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Palmophyllum Crassum , a New Record of an Ancient Species In

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ISSN 1226-9999 (print) ISSN 2287-7851 (online) Korean J. Environ. Biol. 35(3) : 319~328 (2017) https://doi.org/10.11626/KJEB.2017.35.3.319 <Original article> Palmophyllum crassum, a New Record of an Ancient Species in Green Algae from Korea Hyung Woo Lee and Myung Sook Kim* Department of Biology, Jeju National University, Jeju 63243, Republic of Korea Abstract - The continuous exploration in deep seawater from Korea makes us lead the discovery of ancient Chlorophyta, Palmophyllum, in the Korean coast. The phylogenetic analyses of 18S rRNA and rbcL genes demonstrate that our specimens are Palmophyllum crassum (Naccari) Rabenhorst, recorded in Japan and clearly distinguished from P. umbracola from New Zealand and California, USA. Palmophyllum crassum grows in the subtidal region, 8-30 m deep, and has a crustose thallus which is closely adherent to substrates such as non-geniculate crustose coralline algae, sponge, shells, or rocks. P. crassum is composed of numerous spherical cells embedded in the gelatinous matrix. The discovery of this ancient green seaweed implies that the Korean coast is one of the hotspots of algal species diversity and has the suitable marine environment for algal speciation. We suggest the grounds to conserve the Korean coast environmentally as the biodiversity center of marine species by studying the phylogeny of seaweeds. Key words : 18S rRNA, molecular phylogeny, Palmophyllophyceae, Palmophyllum crassum, rbcL INTRODUCTION that the earliest-diverging Chlorophyta comprises marine green algae with simple morphology by revealing a deep- The green algae distributed in freshwater and seawater, branching clade which is a macroscopic algal group named even terrestrial habitats, are photosynthetic eukaryotes char- as the order Palmophyllales including Palmophyllum, Ver- acterized by the presence of chloroplast with two envelope digellas and Palmoclathrus, based on the molecular phylo- membranes, stacked thylakoids, and chlorophyll a and b genetic study. with different morphological organizations such as mona- The palmelloid green algae, Palmophyllum, Palmoclathrus doid, palmelloid, coccoid, coenocytic, and filamentous and Verdigellas, thrive in deep seawater up to >100 m deep, (Pröschold and Leliaert 2007). This green lineage has been where has dimly light marine habitat (Womersley 1971; an essential member in the global ecosystem for a long time Nelson and Ryan 1986; Ballantine and Aponte 1996). These as the ancestor of land plants evolved by the early diver- seaweeds are characterized by a unique multicellularity, gence of Streptophyta and Chlorophyta, from an ancestral forming firm and well-defined macroscopic thalli, referred green flagellate unicell (Leliaert et al. 2012). Therefore, it to as palmelloid thallus organization (Zechman et al. 2010). was generally recognized that the ancestral Chlorophyta is Despite the lack of evidence of the systematic position unicellular with the presence of flagella and organic body within the green algae, these genera had been classified into scales, but this concept has been a matter of debate (Leliaert the family Palmellaceae of the chlorophycean order Volvo- et al. 2016). Recently, Zechman et al. (2010) challenged cales (Fritsch 1935), the family Palmellaceae of the order Tetrasporales (Womersley 1984), or the family Chlorophy- * ‌Corresponding author: Myung Sook Kim, Tel. 064-754-3523, ceae of the order Chlorococcales (Nelson and Ryan 1984). Fax. 064-756-3541, E-mail. [email protected] Recently, since the molecular phylogenetic assessment of ⓒ2017. Korean Society of Environmental Biology. 320 Hyung Woo Lee and Myung Sook Kim Table 1. ‌Collection information and GenBank accession number of Palmophyllum crassum (Naccari) Rubenhorst specimens analyzed in this study GenBank accession No. Taxa Collection information Habit (depth/substratum) Voucher 18S rRNA rbcL Gwideok 1-ri, Jeju, Korea; 25-30 m deep / reef with MSK-GA00830 - MF769365 31 May 2011 crustose coralline algae Chujado, Jeju, Korea; 13-15 m deep / reef with MSK-GA00915 MF769362 MF769367 1 Oct. 2011 crustose coralline algae Udo, Jeju, Korea; 18-25 m deep / reef with MSK-GA00912 - MF769366 1 Nov. 2011 crustose coralline algae Udo, Jeju, Korea; 18-25 m deep / reef with MSK131101-10 MF769361 MF769368 Palmophyllum crassum 1 Nov. 2011 crustose coralline algae (Naccari) Rubenhorst Udo, Jeju, Korea; 18-25 m deep / reef with MSK131101-11 - MF769369 1 Nov. 2011 crustose coralline algae Hyeongjeseom, Busan, Korea; 10-15 m deep / reef with MSK160728-02 MF769363 - 28 Jul. 2016 sponge Shimoda, Shizuoka, Japan; 8-15 m deep / reef with MSK170417-01 MF769364 - 17 Apr. 2017 crustose coralline algae Shimoda, Shizuoka, Japan; 8-15 m deep / reef with MSK170417-03 - MF769370 17 Apr. 2017 sponge the plastid-encoded atpB and rbcL genes and the nuclear- analyses. In addition, to compare with the entities from encoded 18S rRNA gene resolved that these palmelloid Korea, we carried out a collection in Japan. The aims of this genera are positioned to the early diverged lineage in Chlo- study are to identify new green algal entities collected from rophyta forming monophyly in order level, the order Palmo- deep subtidal and to resolve the species diversity of Korean phyllales and the family Palmophyllaceae were established green seaweed by reconstructing the green algal phylogeny (Zeckman et al. 2010). Further, this early evolutionary lin- with recognition of ancient lineage. eage was elevated to the class Palmophyllophyceae, based on the chloroplast phylogenomic analyses (Leliaert et al. 2016). MATERIALS AND METHODS The genus Palmophyllum is reported only two species, P. crassum (Naccari) Rabenhorst and P. umbracola Nelson et The samples were collected using SCUBA (from depths Ryan, all over the world (Guiry and Guiry 2017). P. crassum of 8-30 m) in the southern part of Korea including Jeju has been known as the cosmopolitan species, unlike P. Island and the central coast of Japan (Table 1). Underwater umbracola, which is mainly restricted in the Southern images were obtained using a digital camera (Stylus TG-4, hemisphere (Nelson and Ryan 1984). Although it has been Olympus, Japan). Samples were transported to the labora- recorded in Japan (Yoshida et al. 1990), several investiga- tory and photographed by Canon Powershot G7X camera tions of Korean algal flora have not recognized P. crassum (Canon, Japan). After describing the external morphology, distributed in the deep region (Kang et al. 2011; Kang and voucher specimens were made into pressed ones on the her- Kim 2012). barium sheets. Samples for DNA analyses were detached Recently, the molecular methods have been applied to from the thallus and dried via silica-gel. Samples for ana- green seaweeds from Korean coasts to conduct taxonomic tomical investigations were preserved in 5.0% formalin in reexamination or to describe species diversity (Lee and Kim seawater. Sections were done by a bench-top freezing micro- 2011, 2015). By continuous exploration of deep subtidal tome (NK-101-II; Nippon Optical Works Co., Ltd., Tokyo, regions from Korean coastlines, we obtained crustose and Japan). Photomicrographs were obtained using a BX43 firmly gelatinous green algal specimens unrecognized pre- microscope (Olympus, Tokyo, Japan), with an EOS 600D viously and undertook the molecular and morphological digital camera (Canon, Japan). The digitized images were Palmophyllum crassum from Korea 321 imported into Adobe Photoshop ver. 6.1 software (Adobe RESULTS Systems Inc., San Jose, CA, USA). Voucher specimens were deposited in the herbarium of Jeju National University We analyzed a set of 41 SSU 18S rRNA gene sequences (JNUB), Korea and the National Institute of Biological Re- including the four Palmophyllum crassum (MF769361- sources (NIBR), Incheon, Korea. MF769364) collected from Korea and Japan (Table 1), the DNA was extracted using the DNeasy Plant Mini Kit representative taxa in charophytes, prasinophytes, and core (Qiagen, Hilden, Germany) following the manufacturer’s chlorophytes with Palmophyllophyceae, Palmophyllum instructions. Following DNA extraction, the polymerase umbracola (FJ619275 and FJ619276) and Verdigella peltata chain reaction (PCR) were conducted to amplify the nuclear- (FJ619277 and LT174528). The SSU 18S rRNA data set encoded small subunit (SSU) 18S rRNA gene and the consisted of 1897 characters. Among all sites, 758 (56.1%) ribulose-1, 5-biphospate carboxylase/oxygenage (rbcL). were variable and 506 (26.7%) were parsimoniously infor- Amplification was performed in a 20-μL reaction, using mative. The phylogenetic tree constructed by ML and BI AccuPower PCR PreMix (Bioneer, Daejeon, Korea) and was congruent, and we exhibited the ML topology including Swift MaxPro thermal cyclers (ESCO, Singapore). The pri- the bootstrap (BS) value in ML and posterior probability (PP) mer and PCR protocols for SSU 18S rRNA were followed in BI (Fig. 1). Ulvophyceae-Trebouxiophyceae-Chlorophy- by Saunders and Moore (2013), and those for rbcL were ceae (UTC) and Streptophyta formed each distinct clade in followed by Heesch et al. (2009). PCR products were pu- the SSU phylogenetic tree, but prasinophytes were polyphy- rified using the AccuPrep Purification Kit (Bioneer) and letic. Our four P. crassum specimens collected from Korea sequenced commercially at Macrogen (Seoul, Korea). and Japan were identical, and they formed an independent Sequence edition and alignment were carried out using clade with Palmophyllum umbracola from USA (FJ619275) Chromas version 1.45 software (Queensland,
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    bioRxiv preprint doi: https://doi.org/10.1101/668475; this version posted June 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Andrea Del Cortonaa,b,c,d,1, Christopher J. Jacksone, François Bucchinib,c, Michiel Van Belb,c, Sofie D’hondta, Pavel Škaloudf, Charles F. Delwicheg, Andrew H. Knollh, John A. Raveni,j,k, Heroen Verbruggene, Klaas Vandepoeleb,c,d,1,2, Olivier De Clercka,1,2 Frederik Leliaerta,l,1,2 aDepartment of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium bDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium cVIB Center for Plant Systems Biology, Technologiepark 71, 9052 Zwijnaarde, Belgium dBioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium eSchool of Biosciences, University of Melbourne, Melbourne, Victoria, Australia fDepartment of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800 Prague 2, Czech Republic gDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA hDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA. iDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK jSchool of Biological Sciences, University of Western Australia (M048), 35 Stirling Highway, WA 6009, Australia kClimate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia lMeise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium 1To whom correspondence may be addressed. Email [email protected], [email protected], [email protected] or [email protected].
  • Refinements for the Amplification and Sequencing of Red Algal DNA Barcode and Redtol Phylogenetic Markers: a Summary of Current Primers, Profiles and Strategies

    Refinements for the Amplification and Sequencing of Red Algal DNA Barcode and Redtol Phylogenetic Markers: a Summary of Current Primers, Profiles and Strategies

    Review Algae 2013, 28(1): 31-43 http://dx.doi.org/10.4490/algae.2013.28.1.031 Open Access Refinements for the amplification and sequencing of red algal DNA barcode and RedToL phylogenetic markers: a summary of current primers, profiles and strategies Gary W. Saunders1,* and Tanya E. Moore1 1Centre for Environmental and Molecular Algal Research, Department of Biology, University of New Brunswick, Frederic- ton, NB E3B 5A3, Canada This review provides a comprehensive summary of the PCR primers and profiles currently in use in our laboratory for red algal DNA barcoding and phylogenetic research. While work focuses on florideophyte taxa, many of the markers have been applied successfully to the Bangiales, as well as other lineages previously assigned to the Bangiophyceae sensu lato. All of the primers currently in use with their respective amplification profiles and strategies are provided, which can include full fragment, overlapping fragments and what might best be called “informed overlapping fragments”, i.e., a fragment for a marker is amplified and sequenced for a taxon and those sequence data are then used to identify the best primers to amplify the remaining fragment(s) for that marker. We extend this strategy for the more variable markers with sequence from the external PCR primers used to “inform” the selection of internal sequencing primers. This summary will hopefully serve as a useful resource to systematists in the red algal community. Key Words: DNA barcode; Florideophyceae; molecular markers; phylogeny; polymerase chain reaction; primers; RedToL INTRODUCTION There can be little question that molecular techniques redtol/) (Vis et al. 2010).