective protein products or reduced translational efficiency.

scholarly journals Regions of very low H3K27me3 partition the Drosophila genome into topological domains

2016 ◽  
Author(s):  
Sherif El-Sharnouby ◽  
Bettina Fischer ◽  
Jose Paolo Magbanua ◽  
Benjamin Umans ◽  
Rosalyn Flower ◽  
...  
Keyword(s):  
Domain Architecture ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Drosophila Genome ◽  
Topological Domains ◽  
Transcription Start Sites ◽  
Genome Wide ◽  
Domain Boundaries ◽  
Topologically Associated Domains ◽  
Architectural Organization

AbstractBackgroundIt is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood.ResultsWe have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing mid-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries.ConclusionsWe suggest that the D domain chromatin state, characterised by very low H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome.

Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes

Chromosoma ◽  
2019 ◽  
Vol 129 (1) ◽  
pp. 25-44 ◽  
Author(s):  
Olga V. Demakova ◽  
Sergey A. Demakov ◽  
Lidiya V. Boldyreva ◽  
Tatyana Yu. Zykova ◽  
Victor G. Levitsky ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Polytene Chromosomes ◽  
Housekeeping Genes ◽  
Coding Sequences

scholarly journals Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections

Planta ◽  
2021 ◽  
Vol 253 (4) ◽  
Author(s):  
Mingzhao Zhu ◽  
Shujin Lu ◽  
Mu Zhuang ◽  
Yangyong Zhang ◽  
Honghao Lv ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Downy Mildew ◽  
Fusarium Wilt ◽  
Black Spot ◽  
Housekeeping Genes ◽  
Chitinase Gene ◽  
Genome Wide ◽  
A Genome

Abstract Main conclusion Chitinase family genes were involved in the response of Brassica oleracea to Fusarium wilt, powdery mildew, black spot and downy mildew. Abstract Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.

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