scholarly journals Association analysis of repetitive elements and R-loop formation across species

2020 ◽  
Author(s):  
Chao Zeng ◽  
Masahiro Onoguchi ◽  
Michiaki Hamada
Keyword(s):  
Fruit Fly ◽  
Low Complexity ◽  
Repetitive Elements ◽  
S2 Cells ◽  
Loop Formation ◽  
Long Terminal Repeats ◽  
Long Interspersed Nuclear Elements ◽  
Regulatory Effects ◽  
Species Specific ◽  
Simple Repeats

ABSTRACTGenomes are known to have a large number of repetitive elements. Emerging evidence suggests that these non-coding elements may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. In this study, we found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellites, long interspersed nuclear elements (LINEs), and DNAs were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeats (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells. Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.

scholarly journals Association analysis of repetitive elements and R-loop formation across species

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chao Zeng ◽  
Masahiro Onoguchi ◽  
Michiaki Hamada
Keyword(s):  
Fruit Fly ◽  
Low Complexity ◽  
Wide Distribution ◽  
Long Terminal Repeat Retrotransposons ◽  
Repetitive Elements ◽  
Loop Formation ◽  
Genome Wide ◽  
Regulatory Effects ◽  
Species Specific ◽  
Simple Repeats

Abstract Background Although recent studies have revealed the genome-wide distribution of R-loops, our understanding of R-loop formation is still limited. Genomes are known to have a large number of repetitive elements. Emerging evidence suggests that these sequences may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. Results We found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellite, long interspersed nuclear elements (LINEs), and DNA transposons were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeat retrotransposons (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells. Conclusions Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.

Rapid diagnosis of the economically important fruit fly, Bactrocera correcta (Diptera: Tephritidae) based on a species-specific barcoding cytochrome oxidase I marker

2013 ◽  
Vol 103 (3) ◽  
pp. 363-371 ◽  
Author(s):  
F. Jiang ◽  
Z.H. Li ◽  
Y.L. Deng ◽  
J.J. Wu ◽  
R.S. Liu ◽  
...  
Keyword(s):  
Cytochrome Oxidase ◽  
Fruit Fly ◽  
Cytochrome Oxidase I ◽  
Invasive Pest ◽  
Molecular Technique ◽  
Life Stages ◽  
Specific Primer ◽  
Mtdna Coi ◽  
Bactrocera Correcta ◽  
Species Specific

AbstractThe guava fruit fly, Bactrocera correcta (Bezzi) (Diptera: Tephritidae), is an invasive pest of fruit and vegetable crops that primarily inhabits Southeast Asia and which has the potential to become a major threat within both the Oriental and Australian oceanic regions as well as California and Florida. In light of the threat posed, it is important to develop a rapid, accurate and reliable method to identify B. correcta in quarantine work in order to provide an early warning to prevent its widespread invasion. In the present study, we describe a species-specific polymerase chain reaction assay for the diagnosis of B. correcta using mitochondrial DNA cytochrome oxidase I (mtDNA COI) barcoding genes. A B. correcta-specific primer pair was designed according to variations in the mtDNA COI barcode sequences among 14 fruit fly species. The specificity and sensitivity of the B. correcta-specific primer pair was tested based on the presence or absence of a band in the gel profile. A pair of species-specific B. correcta primers was successfully designed and named BCOR-F/BCOR-R. An ∼280 bp fragment was amplified from specimens belonging to 17 geographical populations and four life stages of B. correcta, while no such diagnostic bands were present in any of the 14 other related fruit fly species examined. Sensitivity test results demonstrated that successful amplification can be obtained with as little as 1 ng μl−1 of template DNA. The species-specific PCR analysis was able to successfully diagnose B. correcta, even in immature life stages, and from adult body parts. This method proved to be a robust single-step molecular technique for the diagnosis of B. correcta with respect to potential plant quarantine.

scholarly journals Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Peter D. Olson ◽  
Alan Tracey ◽  
Andrew Baillie ◽  
Katherine James ◽  
Stephen R. Doyle ◽  
...  
Keyword(s):  
Complete Genome ◽  
Gene Prediction ◽  
Low Complexity ◽  
Complex Species ◽  
Complete Representation ◽  
Spliced Leader ◽  
Long Read ◽  
Reference Quality ◽  
Species Specific ◽  
Genome Representation

Abstract Background Chromosome-level assemblies are indispensable for accurate gene prediction, synteny assessment, and understanding higher-order genome architecture. Reference and draft genomes of key helminth species have been published, but little is yet known about the biology of their chromosomes. Here, we present the complete genome of the tapeworm Hymenolepis microstoma, providing a reference quality, end-to-end assembly that represents the first fully assembled genome of a spiralian/lophotrochozoan, revealing new insights into chromosome evolution. Results Long-read sequencing and optical mapping data were added to previous short-read data enabling complete re-assembly into six chromosomes, consistent with karyology. Small genome size (169 Mb) and lack of haploid variation (1 SNP/3.2 Mb) contributed to exceptionally high contiguity with only 85 gaps remaining in regions of low complexity sequence. Resolution of repeat regions reveals novel gene expansions, micro-exon genes, and spliced leader trans-splicing, and illuminates the landscape of transposable elements, explaining observed length differences in sister chromatids. Syntenic comparison with other parasitic flatworms shows conserved ancestral linkage groups indicating that the H. microstoma karyotype evolved through fusion events. Strikingly, the assembly reveals that the chromosomes terminate in centromeric arrays, indicating that these motifs play a role not only in segregation, but also in protecting the linear integrity and full lengths of chromosomes. Conclusions Despite strong conservation of canonical telomeres, our results show that they can be substituted by more complex, species-specific sequences, as represented by centromeres. The assembly provides a robust platform for investigations that require complete genome representation.

scholarly journals Sequence and Structure Characteristics of 22 Deletion Breakpoints in Intron 44 of the DMD Gene Based on Long-Read Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Chang Geng ◽  
Yuanren Tong ◽  
Siwen Zhang ◽  
Chao Ling ◽  
Xin Wu ◽  
...  
Keyword(s):  
Becker Muscular Dystrophy ◽  
Repetitive Elements ◽  
Loop Formation ◽  
End Joining ◽  
Origin Firing ◽  
Large Deletions ◽  
Long Read ◽  
Non Homologous End Joining ◽  
Dmd Gene ◽  
Palindromic Sequences

Purpose: Exon deletions make up to 80% of mutations in the DMD gene, which cause Duchenne and Becker muscular dystrophy. Exon 45-55 regions were reported as deletion hotspots and intron 44 harbored more than 25% of deletion start points. We aimed to investigate the fine structures of breakpoints in intron 44 to find potential mechanisms of large deletions in intron 44.Methods: Twenty-two dystrophinopathy patients whose deletion started in intron 44 were sequenced using long-read sequencing of a DMD gene capture panel. Sequence homology, palindromic sequences, and polypyrimidine sequences were searched at the breakpoint junctions. RepeatMasker was used to analyze repetitive elements and Mfold was applied to predict secondary DNA structure.Results: With a designed DMD capture panel, 22 samples achieved 2.25 gigabases and 1.28 million reads on average. Average depth was 308× and 99.98% bases were covered at least 1×. The deletion breakpoints in intron 44 were scattered and no breakpoints clustered in any region less than 500 bp. A total of 72.7% of breakpoints located in distal 100 kb of intron 44 and more repetitive elements were found in this region. Microhomologies of 0–1 bp were found in 36.4% (8/22) of patients, which corresponded with non-homologous end-joining. Microhomologies of 2–20 bp were found in 59.1% (13/22) of patients, which corresponded with microhomology-mediated end-joining. Moreover, a 7 bp insertion was found in one patient, which might be evidence of aberrant replication origin firing. Palindromic sequences, polypyrimidine sequences, and small hairpin loops were found near several breakpoint junctions. No evidence of large hairpin loop formation in deletion root sequences was observed.Conclusion: This study was the first to explore possible mechanisms underlying exon deletions starting from intron 44 of the DMD gene based on long-read sequencing. Diverse mechanisms might be associated with deletions in the DMD gene.

scholarly journals Species-specific transcriptional profiles of the gut and gut microbiome of Ceratitis quilicii and Ceratitis rosa sensu stricto

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Fathiya M. Khamis ◽  
Paul O. Mireji ◽  
Fidelis L. O. Ombura ◽  
Anna R. Malacrida ◽  
Erick O. Awuoche ◽  
...  
Keyword(s):  
Sibling Species ◽  
Gut Microbiome ◽  
De Novo ◽  
Differential Expression Analysis ◽  
Fruit Fly ◽  
Sensu Stricto ◽  
Transcriptional Profiles ◽  
Species Specific ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractThe fruit fly species, Ceratitis rosa sensu stricto and Ceratitis quilicii, are sibling species restricted to the lowland and highland regions, respectively. Until recently, these sibling species were considered as allopatric populations of C. rosa with distinct bionomics. We used deep Next Generation Sequencing (NGS) technology on intact guts of individuals from the two sibling species to compare their transcriptional profiles and simultaneously understand gut microbiome and host molecular processes and identify distinguishing genetic differences between the two species. Since the genomes of both species had not been published previously, the transcriptomes were assembled de novo into transcripts. Microbe-specific transcript orthologs were separated from the assembly by filtering searches of the transcripts against microbe databases using OrthoMCL. We then used differential expression analysis of host-specific transcripts (i.e. those remaining after the microbe-specific transcripts had been removed) and microbe-specific transcripts from the two-sibling species to identify defining species-specific transcripts that were present in only one fruit fly species or the other, but not in both. In C. quilicii females, bacterial transcripts of Pectobacterium spp., Enterobacterium buttiauxella, Enterobacter cloacae and Klebsiella variicola were upregulated compared to the C. rosa s.s. females. Comparison of expression levels of the host transcripts revealed a heavier investment by C. quilicii (compared with C. rosa s.s.) in: immunity; energy production; cell proliferation; insecticide resistance; reproduction and proliferation; and redox reactions that are usually associated with responses to stress and degradation of fruit metabolites.

scholarly journals The 14-3-3 (YWHA) Proteins in Signalling and Development of the Fruit Fly, Drosophila melanogaster

2019 ◽  
Vol 9 (1) ◽  
pp. 80-85 ◽  
Author(s):  
Santanu De
Keyword(s):  
Cell Cycle ◽  
Drosophila Melanogaster ◽  
Cell Signalling ◽  
Fruit Fly ◽  
Model Systems ◽  
Cellular Mechanisms ◽  
Homologous Proteins ◽  
Cellular Events ◽  
Species Specific ◽  
Molecular Bases

The 14-3-3 (YWHA or Tyrosine 3-Monooxygenase/Tryptophan 5-Monooxygenase Activation proteins) are a family of highly conserved, homologous proteins critical to diverse cellular events including cell cycle, signal transduction and embryonic development.  Various species-specific isoforms of 14-3-3 exist, encoded by separate genes.  They are expressed in a wide variety of organisms ranging from plants to animals, including the fruit fly or Drosophila melanogaster.  Drosophila is one of the most universally accepted model systems to study complex cellular mechanisms of signalling and development.  However, regulation of these processes in fruit flies by the 14-3-3 proteins have not been entirely understood.  This mini review encapsulates the expression, distribution, interactions and regulatory roles of the 14-3-3 proteins in Drosophila.  The analysis would help to elucidate some of the molecular bases of key cell-signalling mechanisms and development.

scholarly journals Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection

2020 ◽  
Author(s):  
Peter D. Olson ◽  
Alan Tracey ◽  
Andrew Baillie ◽  
Katherine James ◽  
Stephen R. Doyle ◽  
...  
Keyword(s):  
Complete Genome ◽  
Gene Prediction ◽  
Low Complexity ◽  
Complex Species ◽  
Complete Representation ◽  
Spliced Leader ◽  
Long Read ◽  
Reference Quality ◽  
Species Specific ◽  
Genome Representation

AbstractBackgroundChromosome-level assemblies are indispensable for accurate gene prediction, synteny assessment and understanding higher-order genome architecture. Reference and draft genomes of key helminth species have been published but little is yet known about the biology of their chromosomes. Here we present the complete genome of the tapeworm Hymenolepis microstoma, providing a reference-quality, end-to-end assembly that represents the first fully assembled genome of a spiralian/lophotrochozoan, revealing new insights into chromosome evolution.ResultsLong-read sequencing and optical mapping data were added to previous short-read data enabling complete re-assembly into six chromosomes, consistent with karyology. Small genome size (169 Mb) and lack of haploid variation (1 SNP/3.2 Mb) contributed to exceptionally high contiguity with only 85 gaps remaining in regions of low complexity sequence. Resolution of repeat regions reveals novel gene expansions, micro-exon genes, and spliced leader transsplicing, and illuminates the landscape of transposable elements, explaining observed length differences in sister chromatids. Syntenic comparison with other parasitic flatworms shows conserved ancestral linkage groups indicating that the H. microstoma karyotype evolved through fusion events. Strikingly, the assembly reveals that the chromosomes terminate in centromeric arrays, indicating that these motifs play a role not only in segregation, but also in protecting the linear integrity and full lengths of chromosomes.ConclusionsDespite strong conservation of canonical telomeres, our results show that they can be substituted by more complex, species-specific sequences, as represented by centromeres. The assembly provides a robust platform for investigations that require complete genome representation.

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