Estimating Protistan Diversity Using High-Throughput Sequencing

被引：44

作者：

Hu, Sarah K. ^{[1
]}

Liu, Zhenfeng ^{[1
]}

Lie, Alle A. Y. ^{[1
]}

Countway, Peter D. ^{[2
]}

Kim, Diane Y. ^{[1
]}

Jones, Adriane C. ^{[3
]}

Gast, Rebecca J. ^{[4
]}

Cary, S. Craig ^{[5
,6
]}

Sherr, Evelyn B. ^{[7
]}

Sherr, Barry F. ^{[7
]}

Caron, David A. ^{[1
]}

机构：

[1] Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA

[2] Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA

[3] Mt St Marys Coll, Los Angeles, CA 90049 USA

[4] Woods Hole Oceanog Inst, Woods Hole, MA 02543 USA

[5] Univ Waikato, Sch Sci, Environm Res Inst, Hamilton 3240, New Zealand

[6] Univ Delaware, Coll Earth & Ocean Sci, Newark, DE 19716 USA

[7] Oregon State Univ, Coll Ocean & Atmospher Sci, Corvallis, OR 97331 USA

来源：

JOURNAL OF EUKARYOTIC MICROBIOLOGY | 2015年 / 62卷 / 05期

基金：

美国国家科学基金会;

关键词：

18S rRNA gene; biogeography; microbial eukaryotes; protists; V4 tag sequencing; RIBOSOMAL-RNA; REGIONS; RDNA; COMMUNITY;

D O I：

10.1111/jeu.12217

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

Sequencing hypervariable regions from the 18S rRNA gene is commonly employed to characterize protistan biodiversity, yet there are concerns that short reads do not provide the same taxonomic resolution as full-length sequences. A total of 7,432 full-length sequences were used to perform an in silico analysis of how sequences of various lengths and target regions impact downstream ecological interpretations. Sequences that were longer than 400 nucleotides and included the V4 hypervariable region generated results similar to those derived from full-length 18S rRNA gene sequences. Present high-throughput sequencing capabilities are approaching protistan diversity estimation comparable to whole gene sequences.

引用

页码：688 / 693

页数：6

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