Estimation of 18S Gene Copy Number in Marine Eukaryotic Plankton Using a Next-Generation Sequencing Approach

被引：106

作者：

Gong, Weida ^{[1
]}

Marchetti, Adrian ^{[1
]}

机构：

[1] Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27515 USA

来源：

FRONTIERS IN MARINE SCIENCE | 2019年 / 6卷

关键词：

18S rRNA gene; amplicon sequencing; plankton community composition; bioinforrnatics; microbial ecology; READ ALIGNMENT; GENOME; QUANTIFICATION; DIVERSITY; RDNA;

D O I：

10.3389/fmars.2019.00219

中图分类号：

X [环境科学、安全科学];

学科分类号：

08 ; 0830 ;

摘要：

The small subunit 18S rRNA (18S) gene is the most commonly used marker for taxonomic identification in eukaryotes. However, protists may harbor substantial variation in their 18S gene copy number, which can lead to a rapid decline in concordance between 18S gene sequences and actual organismal abundances. Here we used a computational method to estimate 18S gene copy number in seven species of marine eukaryotic phytoplankton and found large interspecies and strain-level differences across and within the examined species. Our results emphasize that variations in 18S gene copy number need to be taken into consideration and that corrections can improve the accuracy of quantitative eukaryotic microbial community profiles.

引用

页数：5

共 50 条

[1] Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias
Martin, Jon Lapeyra
Santi, Ioulia
Pitta, Paraskevi
John, Uwe
Gypens, Nathalie
METABARCODING AND METAGENOMICS, 2022, 6 : 245 - 259
[2] Copy Number Variation Detection Using Next-Generation Sequencing
Baughn, Linda B.
Onsongo, Getiria
Bower, Matthew
Henzler, Christine
Silverstein, Kevin A. T.
Thyagarajan, Bharat
AMERICAN JOURNAL OF CLINICAL PATHOLOGY, 2015, 143 : A13 - A13
[3] Copy Number Variant Detection by Targeted Gene Next-Generation Sequencing
Myers, C. E.
Nguyen, H. L.
Hauenstein, J.
Saxe, D. F.
Smith, G. H.
Hill, C. E.
Zhang, L.
Deeb, K. K.
JOURNAL OF MOLECULAR DIAGNOSTICS, 2019, 21 (06): : 1150 - 1151
[4] An approach for determination of copy number variation using short-read next-generation sequencing
Reeves, K.
Bourbon, M.
Hurd, D.
Reid, J.
Molha, D.
Houniet, D.
Cousin, J.
EUROPEAN JOURNAL OF HUMAN GENETICS, 2018, 26 : 649 - 649
[5] Personalized copy number and segmental duplication maps using next-generation sequencing
Alkan, Can
Kidd, Jeffrey M.
Marques-Bonet, Tomas
Aksay, Gozde
Antonacci, Francesca
Hormozdiari, Fereydoun
Kitzman, Jacob O.
Baker, Carl
Malig, Maika
Mutlu, Onur
Sahinalp, S. Cenk
Gibbs, Richard A.
Eichler, Evan E.
NATURE GENETICS, 2009, 41 (10) : 1061 - U29
[6] Personalized copy number and segmental duplication maps using next-generation sequencing
Can Alkan
Jeffrey M Kidd
Tomas Marques-Bonet
Gozde Aksay
Francesca Antonacci
Fereydoun Hormozdiari
Jacob O Kitzman
Carl Baker
Maika Malig
Onur Mutlu
S Cenk Sahinalp
Richard A Gibbs
Evan E Eichler
Nature Genetics, 2009, 41 : 1061 - 1067
[7] Copy number variation of individual cattle genomes using next-generation sequencing
Bickhart, Derek M.
Hou, Yali
Schroeder, Steven G.
Alkan, Can
Cardone, Maria Francesca
Matukumalli, Lakshmi K.
Song, Jiuzhou
Schnabe, Robert D.
Ventura, Mario
Taylor, Jeremy F.
Garcia, Jose Fernando
Van Tasse, Curtis P.
Sonstegard, Tad S.
Eichler, Evan E.
Liu, George E.
GENOME RESEARCH, 2012, 22 (04) : 778 - 790
[8] A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing Data
Hill, Tom
Unckless, Robert L.
G3-GENES GENOMES GENETICS, 2019, 9 (11): : 3575 - 3582
[9] Identification of eukaryotic microorganisms with 18S rRNA next-generation sequencing in wastewater treatment plants, with a more targeted NGS approach required for Cryptosporidium detection
Zahedi, Alireza
Greay, Telleasha L.
Paparini, Andrea
Linge, Kathryn L.
Joll, Cynthia A.
Ryan, Una M.
WATER RESEARCH, 2019, 158 : 301 - 312
[10] GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads
Fanny-Dhelia Pajuste
Maido Remm
Scientific Reports, 13

← 1 2 3 4 5 →