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

Geng-Ming Lin,Yu-Heng Lai,Gilbert Audira,Chung-Der Hsiao

doi:10.3390/ijms18112341

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.

Highlights

Green algae, a big group which contains at least 7000 species, has been found in wide range habitats from freshwater to sea water [1]
In this study, we demonstrated a genome skimming method to deduce the complete 18-5.8-28S rRNA repeated sequence, which used as a molecular tool to reveal the relationships between Haemotococcus pluvalis, Chlorella ellipsoidea and Aegagropila linnaei to discuss the relationship between the freshwater and marine algae
Internal transcribed spacers (ITS) are sequences located in eukaryotic rRNA genes between the 18S and 5.8S rRNA coding regions (ITS1) and between the 5.8S and 28S rRNA coding regions (ITS2)

Summary

Introduction

A big group which contains at least 7000 species, has been found in wide range habitats from freshwater to sea water [1]. The rapid increase in genomic data from a wide range of green algae has high potential to resolve large-scale green algal relationships. In this study, we demonstrated a genome skimming method to deduce the complete 18-5.8-28S rRNA repeated sequence (as a nuclear marker), which used as a molecular tool to reveal the relationships between Haemotococcus pluvalis, Chlorella ellipsoidea and Aegagropila linnaei to discuss the relationship between the freshwater and marine algae.

Results

Conclusion