An Sung Min, Choi Dong Han, Lee Jung Ho, Lee Howon, Noh Jae Hoon
Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science & Technology, Ansan, Republic of Korea.
Department of Marine Biology, University of Science and Technology, Daejeon, Republic of Korea.
PLoS One. 2017 Jun 16;12(6):e0179422. doi: 10.1371/journal.pone.0179422. eCollection 2017.
Benthic diatoms isolated from tidal flats in the west coast of Korea were identified through both traditional morphological method and molecular phylogenetic method for methodological comparison. For the molecular phylogenetic analyses, we sequenced the 18S rRNA and the ribulose bisphosphate carboxylase large subunit coding gene, rbcL. Further, the comparative analysis allowed for the assessment of the suitability as a genetic marker for identification of closely related benthic diatom species and as potential barcode gene. Based on the traditional morphological identification system, the 61 isolated strains were classified into 52 previously known taxa from 13 genera. However, 17 strains could not be classified as known species by morphological analyses, suggesting a hidden diversity of benthic diatoms. The Blast search on NCBI's Genebank indicated that the reference sequences for most of the species were absent for the benthic diatoms. Of the two genetic markers, the rbcL genes were more divergent than the 18S rRNA genes. Furthermore, a long branch attraction artefact was found in the 18S rRNA phylogeny. These results suggest that the rbcL gene is a more appropriate genetic marker for identification and classification of benthic diatoms. Considering their high diversity and simple shapes, and thus the difficulty associated with morphological classification of benthic diatoms, a molecular approach could provide a relatively easy and reliable classification system. However, this study suggests that more effort should be made to construct a reliable database containing polyphasic taxonomic data for diatom classification.
通过传统形态学方法和分子系统发育方法对从韩国西海岸潮滩分离出的底栖硅藻进行鉴定，以比较这两种方法。对于分子系统发育分析，我们对18S rRNA和核酮糖二磷酸羧化酶大亚基编码基因rbcL进行了测序。此外，通过比较分析可以评估其作为鉴定近缘底栖硅藻物种的遗传标记以及潜在条形码基因的适用性。基于传统形态学鉴定系统，61株分离菌株被归类为13个属中的52个已知分类单元。然而，17株菌株通过形态学分析无法归类为已知物种，这表明底栖硅藻存在隐藏的多样性。在NCBI的基因库上进行的Blast搜索表明，底栖硅藻的大多数物种缺乏参考序列。在这两个遗传标记中，rbcL基因比18S rRNA基因的差异更大。此外，在18S rRNA系统发育中发现了长枝吸引假象。这些结果表明，rbcL基因是用于底栖硅藻鉴定和分类的更合适的遗传标记。考虑到底栖硅藻的高度多样性和简单形状，以及因此与底栖硅藻形态分类相关的困难，分子方法可以提供一个相对简单可靠的分类系统。然而，这项研究表明，应该做出更多努力来构建一个包含多相分类数据的可靠数据库，用于硅藻分类。
