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Int. J. Mol. Sci. 2017, 18(11), 2341; https://doi.org/10.3390/ijms18112341

A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming

1
Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
2
Department of Chemistry, Chinese Culture University, Taipei 11114, Taiwan
3
Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan
4
Center for Biomedical Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan
5
Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 32023, Taiwan
*
Author to whom correspondence should be addressed.
Received: 16 October 2017 / Revised: 2 November 2017 / Accepted: 3 November 2017 / Published: 6 November 2017
(This article belongs to the Special Issue Chloroplast)
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Abstract

Green algae, Chlorella ellipsoidea, Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5–0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time. View Full-Text
Keywords: green algae; rRNA repeated unit; phylogeny; genome skimming green algae; rRNA repeated unit; phylogeny; genome skimming
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Lin, G.-M.; Lai, Y.-H.; Audira, G.; Hsiao, C.-D. A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming. Int. J. Mol. Sci. 2017, 18, 2341.

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