Optimized Metavirome Analysis of Marine DNA Virus Communities for Taxonomic Profiling SCIE SCOPUS KCI

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Title
Optimized Metavirome Analysis of Marine DNA Virus Communities for Taxonomic Profiling
Alternative Title
Optimized Metavirome Analysis of Marine DNA Virus Communities for Taxonomic Profiling
Author(s)
Kim, Kang Eun; Jung, Seung Won; Park, Joon Sang; Kim, Hyun Jung; Lee, Chol Young; Ha, Sun-Yong; Lee, Taek Kyun
KIOST Author(s)
Kim, Kang Eun(김강은)Jung, Seung Won(정승원)Park, Joon Sang(박준상)Lee, Chol Young(이철용)Lee, Taek Kyun(이택견)
Alternative Author(s)
김강은; 정승원; 박준상; 김현정; 이철용; 이택견
Publication Year
2022-06
Abstract
Recent advances in metavirome technology have provided new insights into viral diversity and function. The bioinformatic process of metavirome study is generally divided into two (or three) steps: assembly and taxonomic profiling including nucleotide alignment. Moreover, k-mer size and contig length are known to considerably affect the results of the assembly and consequently those of taxonomic profiling; however, the optimal k-mer size and contig length have not been established. In the present study, we analyzed marine virus DNA datasets with three different k-mer sizes using different assemblers: 1 k-mer (20) in the CLC Genomics Workbench, and 4 (21, 33, 55, and 77) and 5 (21, 33, 55, 77, and 99) k-mers in metaSPAdes. The use of large k-mers had the advantage of resolving more repeat regions, with higher N50 values and average contig lengths. The contig length helps reduce the error of continuous sequences and determine the number of viral operational taxonomic units. Our analysis suggested that 300 bp may be an appropriate minimum contig length, depending on the characteristics of viral samples. Based on the assembly result using metaSPAdes, we analyzed the DNA virus community using three taxonomic profiling tools: MG-RAST online server, the taxonomic profiling tools function in the CLC microbial module, and customized taxonomic assignment coding (CUTAXAC) using RStudio based on the BLASTn analysis. CUTAXAC showed the most diverse viral composition at the family and species levels along with the highest Shannon diversity index and fastest analysis time.
ISSN
1738-5261
URI
https://sciwatch.kiost.ac.kr/handle/2020.kiost/42480
DOI
10.1007/s12601-022-00064-0
Bibliographic Citation
OCEAN SCIENCE JOURNAL, v.57, no.2, pp.259 - 268, 2022
Publisher
한국해양과학기술원
Keywords
Customized taxonomic assignment coding (CUTAXAC); Marine metavirome; Taxonomy profiling; Fast analysis time; High Shannon diversity
Type
Article
Language
English
Document Type
Article; Early Access
Publisher
한국해양과학기술원
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