scholarly journals Erratum: The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Ilnam Kang ◽  
Suhyun Kim ◽  
Md. Rashedul Islam ◽  
Jang-Cheon Cho
Keyword(s):  
Complete Genome ◽  
Whole Genome Amplification ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Amplification

scholarly journals The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Ilnam Kang ◽  
Suhyun Kim ◽  
Md. Rashedul Islam ◽  
Jang-Cheon Cho
Keyword(s):  
Metabolic Pathways ◽  
Complete Genome ◽  
Whole Genome Amplification ◽  
Whole Genome ◽  
Bacterial Group ◽  
Freshwater Lakes ◽  
Genome Sequences ◽  
Genome Amplification ◽  
Axenic Cultures ◽  
Niche Diversification

Abstract The acI lineage of the phylum Actinobacteria is the most abundant bacterial group in most freshwater lakes. However, due to difficulties in laboratory cultivation, only two mixed cultures and some incomplete single-amplified or metagenome-derived genomes have been reported for the lineage. Here, we report the initial cultivation and complete genome sequences of four novel strains of the acI lineage from the tribes acI-A1, -A4, -A7, and -C1. The acI strains, initially isolated by dilution-to-extinction culturing, eventually failed to be maintained as axenic cultures. However, the first complete genomes of the acI lineage were successfully obtained from these initial cultures through whole genome amplification applied to more than hundreds of cultured acI cells. The genome sequences exhibited features of genome streamlining and showed that the strains are aerobic chemoheterotrophs sharing central metabolic pathways, with some differences among tribes that may underlie niche diversification within the acI lineage. Actinorhodopsin was found in all strains, but retinal biosynthesis was complete in only A1 and A4 tribes.

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 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 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

scholarly journals Complete Genome Sequences of Campylobacter hyointestinalis subsp. hyointestinalis Strain LMG 9260 and C. hyointestinalis subsp. lawsonii Strain LMG 15993

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
William G. Miller ◽  
Emma Yee ◽  
Mary H. Chapman
Keyword(s):  
Complete Genome ◽  
Whole Genome ◽  
Genome Sequences

Campylobacter hyointestinalis is isolated primarily from ruminants and swine, but is also occasionally isolated from humans. C. hyointestinalis is currently divided into two subspecies, C. hyointestinalis subsp. hyointestinalis and C. hyointestinalis subsp. lawsonii . This study describes the first closed whole-genome sequences of C. hyointestinalis subsp. hyointestinalis isolate LMG 9260 and C. hyointestinalis subsp. lawsonii isolate LMG 15993.

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