Preliminary comparison of quantification efficiency between DNA-derived dataset and cell-derived dataset of mixed diatom sample based on rDNA-ITS sequence analysis

Quantification of eukaryotes, such as diatom within a water community is extremely difficult due to the different copy number of the measured gene. ITS sequence was considered to be useful in defining intra-specific or population-level differences for their fast evolving. To assess the possibility o...

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Bibliographic Details
Published in:Biochemical systematics and ecology 2014-12, Vol.57, p.183-190
Main Authors: Guo, Liliang, Sui, Zhenghong, Zhang, Shu, Liu, Yuan, Du, Qingwei
Format: Article
Language:English
Subjects:
Bacillariophyceae
Community structure
Diatom
Diversity
OTUs
Quantification
rDNA
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Summary:Quantification of eukaryotes, such as diatom within a water community is extremely difficult due to the different copy number of the measured gene. ITS sequence was considered to be useful in defining intra-specific or population-level differences for their fast evolving. To assess the possibility of exploring rDNA-ITS region in quantification analysis of environment samples, the fragment of 5.8S + ITS-2 was amplified from extracted DNA and sedimental cell samples derived from the same natural-simulated water community, respectively. Two clone libraries were built from the above DNA-derived (DD) and cell-derived (CD) amplifications. The operational taxonomic units (OTUs) of the libraries were calculated. In most cases, number of OTUs for CD dataset was smaller than DD dataset. For the DD and CD datasets, 112 sequences yielded 6 OTUs-96 and 4 OTUs-97 and were assigned to six and four species, respectively. Intraspecific variations existed in these cultivations. The sequences percentage in datasets did not match with the cell portions in mixed sample, which revealed that 5.8S + ITS-2 copies varied between different diatom species, and it was not suitable for quantitative analysis of diatom community structures in mixed sample. More researches are necessary to seek for proper gene to quantify diatoms in the environmental samples. •DNA extracting was a necessary processing for microbial diversity analysis based clone.•There were intraspecific variations in these cultivations.•rDNA-ITS was not suitable for analysis of diatom community structures in mixed sample.
ISSN:0305-1978
1873-2925
DOI:10.1016/j.bse.2014.08.026