scholarly journals Genome-Wide Identification and Analysis of High-Copy-Number LTR Retrotransposons in Asian Pears

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 156
Author(s):  
Shuang Jiang ◽  
Xiaoqing Wang ◽  
Chunhui Shi ◽  
Jun Luo
Keyword(s):  
Copy Number ◽  
Long Terminal Repeat Retrotransposons ◽  
High Copy Number ◽  
Pyrus Pyrifolia ◽  
Origin And Evolution ◽  
Asian Pear ◽  
Copy Numbers ◽  
Genome Wide ◽  
History Of ◽  
Insertion Sites

A large proportion of the genome of ‘Suli’ pear (Pyrus pyrifolia) contains long terminal repeat retrotransposons (LTR-RTs), which suggests that LTR-RTs have played important roles in the evolution of Pyrus. Further analysis of retrotransposons, particularly of high-copy-number LTR-RTs in different species, will provide new insights into the evolutionary history of Pyrus. A total of 4912 putative LTR-RTs classified into 198 subfamilies were identified in the ‘Suli’ pear genome. Six Asian pear accessions, including cultivars and wild species, were resequenced. The comparison of copy number for each LTR-RT subfamily was evaluated in Pyrus accessions, and data showed up to four-fold differences for some subfamilies. This contrast suggests different fates for retrotransposon families in the evolution of Pyrus. Fourteen high-copy-number subfamilies were identified in Asian pears, and more than 50% of the LTR-RTs in the genomes of all Pyrus accessions were from these 14 identified LTR-RT subfamilies. Their average insertion time was 3.42 million years ago, which suggests that these subfamilies were recently inserted into the genome. Many homologous and specific retrotransposon insertion sites were identified in oriental and occidental pears, suggesting that the duplication of retrotransposons has occurred throughout almost the entire origin and evolution of Pyrus species. The LTR-RTs show high heterogeneity, and their copy numbers vary in different Pyrus species. Thus, our findings suggest that LTR-RTs are an important source of genetic variation among Pyrus species.

scholarly journals Genome-Wide Somatic Copy Number Alterations in Low-Grade PanINs and IPMNs from Individuals with a Family History of Pancreatic Cancer

2012 ◽  
Vol 18 (16) ◽  
pp. 4303-4312 ◽  
Author(s):  
Seung-Mo Hong ◽  
Audrey Vincent ◽  
Mitsuro Kanda ◽  
Julie Leclerc ◽  
Noriyuki Omura ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Family History ◽  
Copy Number ◽  
Low Grade ◽  
Copy Number Alterations ◽  
Genome Wide ◽  
History Of ◽  
Somatic Copy Number Alterations

Retrotransposon-based molecular markers for assessment of genomic diversity

2014 ◽  
Vol 41 (8) ◽  
pp. 781 ◽  
Author(s):  
Ahmed M. Alzohairy ◽  
Gábor Gyulai ◽  
Mohamed F. Ramadan ◽  
Sherif Edris ◽  
Jamal S. M. Sabir ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Copy Number ◽  
Long Terminal Repeat Retrotransposons ◽  
Genomic Diversity ◽  
Insertion Polymorphism ◽  
Sequence Motifs ◽  
History Of ◽  
Copy And Paste ◽  
Binding Sequence ◽  
Genomic Insertions

Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in ‘repeat seas’ or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).

scholarly journals Construction of high copy number and highly stable Escherichia coli-Bacillus subtilis shuttle plasmids based on pWB980

2019 ◽  
Author(s):  
XingYa Zhao ◽  
JianYong Xu ◽  
Ming Tan ◽  
Jie Zhen ◽  
WenJu Shu ◽  
...  
Keyword(s):  
Copy Number ◽  
Insertion Site ◽  
Pectate Lyase ◽  
High Copy Number ◽  
Expression Vectors ◽  
Upstream Region ◽  
Transformation Rate ◽  
E Coli ◽  
Shuttle Plasmid ◽  
Insertion Sites

Abstract Background: pWB980 derived from pUB110 is a promising expression vector in Bacillus for its high copy number and high stability. However, the low transformation rate of recombinant plasmids to the wild cells limited the application of it. On the basis of pWB980, constructing an E. coli - B. subtilis shuttle plasmid could facilitate the transformation rate to Bacillus cells. Because the insertion site for E. coli replication origin sequence ( ori ) is not unique in pWB980, in order to investigate the best insertion site, eight shuttle plasmids (pUC980-1~pUC980-8) containing all possible insertion sites and directions were constructed.Results: The results showed that all the selected insertion sites could be used to construct shuttle plasmid but some sites required a specific direction. And different insertion sites led to different properties of the shuttle plasmids. The best shuttle plasmids pUC980-1 and pUC980-2, which showed copies more than 450 per cell and segregational stabilities up to 98%, were selected for heterologous expressions of an alkaline pectate lyase gene pelN , an alkaline protease spro1 and a pullulanase gene pulA11 , respectively. The highest extracellular activities of PelN, Spro1 and PulA11 were upto 5200 U/mL, 21537 U/mL and 504 U/mL correspondingly after 54 h, 60 h and 48 h fermentation in a 10 L fermentor. Notably, PelN and Spro1 showed remarkably higher yields in Bacillus than previous reports.Conclusion: In this work we can conclude that the optimum ori insertion site was the upstream region of BA3-1 in pWB980 which resulted in shuttle plasmids with higher copy numbers and higher stabilities. The novel shuttle plasmids pUC980-1 and pUC980-2 will be promising expression vectors in B. subtilis . And the ori insertion mechanism revealed in this work could provide theoretical guidance for further studies of pWB980 and constructions of other shuttle plasmids.

Somatic Mosaicism in Bulls Estimated from Genome-Wide CNV Array and TSPY Gene Copy Numbers

2016 ◽  
Vol 149 (3) ◽  
pp. 176-181 ◽  
Author(s):  
Olutobi A. Oluwole ◽  
Tamas Revay ◽  
Kiana Mahboubi ◽  
Laura A. Favetta ◽  
W. Allan King
Keyword(s):  
Copy Number ◽  
De Novo ◽  
Somatic Mosaicism ◽  
Copy Number Variations ◽  
Tissue Type ◽  
Gene Copy ◽  
Copy Numbers ◽  
Genome Wide ◽  
Wide Range ◽  
Tspy Gene

Somatic mosaicism has become a focus in human research due to the implications of individual genetic variability in disease. Here, we assessed somatic copy number variations (CNVs) in Holstein bulls in 2 respects. We estimated genome-wide CNVs and assayed CNVs of the TSPY gene, the most variable bovine gene from the Y chromosome. Somatic tissues (blood, lung, heart, muscle, testis, and brain) of 4 bulls were arrayed on the Illumina Bovine SNP50k chip and qPCR tested for TSPY copy numbers. Our results showed extensive copy number divergence in tissues within the same animal as well as significant copy number alterations of TSPY. We detected a mean of 31 CNVs per animal among which 14 were of germline origin, as they were constantly present in all investigated tissues of the animal, while 18 were specific to 1 tissue. Thus, 57% of the total number of detected CNVs was the result of de novo somatic events. Further, TSPY copy number was found to vary significantly among tissues as well as among the same tissue type from different animals in a wide range from 7 to 224% of the calibrator. Our study shows significant autosomal and Y-chromosomal de novo somatic CNV in bulls.

Differences in the prevalence of IS6110 insertion sites in Mycobacterium tuberculosis strains: low and high copy number of IS6110

1998 ◽  
Vol 78 (2) ◽  
pp. 109-116 ◽  
Author(s):  
N. Fomukong ◽  
M. Beggs ◽  
H. El Hajj ◽  
G. Templeton ◽  
K. Eisenach ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Copy Number ◽  
High Copy Number ◽  
Insertion Sites

scholarly journals Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

DNA Research ◽  
2021 ◽  
Author(s):  
Kenta Shirasawa ◽  
Akihiro Itai ◽  
Sachiko Isobe
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Genetic Maps ◽  
Japanese Pear ◽  
Pyrus Pyrifolia ◽  
Breeding Programs ◽  
Genome Wide ◽  
Protein Encoding ◽  
History Of ◽  
Encoding Genes

Abstract Aim We analyzed the genome sequence of a Japanese pear (Pyrus pyrifolia) to facilitate its genetics and genomics as well as breeding programs, in which a variety ′Nijisseiki′ with superior flesh texture has been used as a parent for most Japanese pear cultivars. Methods and results De novo assembly of long sequence reads covered 136× of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6 Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 high-confidence protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of genome-wide duplication was observed, consistent with related species. Conclusion and Perspective This is the first chromosome-scale genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

scholarly journals Characterization of a Large, Stable, High-Copy-Number Streptomyces Plasmid That Requires Stability and Transfer Functions for Heterologous Polyketide Overproduction

2006 ◽  
Vol 73 (4) ◽  
pp. 1296-1307 ◽  
Author(s):  
Ryan Fong ◽  
Zhihao Hu ◽  
C. Richard Hutchinson ◽  
Jianqiang Huang ◽  
Stanley Cohen ◽  
...  
Keyword(s):  
Copy Number ◽  
Transfer Functions ◽  
Biosynthetic Gene Cluster ◽  
Plasmid Copy Number ◽  
High Copy Number ◽  
Plasmid Replication ◽  
Biosynthetic Genes ◽  
Plasmid Copy ◽  
Metabolite Production ◽  
Copy Numbers

ABSTRACT A major limitation to improving small-molecule pharmaceutical production in streptomycetes is the inability of high-copy-number plasmids to tolerate large biosynthetic gene cluster inserts. A recent finding has overcome this barrier. In 2003, Hu et al. discovered a stable, high-copy-number, 81-kb plasmid that significantly elevated production of the polyketide precursor to the antibiotic erythromycin in a heterologous Streptomyces host (J. Ind. Microbiol. Biotechnol. 30:516-522, 2003). Here, we have identified mechanisms by which this SCP2*-derived plasmid achieves increased levels of metabolite production and examined how the 45-bp deletion mutation in the plasmid replication origin increased plasmid copy number. A plasmid intramycelial transfer gene, spd, and a partition gene, parAB, enhance metabolite production by increasing the stable inheritance of large plasmids containing biosynthetic genes. Additionally, high product titers required both activator (actII-ORF4) and biosynthetic genes (eryA) at high copy numbers. DNA gel shift experiments revealed that the 45-bp deletion abolished replication protein (RepI) binding to a plasmid site which, in part, supports an iteron model for plasmid replication and copy number control. Using the new information, we constructed a large high-copy-number plasmid capable of overproducing the polyketide 6-deoxyerythronolide B. However, this plasmid was unstable over multiple culture generations, suggesting that other SCP2* genes may be required for long-term, stable plasmid inheritance.

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