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Ribulose-1, 5-Bisphosphate Carboxylase/Oxygenase Gene Sequencing in Taxonomic Delineation of Padina Species in the Northern Coast of the Persian Gulf, (IRAN)

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Ribulose-1, 5-Bisphosphate Carboxylase/Oxygenase Gene Sequencing in Taxonomic Delineation of Padina Species in the Northern Coast of the Persian Gulf, (IRAN) Journal of the Persian Gulf (Marine Science)/Vol. 4/No. 13/September 2013/11/47-57Journal of the Persian Gulf Ribulose-1, 5-Bisphosphate Carboxylase/Oxygenase Gene Sequencing in Taxonomic Delineation of Padina Species in the Northern Coast of the Persian Gulf, (IRAN). Amini, Faedeh1*; Riahi, Hossein1; Zolgharnain, Hossein2 1- Faculty of Biosciences, Shahid Beheshti University, G.C., Tehran, IR Iran 2- Faculty of Marine Biology. Khorramshahr Marine Science and Technology University, Khorramshahr, IR Iran Received: May 2013 Accepted: August 2013 © 2013 Journal of the Persian Gulf. All rights reserved. Abstract Taxonomic study of the genus Padina (Dictyotales, Phaeophyceae) from the Persian Gulf coast was conducted based on morphology and molecular phylogenetic analyses using chloroplast encoded large subunit RuBisCo (rbcL) gene sequences. Detailed descriptions of each species found in this study are described. Several morphological characters, such as number of cell layers composing the thallus, presence or absence and degree of calcification, presence or absence of small groups of rhizoid-like hairs, structure, position and arrangement of hairlines, presence or absence of indusium and reproductive sori, are considered to be reliable morphological characters for species delineation. In this study, it was realized there were 12 new sequences among the samples examined and as such, based on the rbcL sequences, four species could be tentatively delineated along the Persian Gulf coast: Padina sp.FA, Padina sp.PG, Padina sp. INDEGR032 and Dictyota ciliolate Sonder ex Kützing 1859. Further work is required to complete description of new species based on morphology and molecular analyses. Keywords: Macroalgae, Padina genus, Systematic, Molecular studies, rbcL gene. 1. Introduction and Rabii 1996, 1999, 2004, 2008). There are articles about taxonomy of macroalgae on Arabian coasts of Species of the marine brown algal genus Padina Persian Gulf, (Al-Hasan and Jones, 1989, Basson et are widely distributed throughout the tropics and are al., 1977, 1989., Basson etal,. 1992, Basson, 1979a., very easy to recognize in the field with their "fan- 1979b., Børgesen, 1939., DeClerk et al., 1996, like" blade. According to Algae Base (Guiry&Guiry, Newton, 1955a., 1955b., and Abdel-Kareem, 2009). 2013: http://www.algaebase.org), 37 species are Taxonomic studies of Padina species in the coast of currently recognized worldwide, in which 6 species the Persian Gulf were, until recently, usually dealt were recorded in the northern of Persian Gulf coast with revisions or descriptions exclusively based on of Iran based on morphological studies (Børgesen, somewhat variable morphological characters, e.g., 1939., Nizamuddin and Gesner 1970., Sohrabipour thallus shape, size and color (Trono, 1969 and Ni-Ni- Win et al., 2011). Furthermore, several recent studies 1* E-mail: [email protected] dealing with European and Mediterranean taxa 47 Amini et al. / Ribulose-1, 5-Bisphosphate Carboxylase/Oxygenase Gene Sequencing in Taxonomic Delineation… indicated that common morphological data without in December 2009, August and March 2010, August the support of DNA sequence data were insufficient and September 2011 (Figure 1). basis for estimating species diversity and knowledge of species boundaries (De Clerck et al., 2005 and 2006). However, a few papers based on taxonomic sources, were published dealing with the marine algal flora of the Persian Gulf, for example, the molecular RAPD and ISSR markers studies on three Sargassum species (Noormohammadi et al., 2011b). In addition, Padina could be employed as a possible environmental bioindicator in the Persian Gulf (Amini et al., 2013); therefore it is very important to identify the Padina species. The chloroplast-encoded Fig. 1. Locations of sampling for seaweeds on the intertidal Coast of Persian Gulf of Iran. 1. Kish island, 2. Lengeh area, 3. large subunit of the RUBISCO gene (rbcL) has been Shib Deraz (Qeshm island), 4. Messen(Qeshm island), 5. used in molecular phylogenetic studies of brown Behined Farmandari (Qeshm island) algae and has been demonstrated to be a useful molecular marker by many authors (Cho et al., 2004, The samples were obtained by hand and diving Hoshina et al., 2004, De Clerck et al., 2006, Cho et preserving proceeds followed (Tsuda, 1972) and al., 2007, Bittner et al., 2008, Ni-Ni-Win et al., 2008, DNA extraction, amplification (PCR) of rbcL 2010, 2011, Phillips et al., 2008). Thus, in this study, region, and sequencing followed (Siemer et al., rbcL is used as molecular marker combined with 1998 and Ni-Ni-Win et al., 2008). For anatomical morphological observations to clarify the taxonomy observations, specimens were hand-sectioned and of Padina species and evaluate taxonomically micrographed using a Dino Capture Ver.3 Digital important morphological characters. We infer a Camera attached to a microscope CH 40 (Olympus, phylogeny of the genus with 12 newly generated Japan). For each specimen, the morphological and sequences plus already available sequence data, anatomical characteristics (vegetative and discuss the molecular taxonomy of the genus, and reproductive) were analyzed. According to (Ni-Ni- suggest possibility of describing new species based Win et al., 2011) some of the morphological on combined morphological and molecular analyses. characters like shape, size, color, and thickness of In this study detailed descriptions of all species the thallus, are highly variable within the species examined are provided based on recently collected and are dependent to environmental conditions and samples and type specimens. age of the individual. But other characters like the number of cell layers, presence or absence and 2. Materials and Methods degree of calcification, the structure and the position arrangement of hair lines and arrangement The brown algae Padina species (Phaeophyceae, of them with sporangial sori, presence or absence of Dictyotales, Dictyotaceae) were collected from an indusium, the presence or absence of groups of Persian Gulf in the intertidal regions along the rhizoid-like hairs on the thallus surface, and southern coast of Iran, namely: Kish island (26° 51' reproductive sori were considered stable within the N, 53°59' E), Lengeh area (26° 28' N, 54°78' E ), species. The collected samples were deposited in Shib Deraz (26° 42' N, 56°04' E), Messen (26° 49' N, HSBU Bioscience Faculty (Beheshti University 53°23' E), Behind Farmandari (27° 04' N, 56°59' E) Herbarium). Total genomic DNA was extracted 48 Journal of the Persian Gulf (Marine Science)/Vol. 4/No. 13/September 2013/11/47-57 from tissue samples, dried in a silica gel DNA heuristic search with tree-bisection-reconnection extraction, with amplification (PCR) of the rbcL (TBR) branch swapping options. Bootstrap region and sequencing using an extraction protocol resampling was carried out with 100 replicates for detailed by (Ni-Ni-Win et al., 2008, 2011a and ML and 1000 replicates for NJ and MP (Felsenstein, 2011b). The PCR conditions for rbcL were as 1985). Dictyota ciliolata and Dictyota dicotoma follows: an initial denaturation step at 94°C for 3 (Dictyotales) were considered as outgroup to root the min, followed by 94°C for 0.5 min, annealing at trees. 58°C for 0.5 min, extension at 72°C for 2 min for 28 cycles, and final extension at 72°C for 10 min. 3. Results PCR products were checked for length and yielded by electrophoresis on 1.5% agarose gels dyed with 3.1. Morphological Observations ethidium bromide. In order to minimize possible errors during PCR, three independent PCR reactions All specimens used for this study are listed in were performed for each DNA sample. Primer Tables 2 and 3. The major morphoanatomical sequences, annealing temperatures and characters used for species identification are been bibliographic sources are provided in Table 1. summarized in Table 4. Table 1.The Primers that used in this study Padin sp. PG, haplotype 1 nov. AB793713 HSBU- Primer Sequence Annealing Gene Direction Reference name (5'a→3') T°C 2011300 GGGTAATTTGT Ni-Ni-Win et al., 2008 rbcL-P1 rbcL Forward 64 AAGTGGATGCG and Kawai et al., 2007 CGACGAAGTCA Ni-Ni-Win et al., 2008 rbcL-D2 rbcL Reversed 61.4 GGAGTATCTG and Kawai et al., 2007 GTGGACTGTTG The erect thalli with 2-4 cell layers, (4 cells Fa(57-76) rbcL Forward 60.6 Present study TTTGGACTG ACATTTACGAA Ra500-519 rbcL Reverse 59.7 Present study layered at the base) is yellowish brown in color, GAGAAGCCC attached by branched rhizoidal stipe. Thalli DNA sequences are deposited in DNA Data Bank moderately calcified on both surfaces, blades are of Japan (DDBJ). The 12 newly generated sequences divided deeply into 5 fan-shaped segments, the were complemented with 31 sequences downloaded length of each segment is between 5 to 10 cm, and from Genbank and aligned using (Thompson et al., the width up to 4 cm. The stipe is up to 5 cm long 1994) and the alignment was refined manually. and 0.2 cm wide. Sporangia rows are closely Phylogenetic analyses were carried out by maximum alternate with hair rows at different intervals parsimony (MP), maximum likelihood (ML) and without indusia, sometimes as isolated patches neighbor joining (NJ) methods, using MEGA5.1 between two hair lines on the lower surface when (Tamura et al., 2011). An appropriate model of both surfaces are viewed together. The species sequence evolution for maximum likelihood (ML) resembles P. tetrastromatica Hauck but the blades analysis was selected the best-fit models based on of P. tetrastromatica Hauck showed no AICc values criterion with MEGA’s built-in model calcification (Wynne et al., 1998) but this species testing suite. A ML tree was inferred using the has light calssification on two sides. In cross selected GTR model using nearest neighbor sections of the blades, both in mid region and in interchange tree rearrangements. A neighbour- more basal portions showed a 4 layered joining (NJ) distance-based tree was constructed organization but Padina sp. PG has 2 cell layer (Saitou and Nei etal., 1987 and Nei etal., 2000) using and 4 layers at the base.
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