Selection of suitable fragment from rbcl gene for dna barcode analysis of family halymeniaceae, rhodophyta

201 Vietnam Journal of Marine Science and Technology; Vol. 19, No. 4A; 2019: 201–213 DOI: https://doi.org/10.15625/1859-3097/19/4A/14592 https://www.vjs.ac.vn/index.php/jmst Selection of suitable fragment from rbcL gene for DNA barcode analysis of family Halymeniaceae, Rhodophyta Nguyen Xuan Vy 1,2,* , Nguyen Nhat Nhu Thuy 1 , Nguyen Trung Hieu 1 , Nguyen Thi Xuan Thuy 1 1 Department of Marine Botany, Institute of Oceanography, VAST, Vietnam 2 Faculty of Marine Science and Technology, Graduate University of Science and Technology, VAST, Vietnam * E-mail: nguyenxuanvi@gmail.com Received: 30 July 2019; Accepted: 6 October 2019 ©2019 Vietnam Academy of Science and Technology (VAST) Abstract Among the members of Halymeniaceae family, Grateloupia sensu lato occupies the largest composition in species. Classification based on morphological traits is difficult due to the highly variable terete to blade-like thalli among the members of this genus that usually leads to misidentification. Molecular systematics has been applied to classify Grateloupia sensu lato so that the taxonomists acquire a better understanding of the species diversity in general. The plastid gene encoding the large subunit of ribulose-1,5-bisphosphate- carboxylase-oxygenase (rbcL) was the focus of numerous marine algal studies concerning phylogeny and molecular evolution. However, using the full length of rbcL showed disadvantages such as cost and time consuming due to two times of sequencing and two times of PCR. In the present study, the shorter sequence, fragment 773 bp at 5’ end and fragment 579 bp at 3’ end of rbcL were applied and compared for the phylogenetic analysis of Halymeniaceae members. The results indicated there are no differences of topological phylogenetic trees, species resolution within genus and genus resolution within the family between fragment 773 bp at 5’ and the full length of rbcL. Therefore, we conclude that fragment 773 bp at 5’ should be used as DNA barcodes for the Halymeniaceae to reduce the cost and time during phylogenetic analysis. Two taxa Grateloupia newly collected in Vietnam were grouped to the known Phyllymenia, a new genus in Vietnam. Keywords: DNA barcodes, fragments, Halymeniaceae, Phyllymenia, rbcL. Citation: Nguyen Xuan Vy, Nguyen Nhat Nhu Thuy, Nguyen Trung Hieu, Nguyen Thi Xuan Thuy, 2019. Selection of suitable fragment from rbcL gene for DNA barcode analysis of family Halymeniaceae, Rhodophyta. Vietnam Journal of Marine Science and Technology, 19(4A), 201–213. Nguyen Xuan Vy et al. 202 INTRODUCTION Halymeniaceae was considered as the highest species diversity family in Rhodophyta with 343 species which belong to 37 genera. Grateloupia senso lato shows the largest number in species (97 species) [1]. However, members of Grateloupia and closely related genera show highly diverse morphological traits, and it is one of the genera that present a difficult species classification. Therefore, it leads to misidentification among species within the genus and different genera [2]. Based on reproductive anatomy and postfertilization development of cystocarp, Gargiulo et al. [3] indicated that genus Grateloupia should be segregated into multiple genera including Dermocorynus P. L. Crouan et H. M. Crouan, Pachymeniopsis Y. Yamada ex S. Kawabata, Phyllymenia J. Agardh and Prionitis J. Agardh, all of which have been subsumed in Grateloupia by previous authors. In the recent studies of taxonomy based on detailed morphological observations, Grateloupia senso lato was segregated into eight genus including Neorubra M. S. Calderon, G. H. Boo et S. M. Boo; Phyllymenia [4]; Prionitis; Pachymeniopsis; Grateloupia C. Agardh; Mariramirezia M. S. Calderon, G. H. Boo, A. Mansilla et S. M. Boo [5]; Yonagunia (Okamua) Kawaguchi et Masuda and Dermocarpus. Molecular systematics has been applied to classify marine plants so that the taxonomists acquire a better understanding of the species diversity in general. The plastid gene encoding PSII thylakoid protein D1 (psbA) was the focus of numerous brown algal studies concerning phylogeny and molecular evolution [6, 7] whereas, elongation factor Tu gene (tufA) and the large subunit of ribulose-1,5-bisphosphate- carboxylase-oxygenase (rbcL) were used as DNA barcodes for green and red algae, respectively [8, 9]. In contrast, the nuclear internal transcribed spacer (ITS) region including the 5.8S sequence was applied to the molecular systematic of seagrass [10], mangroves [11] and phytoplankton [12]. Nowadays, molecular systematics and detailed morphological observations are two main tools for taxonomic studies. Recently, molecular systematics was applied to study the taxonomy of various marine macrophytes in Vietnam such as seagrass [10, 13], mangroves [14]. Based on phylogenetic analysis of rbcL gene, Nguyen et al. [13] indicated that the red Grateloupia taiwanensis S. M. Lin et H. Y. Liang, the common species in Taiwan and USA was also found at Da Nang, Vietnam. The rare brown alga Dictyota hauckiana Nizamuddin was also recorded in Vietnam for the first time based on the concatenated psbA and rbcL genes [15]. Le et al., [16] published the new description of Gracilaria phuquocensis N. H. Le, N., Muangmai et G.C. Zuccarello with validation of rbcL gene. Therefore, DNA barcoding is an indispensable tool in term of classification of marine algae. DNA barcoding is an approach to identify and recognize species by using short orthologous DNA sequences, known as “DNA barcodes”. The criteria for the development of reliable barcode data are that candidate loci should be suitable for a wide range of taxa, show a high variation between species, but should be conserved within species, so that the intra-specific variation will be insignificant [17]. It is well-known that the full length of rbcL was normally used for the phylogenetic analysis of the Halymeniaceae family, Rhodophyta. However, the disadvantages of the full length of rbcL (1,257 bp) approach were: (i) using three (Wang et al. [9]) or two (Lin et al., [18]) primer pairs for PCR of rbcL, (ii) costly and time consuming due to sequencing cost and two/three times of PCR and (iii) forming long concatenated sequences that increase and prolong steps in the bioinformatic analysis. This led to the hypothesis that phylogenetic analysis based on a short sequence (< 1,000 bp) of rbcL would resolve the taxonomy among members of Halymeniaceae, Rhodophyta instead of using the full length of rbcL (1,257 bp). MATERIALS AND METHODS Sample collection The algal samples were collected at Da Nang City (16 o08’N; 108o07’) and Nha Trang City (12 o15’N; 109o15’), Vietnam (fig. 1) in February 2019. Snorkelling was used to collect Selection of suitable fragment from rbcL gene 203 the samples in the shallow water (3–5 m). Algal materials were washed with seawater in the field to remove the epiphytes and debris that were commonly attached to the algae. Each specimen was placed in a single plastic bag and kept on ice. Materials were transferred to the laboratory within one or two days. In the laboratory, materials were re-washed with de- ionized water to remove seawater. One specimen was divided into three parts, one part was pressed as a herbarium voucher specimen (G04-06DN; G40-42NT) deposited in the Museum of Oceanography, Nha Trang City, Vietnam, another part was fixed in formalin 7% for morphological observation later, and the small blades of herbarium voucher specimen were used for DNA extraction. Information of the samples is presented in Appendix 1. Fig. 1. The map of Vietnam and sampling sites (the black solid rounds). The map was processed by MapInfor Pro TM , version 12.5.5 (Pitney Bowes Software Inc., NY, USA) DNA extraction, polymerase chain reaction (PCR) and sequencing The dried materials were rehydrated in sterile water for one hour. The materials were homogenized by a mortar and pestle in liquid nitrogen, and 100 mg of the finely powdered algal material was used for DNA extraction. The DNA extraction was carried out using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instruction. DNA quality was checked on agarose gels stained with Midori Green Advance (Nippon Genetics Europe GmbH, Düren) and the concentration was measured by a spectrophotometer U-2900 (Hitachi, Tokyo, Japan). The primer pairs of F7 (5’- AACTCTGTAGAACGNACAAG-3’) [19] and R898 (5’-GACGAGAATAAGTTGARTTAC C-3’) [20], and the primer pairs of F762 (5’- GTATGAAAGAGCTGAATTTG-3’) [20] and R1381 (5’-ATCTTTCCATAGATCTAAAGC- 3’) [21] were used to amplify the fragment of 773 bp at 5’ end (Fragment 773 bp-F773) and 597 bp at 3’ end (Fragment 597 bp-F597), respectively. Full length of rbcL (F1257) is a combination of F773 and F597. The PCR compositions and PCR conditions were followed in our previous study [13]. Two fragments were achieved from two independent PCR. All PCR reactions were repeated two to four times independently with the same individual to keep errors (possibly created by the Taq polymerase) in the final consensus sequence to a minimum. PCR products were cleaned using a GenEluteTM PCR Clean-Up kit (Sigma Aldrich, St. Louis, MI, USA) following the manufacturer’s instruction. Direct sequencing of PCR product was done by 1ST BASE (Selangor, Malaysia) from both directions. The consensus sequence was achieved by Clone Manager 9 (Sci-Ed, Cary, NC, USA). For comparison, known rbcL sequences of members of Halymeniaceae were added to the dataset (Appendix 1). Bioinformatics analysis Six F773 sequences and six F597 sequences from three different taxa (from this study) and 62 rbcL sequences of Halymeniaceae were retrieved from the GenBank (Appendix 1). Three datasets (F773, F579 and F1257) were independently analyzed. For each dataset, 68 sequences were aligned by CLUSTAL W using MEGA X [21], and the alignment was further modified by eye. Gaps were considered as missing data. Identical Nguyen Xuan Vy et al. 204 sequences within each species were excluded from the alignment. jModelTest [22] and the corrected AIC were used to find the best model for the analysis. Phylogenetic analyses were performed using Maximum Likelihood (ML) in RAxML version 8.1 with the General Time Reversible (GTR) model, and Bayesian Inference (BI) (Metropolis Coupled Markov- chain Monte-Carlo method, GTR+G model) performed in MrBayes v.3.2.2 [23]. In the BI, the two parallel runs with four chains each (three heated and one cold) were performed for 1 million generations, sampling a tree every 100 generations. Only trees sampled after convergence were used to make inferences about the phylogeny and to compute a 50% majority-rule consensus tree. In the analyses, trees were tested by the bootstrapping method with 1,000 replications. The consensus tree based on two different trees (achieved from the two methods) was constructed by Dendro Scope software, version 3.2.10 [24]. Comparisons of species boundaries among species within a genus, among genera within the family between two phylogenetic trees (F773 vs F1257; F579 vs F1257) were also performed by the tanglegram option in the Dendro Scope software. RESULTS AND DISCUSSION Phylogenetic analysis based on F1257, F773 and F579 fragments Results of the phylogenetic analyses (Maximum Likelihood and Bayesian Inference) based on F1257 showed that all sequences were distributed into 18 main clades. Grateloupia sensu lato was segregated into nine clades consisting of Phyllymenia (I), Neorubra (II), Pachymeniopsis (III), Prionitis (IV), Grateloupia stipitata group (V), Democorynus (VI), Grateloupia carnosa (VII), Grateloupia (VIII) and Mariramirezia (IX). The unknown Grateloupia sp1 (G04DN-G06DN) specimen is sister species to Phyllymenia huangiae S. M. Lin et H. Y. Liang and Grateloupia sp2 (G40NT-G41NT) is sister species to Phyllymenia proteus Kützing. Specimen of Grateloupia ramosissima Okamura collected at Nha Trang was grouped to known G. ramosissima. The bootstrap values and posterior probability are very high (> 80% and 1.0, respectively) (fig. 2). So far, Phyllymenia was based on a single species, Phyllymenia hieroglyphica J. Agardh (1848), described from South Africa [25]. Several studies later placed Phyllymenia in different names such as Iridaea Bory., Cryptymenia, Schmitz, Pachymenia, Grateloupia [2]. Lin et al. [18, 26] suggested that Grateloupia taiwanensis and G. huangiae could be treated as Phyllymenia members due to similarities of cystocarp development. Based on morphological observation of vegetative and reproductive structures as well as phylogenetic analysis of the large subunit of ribulose-1,5- bisphosphate carboxylase-oxygenase (rbcL) sequence, Calderon et al. [4] suggested that Grateloupia taiwanensis, G. huangiae, G. phuquocensis Tanaka et Pham-Hoang, G. sparsa (Okamura) Chiang, G. turuturu Yamada, G. subpectinata Holmes, G. proteus and G. capensis O. De Clerck are members of Phyllymenia. Results of the phylogenetic analyses (Maximum Likelihood and Bayesian Inference) based on F773 indicated that there is no difference of topology from the F1257. Briefly, Grateloupia sensu lato was also segregated into nine clades consisting of Phyllymenia (I), Neorubra (II), Pachymeniopsis (III), Prionitis (IV), Grateloupia stipitata group (V), Democorynus (VI), Grateloupia carnosa (VII), Grateloupia (VIII) and Mariramirezia (IX). Grateloupia ramosissima collected at Nha Trang was grouped to known Grateloupia ramosissima, whereas Grateloupia sp1 and Grateloupia sp2 are sister species of Phyllymenia huangiae and P. proteus, respectively. The bootstrap values and posterior probability at the node Grateloupia sp1/ Phyllymenia huangiae are very high (100% and 1.0, respectively) whereas bootstrap values and posterior probability at the node Grateloupia sp2/ P. proteus are lower (< 50% and 0.75, respectively) (fig. 3). For the result of the phylogenetic analyses based on F579, Grateloupia sensu lato was segregated into eight clades instead of nine clades. Grateloupia stipitata group and Democorynus formed a distinct clade, whereas the six remaining clades formed six distinct genera. Grateloupia sp1 and Phyllymenia Selection of suitable fragment from rbcL gene 205 huangiae are sister species. However, Grateloupia sp2 is sister species with Phyllymenia belangeri instead of sister species of P. proteus like phylogenetic trees based on F1257 and F773. Grateloupia ramosissima collected at Nha Trang was also grouped to known Grateloupia ramosissima (fig. 4). Fig. 2. Phylogeny of members of Halymeniaceae inferred from Bayesian Inference, Maximum Likelihood. The dataset is based on 1257 bp of rbcL. The posterior probability and bootstrap values of each method are shown in each node. Bold, samples collected at Vietnam. The consensus tree was constructed by Dendro Scope software. See Appendix 1 for the number in front of each taxon Nguyen Xuan Vy et al. 206 Fig. 3. Phylogeny of members of Halymeniaceae inferred from Bayesian Inference, Maximum Likelihood. The dataset is based on 773 bp of rbcL. The posterior probability and bootstrap values of each method are shown in each node. Bold, samples collected at Vietnam. The consensus tree was constructed by Dendro Scope software. See Appendix 1 for the number in front of each taxon Selection of suitable fragment from rbcL gene 207 Fig. 4. Phylogeny of members of Halymeniaceae inferred from Bayesian Inference, Maximum Likelihood. The dataset is based on 579 bp of rbcL. The posterior probability and bootstrap values of each method are shown in each node. Bold, samples collected at Vietnam. The consensus tree was constructed by Dendro Scope software. See Appendix 1 for the number in front of each taxon Nguyen Xuan Vy et al. 208 Comparison of species resolution between F1257 and F773, between F1257 and F579 The results of tanglegram phylogenetic tree indicated that there is no difference of topology of phylogenetic trees based on F1257 and F773. All species in this family are resolved in both F1257 (Panel A) and F773 (Panel B). Notably, the boundaries among genus based on F773 is very clear, it is similar to the phylogenetic tree based on F1257. Wang et al. [9] used three primer pairs to apply the full length of rbcL sequence. In the same way, the later studies used two different primer pairs to amplify the full length of rbcL sequence [13, 28]. That leads to cost and time consuming due to two times of sequencing and two times of PCR. Fig. 5. Tanglegram of phylogenetic trees based on different fragments of rbcL. Panel A is phylogenetic tree based on 1,257 bp (including gaps). Panel B is phylogenetic tree based on 773 bp (including gaps) of rbcL. See Appendix 1 for the number in front of each taxon. See figures 3 and figures 4 for bootstrap values and posterior probability. The tanglegram phylogenetic tree was constructed by tanglegram method in Dendro Scope software Comparison of phylogenetic trees based on F1257 and F579 indicated that there are two disadvantages of phylogenetic tree based on F579. The disadvantages are: (i) Grateloupia stipitata was grouped to members of genus Democorynus (Panel B, fig. 6) instead of being grouped to distinct Grateloupia stipitata group (Panel A, fig. 6); (ii) the bootstrap values and Selection of suitable fragment from rbcL gene 209 posterior probability were much lower than F1257 although the species of two markers F1257 and F579 are the same. The main information, advantages and disadvantages among F1257, F773 and F579 were presented in table 1. Fig. 6. Tanglegram of phylogenetic trees based on different fragments of rbcL. Panel A is phylogenetic tree based on 1,257 bp (including gaps). Panel B is phylogenetic tree based on 579 bp (including gaps) of rbcL. See Appendix 1 for the number in front of each taxon. See fig. 3 and 5 for bootstrap values and posterior probability The tanglegram phylogenetic tree was constructed by tanglegram method in Dendro Scope software For other macrophytes like seagrass and mangroves, Nguyen et al. [10, 11] found that rDNA (ITS1-5.8S-ITS2) with the length of 699 bp had more advantages in species resolution than longer length of the concatenated rbcL and matK (1,470 bp). Therefore, ITS could be Nguyen Xuan Vy et al. 210 applied as a DNA barcode for seagrass and mangroves instead of the rbcL/matK system previously proposed. Among three markers, F773 seems to be the best selection because it overcomes the disadvantages of both F579 and F1250. The cost and time consuming and species resolution are similar to F579, but the boundary of the genus is clearer than F579. Compared to F1257, the results of phylogenetic analysis are the same between F773 and F1257, but the cost to carry out the experiments of F1257 is two times higher than F773 due to two times of PCR and sequencing to achieve the length of 1.257 bp. The primers used for F773 can be applied to order family Gigartinales (personal information). Using a single primer pair from this study may fix the criteria of DNA barcoding [17]. The development of reliable barcode data is that candidate loci should be suitable for a wide range of taxa, show a high variation between species, but should be conserved within species, so that the intra-specific variation will be insignificant. Table 1. Main information, advantages and disadvantages among three fragments: F1257, F773 and F579. Bold: Important information Markers Name F773 F579 F1257 Length (bp) 773 597 1,257 Conservation site (%) 62.1 61.1 61.9 Variable sites (%) 37.9 38.9 38.1 Parsimony informative characters (%) 31.7 32.8 32.1 Singleton sites (%) 6.2 6.0 6.0 Genus resolution (%) 100 77 100 Species resolution (%) 100 100 100 Bootstrap values (%) 58–67 < 62 53–96 Posterior probability > 0.5 0.5 Advantages -Full species resolution -Full species resolution -Full species resolution -Full genus resolution -Full genus resolution -Low cost and time consuming -Low cost and time consuming -High bootstrap values and posterior probability -High bootstrap values and posterior probability Disadvantages -Not full genus resolution -High cost and time consuming CONCLUSION The results and discussion presented above prove that i) F773 should be used as DNA barcodes for Halymeniaceae instead of the full length of rbcL to reduce cost and time consuming. ii) Fragment F571 should not be used as DNA barcodes for Halymeniaceae, and iii) Specimens of putative Grateloupia sp1 collected at Da Nang and Grateloupia sp2 collected at Nha Trang should be treated as Phyllymenia sp1 and Phyllymenia sp2, respectively. 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Journal of phycology, 37(3), 433–442. [27] Lin, S. M., and Liang, H. Y., 2011. Grateloupia huangiae (Halymeniaceae, Rhodophyta), a new species from Taiwan previously confused with Polyopes lancifolius, with emphasis on the development of the auxiliary-cell ampullae. Phycologia, 50(3), 232–240. Appendix 1. List of the species included in the molecular analysis done in this study No. Taxa Locations Voucher specimens/GB number 1 Phyllymenia sp1. Da Nang - Vietnam G04DN 2 Phyllymenia sp1. Da Nang - Vietnam G05DN 3 Phyllymenia sp1. Da Nang - Vietnam G06DN 4 Phyllymenia sp2. Nha Trang - Vietnam G40NT 5 Phyllymenia sp2. Nha Trang - Vietnam G41NT 6 Grateloupia ramosissima Nha Trang - Vietnam G43NT 7 Phyllymenia acletoi Peru KF363925 8 Phyllymenia belangeri South Africa AY772035 9 Phyllymenia capensis South Africa AJ868467 10 Pachymeniopsis lanceolata Japan AB055477 11 Phyllymenia longifolia South Africa AY772023 12 Phyllymenia sp Chile KF363932 13 Phyllymenia huangiae Taiwan HM590410 14 Phyllymenia phuquocensis Hawai’i AY772022 Selection of suitable fragment from rbcL gene 213 15 Phyllymenia proteus Italia JX070626 16 Phyllymenia sparsa Japan AB055473 17 Phyllymenia subpectinata Australia AJ868489 18 Phyllymenia taiwanensis Taiwan EU292742 19 Phyllymenia taiwanensis Da Nang - Vietnam MK167364 20 Phyllymenia turuturu Japan AB038611 21 Pachymeniopsis sp Italy AY651060 22 Phyllymenia lanceolata Chile KJ561159 23 Pachymeniopsis chiangii China AB061386 24 Pachymeniopsis imbricata Japan AB038607 25 Pachymeniopsis cornea China AB061381 26 Pachymeniopsis kurogii Japan AB038606 27 Pachymeniopsis elliptica Japan AB038605 28 Pachymeniopsis angusta Japan AB061378 29 Neorubra decipiens Peru KJ561157 30 Mariramirezia lapathifolia Chile KF363928 31 Mariramirezia orsonoensis Chile KF601434 32 Prionitis asiatica Japan AB055487 33 Prionitis livida Japan AB038610 34 Prionitis acuminata Japan SAP 088107 35 Prionitis schmitziana China AB061398 36 Prionitis elata China AB061389 37 Prionitis patens China AB061391 38 Prionitis divaricata Japan AB038609 39 Grateloupia filicina South Africa AY772036 40 Grateloupia nodifera South Africa AY772032 41 Grateloupia stipitata Peru AF488816 42 Grateloupia ramosissima China AB061396 43 Grateloupia catenata Japan AB038613 44 Grateloupia filicina China AB055472 45 Grateloupia hawaiana Hawaii AY772030 46 Grateloupia yangjiangensis China HQ324236 47 Grateloupia yinggehaiensis China HQ332514 48 Grateloupia orientalis Taiwan EU292744 49 Grateloupia carnosa Japan AB038608 50 Mariramirezia doryphora Peru AF488817 51 Mariramirezia doryphora Iberian AM422892 52 Mariramirezia schizophylla Peru KF601431 53 Mariramirezia orsonoensis Chile MG191653 54 Mariramirezia schizophylla Peru KF601430 55 Democorynus dichotoma Italy JX070628 56 Democorynus horrida Italy JX070627 57 Democorynus montagnei Ireland AY435171 58 Yonagunia formosana Vietnam AB116240 59 Yonagunia tenuifolia Japan AB116248 60 Yonagunia zollingerii Indonesia JX627434 61 Cryptonemia lomation France FN908155 62 Halymenia floresii Spain AY772019 63 Carpopeltis phyllophora Australia AB116364 64 Corynomorpha clavata Mexico AY294360 65 Glaphyrosiphon intestinales South Africa AF385639 66 Polyopes constrictus Japan AB055468 67 Aeodes nitidissiama New Zealand GU252161 68 Pachymenia carnosa South Africa AF385640