Sequence Evolution, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in the Saccharum spontaneum Genome

2020 ◽  
Vol 160 (5) ◽  
pp. 272-282
Author(s):  
Shan Yang ◽  
Kai Zeng ◽  
Ke Chen ◽  
Xinwang Zhao ◽  
Jiayun Wu ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Copy Number ◽  
Blot Hybridization ◽  
Sequence Evolution ◽  
Saccharum Spontaneum ◽  
Dot Blot ◽  
Chromosomal Distribution ◽  
Sequence Organization ◽  
Blast Analysis ◽  
Copia Retrotransposons

Saccharum spontaneum is a wild germplasm resource of the genus Saccharum that has many valuable traits. Ty1-copia retrotransposons constitute a large proportion of plant genomes and affect genome sequence organization and evolution. This study aims to analyze the sequence heterogeneity, phylogenetic diversity, copy number, and chromosomal dispersion patterns of Ty1-copia retrotransposons in S. spontaneum. A total of 44 Ty1-copia reverse transcriptase subclones isolated from S. spontaneum showed a range of heterogeneity, and all sequences were A-T rich, averaging approximately 54.59%. Phylogenetic analysis divided the 44 reverse transcriptase sequences into 5 distinct lineages (Retrofit/Ale, Sire/Maximus, Bianca, Tork/TAR, and Ty1-copia like). Dot-blot hybridization revealed that Ty1-copia retrotransposons consisted of a significant component of approximately 38,900 copies and 16,300 copies per genome in the accessions YN82-114 (2n = 10x = 80) and AP85-441 (2n = 4x = 32), respectively. The results of a local blast analysis showed that there are 15,069 Ty1-copia retrotransposon copies in the genome of AP85-441, of which the Retrofit/Ale lineage had the highest copy number, followed by the Tork/TAR, Sire/Maximus, and Bianca lineages. Furthermore, both FISH and the local blast analysis with AP85-441 genomic data demonstrated that the Ty1-copia retrotransposons were unevenly distributed throughout the chromosomes. Taken together, this study provides insights into the role of Ty1-copia retrotransposons in the evolution and organization of the S. spontaneum genome.

Identification and chromosomal localization of a transcriptionally active retrotransposon of Ty3-gypsy type in rice

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 404-408 ◽  
Author(s):  
Zi-Yin Li ◽  
Shou-Yi Chen ◽  
Xian-Wu Zheng ◽  
Li-Huang Zhu
Keyword(s):  
Oryza Sativa ◽  
Copy Number ◽  
Oryza Sativa L ◽  
Blot Hybridization ◽  
Rice Genome ◽  
Rnase H ◽  
Northern Blot Hybridization ◽  
Japonica Rice ◽  
Terminal Part ◽  
Dot Blot

A DNA fragment representing a transcriptionally active retrotransposon of Ty3-gypsy type was isolated and characterized from rice (Oryza sativa L.). The fragment (named RIRE9) includes the coding sequences for the C-terminal part of the RNase H domain and the N-terminal part of the integrase domain in the polyprotein region. Northern blot hybridization indicated that this element was expressed in rice leaves and stems, suggesting that it is potentially active to transpose under normal growth conditions. Using dot-blot hybridization, the copy number of RIRE9 was estimated to be about 1600 copies per haploid rice genome. Five homologous copies of RIRE9 were assigned to five distinct positions of four chromosomes by restriction fragment length polymorphism (RFLP) mapping approach using an indica-japonica rice doubled-haploid (DH) population and its molecular linkage map. Key words: Oryza sativa L., Ty3-gypsy-like retrotransposon, copy number, chromosomal location.

Development of DNA probes for the identification of sibling species A of the Anopheles culicifacies (Diptera: Culicidae) complex

1995 ◽  
Vol 85 (3) ◽  
pp. 345-353 ◽  
Author(s):  
Maya B. Gunasekera ◽  
B.G.D.N.K. de Silva ◽  
W. Abeyewickreme ◽  
S.K. Subbarao ◽  
H.G. Nandadasa ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Rapid Detection ◽  
Copy Number ◽  
Blot Hybridization ◽  
Dna Probes ◽  
Anopheles Culicifacies ◽  
Dot Blot ◽  
Dot Blot Hybridization ◽  
Field Investigations ◽  
Highly Repetitive Dna

AbstractThree highly repetitive DNA sequences Rp36, Rp217 and Rp234, have been isolated from Anopheles culicifacies Giles sensu lato. The cloned DNA sequences were found at a higher copy number in species B and C, than in species A of the A. culicifacies complex. These sequences may therefore be used as DNA probes to distinguish species A from the other two species, using a 200-fold dilution of a single mosquito DNA extract in a dot-blot hybridization assay. Rp36 and Rp217 have been completely sequenced. Internal repeats were absent in Rp36. Two related core sequences of 13 and 16 bp were found tandemly repeated in Rp217. These probes enable the rapid detection of species A of A. culicifacies in field investigations.

scholarly journals Isolation and characterization of Ty1-copia retrotransposons in Saccharum officinarum

2018 ◽  
Author(s):  
Ke Chen ◽  
Fan Yu ◽  
Yongji Huang ◽  
Xianglin Wu ◽  
Shan Yang ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Saccharum Officinarum ◽  
Plant Genome ◽  
High Yield ◽  
Dot Blot ◽  
Chromosomal Distribution ◽  
Breeding Programs ◽  
Sugarcane Breeding ◽  
Isolation And Characterization

Background. Saccharum officinarum is the most significant resource for sugar and high-yield genes in sugarcane breeding programs. However, the unknown information of evolution and genome organization remain largely in the sugarcane, which has limited progress in sugarcane breeding. Retrotransposons occupy a large proportion of the plant genome; therefore, characterization of Ty1-copia retrotransposons will improve understanding of the evolution and organization of plant genomes. Methods. The present study isolated conserved domains of Ty1-copia retrotransposon-encoded reverse transcriptase genes from S. officinarum to characterize their phylogenetic diversity, genomic abundance, and chromosomal distribution. Results. In total, 42 Ty1-copia reverse transcriptase sequences with 35-100% similarity and high levels of heterogeneity were obtained. Of them, 11 (26%) were disrupted by stop codons and/or frameshift mutations. Phylogenetic analysis revealed these sequences could be split into four distinct evolutionary lineages (Tork/TAR, Tork/Angela, Sire/Maximus, and Retrofit/Ale). Dot blot analysis showed that Ty1-copia retrotransposons represent a significant portion of the S. officinarum genome, with copy numbers as high as 1.7 × 105. Fluorescence in situ hybridization revealed that Ty1-copia retrotransposons were dispersed within heterochromatic regions among all S. officinarum chromosomes, with around 30 obvious signals clustering in terminal regions. However, Ty1-copia retrotransposons were not found in nucleolar organizing regions of 45S rDNA. Discussion. These results serve to enhance our understanding of the chromosomal distribution and evolution of the S. officinarum genome as well as promote possible utilization of retrotransposons in sugarcane breeding programs.

scholarly journals Isolation and characterization of Ty1-copia retrotransposons in Saccharum officinarum

2018 ◽  
Author(s):  
Ke Chen ◽  
Fan Yu ◽  
Yongji Huang ◽  
Xianglin Wu ◽  
Shan Yang ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Saccharum Officinarum ◽  
Plant Genome ◽  
High Yield ◽  
Dot Blot ◽  
Chromosomal Distribution ◽  
Breeding Programs ◽  
Sugarcane Breeding ◽  
Isolation And Characterization

Background. Saccharum officinarum is the most significant resource for sugar and high-yield genes in sugarcane breeding programs. However, the unknown information of evolution and genome organization remain largely in the sugarcane, which has limited progress in sugarcane breeding. Retrotransposons occupy a large proportion of the plant genome; therefore, characterization of Ty1-copia retrotransposons will improve understanding of the evolution and organization of plant genomes. Methods. The present study isolated conserved domains of Ty1-copia retrotransposon-encoded reverse transcriptase genes from S. officinarum to characterize their phylogenetic diversity, genomic abundance, and chromosomal distribution. Results. In total, 42 Ty1-copia reverse transcriptase sequences with 35-100% similarity and high levels of heterogeneity were obtained. Of them, 11 (26%) were disrupted by stop codons and/or frameshift mutations. Phylogenetic analysis revealed these sequences could be split into four distinct evolutionary lineages (Tork/TAR, Tork/Angela, Sire/Maximus, and Retrofit/Ale). Dot blot analysis showed that Ty1-copia retrotransposons represent a significant portion of the S. officinarum genome, with copy numbers as high as 1.7 × 105. Fluorescence in situ hybridization revealed that Ty1-copia retrotransposons were dispersed within heterochromatic regions among all S. officinarum chromosomes, with around 30 obvious signals clustering in terminal regions. However, Ty1-copia retrotransposons were not found in nucleolar organizing regions of 45S rDNA. Discussion. These results serve to enhance our understanding of the chromosomal distribution and evolution of the S. officinarum genome as well as promote possible utilization of retrotransposons in sugarcane breeding programs.

Detection of Hepatitis a Virus and other Enteroviruses in Wastewater and Surface Water Samples by Gene Probe Assay

1991 ◽  
Vol 24 (2) ◽  
pp. 267-272 ◽  
Author(s):  
S. Dubrou ◽  
H. Kopecka ◽  
J. M. Lopez Pila ◽  
J. Maréchal ◽  
J. Prévot
Keyword(s):  
Surface Water ◽  
Cell Cultures ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Limit Of Detection ◽  
Blot Hybridization ◽  
Noncoding Region ◽  
Gene Probe ◽  
Dot Blot ◽  
Lower Efficiency

Enteroviruses were specifically detected by dot blot hybridization when using poliovirus type 1 (PV1) derived subgenomic radiolabeled cRNA probes (riboprobes) in environmental water specimens and in the cell cultures in which the viruses were amplificated. The riboprobe corresponding to the 5' noncoding sequence detected the majority of enteroviruses. Hepatitis A virus (HAV) was specifically detected by an HAV cRNA probe corresponding to the 5' noncoding region of its genome. By this test, the limit of detection of coxsackievirus B5 and echovirus 7 seeded in mineral water was 103 to 104 PFU/spot. In cell cultures, positive signals were observed in the lysates of cells infected by one PFU. Higher positive signals were obtained with a short PV1 probe (nt 221-670) corresponding to the 5' noncoding region, which is a well preserved sequence among the enteroviruses, than with PV1 genomic probe. Hybridization allowed a good detection of enteroviral RNAs in wastewater specimens, but with a lower efficiency in surface water. In this case, amplification of viruses in the cell cultures gave significant hybridization results.

Feasibility of Qualitative Testing of BCR-ABL and JAK2 V617F in Suspected Myeloproliperative Neoplasm (MPN) Using RT-PCR Reversed Dot Blot Hybridization (RT-PCR RDB)

2019 ◽  
Vol 19 (4) ◽  
pp. 220-227
Author(s):  
Najmiatul Masykura ◽  
Ummu Habibah ◽  
Siti Fatimah Selasih ◽  
Soegiarto Gani ◽  
Cosphiadi Irawan ◽  
...  
Keyword(s):  
Blot Hybridization ◽  
Jak2 V617f ◽  
Rt Pcr ◽  
Dot Blot ◽  
Dot Blot Hybridization

scholarly journals Exogenous Isolation of Antibiotic Resistance Plasmids from Piggery Manure Slurries Reveals a High Prevalence and Diversity of IncQ-Like Plasmids

2000 ◽  
Vol 66 (11) ◽  
pp. 4854-4862 ◽  
Author(s):  
Kornelia Smalla ◽  
Holger Heuer ◽  
Antje Götz ◽  
Dagmar Niemeyer ◽  
Ellen Krögerrecklenfort ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Ralstonia Eutropha ◽  
Blot Hybridization ◽  
Restriction Pattern ◽  
Pcr Analysis ◽  
Dot Blot ◽  
High Prevalence ◽  
Resistance Plasmids ◽  
Incq Plasmids ◽  
K 12

ABSTRACT Antibiotic resistance plasmids were exogenously isolated in biparental matings with piggery manure bacteria as plasmid donors inEscherichia coli CV601 and Pseudomonas putidaUWC1 recipients. Surprisingly, IncQ-like plasmids were detected by dot blot hybridization with an IncQ oriV probe in severalP. putida UWC1 transconjugants. The capture of IncQ-like plasmids in biparental matings indicates not only their high prevalence in manure slurries but also the presence of efficiently mobilizing plasmids. In order to elucidate unusual hybridization data (weak or no hybridization with IncQ repB or IncQ oriTprobes) four IncQ-like plasmids (pIE1107, pIE1115, pIE1120, and pIE1130), each representing a different EcoRV restriction pattern, were selected for a more thorough plasmid characterization after transfer into E. coli K-12 strain DH5α by transformation. The characterization of the IncQ-like plasmids revealed an astonishingly high diversity with regard to phenotypic and genotypic properties. Four different multiple antibiotic resistance patterns were found to be conferred by the IncQ-like plasmids. The plasmids could be mobilized by the RP4 derivative pTH10 into Acinetobactersp., Ralstonia eutropha, Agrobacterium tumefaciens, and P. putida, but they showed diverse patterns of stability under nonselective growth conditions in different host backgrounds. Incompatibility testing and PCR analysis clearly revealed at least two different types of IncQ-like plasmids. PCR amplification of total DNA extracted directly from different manure samples and other environments indicated the prevalence of both types of IncQ plasmids in manure, sewage, and farm soil. These findings suggest that IncQ plasmids play an important role in disseminating antibiotic resistance genes.

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