scholarly journals Characterizing Repeats in Two Whole-Genome Amplification Methods in the Reniform Nematode Genome

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
S. T. Nyaku ◽  
V. R. Sripathi ◽  
K. Lawrence ◽  
G. Sharma
Keyword(s):  
Whole Genome Amplification ◽  
Dna Amplification ◽  
Low Complexity ◽  
P Element ◽  
Whole Genome ◽  
Cotton Production ◽  
Reniform Nematode ◽  
Genome Amplification ◽  
Repeat Elements ◽  
Reniform Nematodes

One of the major problems in the U.S. and global cotton production is the damage caused by the reniform nematode, Rotylenchulus reniformis. Amplification of DNA from single nematodes for further molecular analysis can be challenging sometimes. In this research, two whole-genome amplification (WGA) methods were evaluated for their efficiencies in DNA amplification from a single reniform nematode. The WGA was carried out using both REPLI-g Mini and Midi kits, and the GenomePlex single cell whole-genome amplification kit. Sequence analysis produced 4 Mb and 12 Mb of genomic sequences for the reniform nematode using REPLI-g and SIGMA libraries. These sequences were assembled into 28,784 and 24,508 contigs, respectively, for REPLI-g and SIGMA libraries. The highest repeats in both libraries were of low complexity, and the lowest for the REPLI-g library were for satellites and for the SIGMA library, RTE/BOV-B. The same kind of repeats were observed for both libraries; however, the SIGMA library had four other repeat elements (Penelope (long interspersed nucleotide element (LINE)), RTE/BOV-B (LINE), PiggyBac, and Mirage/P-element/Transib), which were not seen in the REPLI-g library. DNA transposons were also found in both libraries. Both reniform nematode 18S rRNA variants (RN_VAR1 and RN_VAR2) could easily be identified in both libraries. This research has therefore demonstrated the ability of using both WGA methods, in amplification of gDNA isolated from single reniform nematodes.

scholarly journals Isothermal DNA amplification using the T4 replisome: circular nicking endonuclease-dependent amplification and primase-based whole-genome amplification

2010 ◽  
Vol 38 (22) ◽  
pp. e201-e201 ◽  
Author(s):  
Yolanda Schaerli ◽  
Viktor Stein ◽  
Michelle M. Spiering ◽  
Stephen J. Benkovic ◽  
Chris Abell ◽  
...  
Keyword(s):  
Whole Genome Amplification ◽  
Dna Amplification ◽  
Whole Genome ◽  
Genome Amplification ◽  
Nicking Endonuclease

scholarly journals Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification

2015 ◽  
Vol 112 (38) ◽  
pp. 11923-11928 ◽  
Author(s):  
Yusi Fu ◽  
Chunmei Li ◽  
Sijia Lu ◽  
Wenxiong Zhou ◽  
Fuchou Tang ◽  
...  
Keyword(s):  
Single Cell ◽  
Whole Genome Amplification ◽  
Multiple Displacement Amplification ◽  
Simultaneous Detection ◽  
Dna Amplification ◽  
Copy Number Variations ◽  
Whole Genome ◽  
Genome Amplification ◽  
High Uniformity

Whole-genome amplification (WGA) for next-generation sequencing has seen wide applications in biology and medicine when characterization of the genome of a single cell is required. High uniformity and fidelity of WGA is needed to accurately determine genomic variations, such as copy number variations (CNVs) and single-nucleotide variations (SNVs). Prevailing WGA methods have been limited by fluctuation of the amplification yield along the genome, as well as false-positive and -negative errors for SNV identification. Here, we report emulsion WGA (eWGA) to overcome these problems. We divide single-cell genomic DNA into a large number (105) of picoliter aqueous droplets in oil. Containing only a few DNA fragments, each droplet is led to reach saturation of DNA amplification before demulsification such that the differences in amplification gain among the fragments are minimized. We demonstrate the proof-of-principle of eWGA with multiple displacement amplification (MDA), a popular WGA method. This easy-to-operate approach enables simultaneous detection of CNVs and SNVs in an individual human cell, exhibiting significantly improved amplification evenness and accuracy.

scholarly journals Quantifying genome DNA during whole-genome amplification via quantitative real-time multiple displacement amplification

RSC Advances ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 4617-4621
Author(s):  
Jing Tu ◽  
Yi Qiao ◽  
Yuhan Luo ◽  
Naiyun Long ◽  
Zuhong Lu
Keyword(s):  
Real Time ◽  
Whole Genome Amplification ◽  
Multiple Displacement Amplification ◽  
Whole Genome ◽  
Genome Amplification

Monitoring multiple displacement amplification by fluorescence signals.

scholarly journals Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): I. CIP Treatment of Samples and Tailing Reaction with Terminal Transferase

2008 ◽  
Vol 2008 (6) ◽  
pp. pdb.prot5002-pdb.prot5002
Author(s):  
C. L. Liu ◽  
B. E. Bernstein ◽  
S. L. Schreiber
Keyword(s):  
Whole Genome Amplification ◽  
Whole Genome ◽  
Linear Amplification ◽  
Genome Amplification ◽  
Terminal Transferase

scholarly journals Species Identification of Pinus Pollen Found in Belukha Glacier, Russian Altai Mountains, Using a Whole-Genome Amplification Method

Forests ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 444
Author(s):  
Fumio Nakazawa ◽  
Yoshihisa Suyama ◽  
Satoshi Imura ◽  
Hideaki Motoyama
Keyword(s):  
Species Identification ◽  
Whole Genome Amplification ◽  
Pollen Grains ◽  
Pollen Grain ◽  
Pinus Sibirica ◽  
Whole Genome ◽  
Accurate Identification ◽  
Closely Related Species ◽  
Genome Amplification ◽  
Amplification Method

Pollen taxa in sediment samples can be identified based on morphology. However, closely related species do not differ substantially in pollen morphology, and accurate identification is generally limited to genera or families. Because many pollen grains in glaciers contain protoplasm, genetic information obtained from pollen grains should enable the identification of plant taxa at the species level. In the present study, species identification of Pinus pollen grains was attempted using whole-genome amplification (WGA). We used pollen grains extracted from surface snow (depth, 1.8–1.9 m) from the Belukha glacier in the summer of 2003. WGA was performed using a single pollen grain. Some regions of the chloroplast genome were amplified by PCR, and the DNA products were sequenced to identify the pollen grain. Pinus includes approximately 111 recognized species in two subgenera, four sections, and 11 subsections. The tree species Pinus sibirica and P. sylvestris are currently found at the periphery of the glacier. We identified the pollen grains from the Belukha glacier to the level of section or subsection to which P. sibirica and P. sylvestris belong. Moreover, we specifically identified two pollen grains as P. sibirica or P. cembra. Fifteen species, including P. sibirica, were candidates for the remaining pollen grain.

scholarly journals A low cost and input tailing method of quality control on multiple annealing, and looping‐based amplification cycles‐based whole‐genome amplification products

2018 ◽  
Vol 33 (3) ◽  
pp. e22697 ◽  
Author(s):  
Changyue Chen ◽  
Jing Li ◽  
JueFeng Wan ◽  
Yuan Lu ◽  
Zhen Zhang ◽  
...  
Keyword(s):  
Quality Control ◽  
Whole Genome Amplification ◽  
Low Cost ◽  
Whole Genome ◽  
Genome Amplification

scholarly journals Correcting palindromes in long reads after whole-genome amplification

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Sven Warris ◽  
Elio Schijlen ◽  
Henri van de Geest ◽  
Rahulsimham Vegesna ◽  
Thamara Hesselink ◽  
...  
Keyword(s):  
Whole Genome Amplification ◽  
Whole Genome ◽  
Genome Amplification ◽  
Long Reads
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