Abstract
The complete plastid genome of Gracilaria textorii, a marine red macroalga, was determined and analyzed. The plastid genome sequence of G. textorii is 179,609 bp. It contains 237 genes, including 203 protein-encoding genes, 30 tRNA genes, 3 rRNA genes, 1 ribonuclease gene, and 1 intron inserted into the trnM gene. Phylogenetic analysis showed that G. textorii clustered together with Gracilaria salicornia, which helps the better understanding of Gracilaria evolution process.
Keywords: Gracilaria textorii, Gracilariaceae, plastid genome, phylogenetic analysis
Gracilaria textorii (Suringar) De Toni is a marine red alga belonging to the family Gracilariaceae (http://www.algaebase.org/). Sphaerococcus textorii Suringar is the basionym of G. textorii. It is a taurine-rich red edible alga which may be used to create functional foods that are rich in naturally occurring taurine. (Kawasaki et al. 2017). The seaweed extract has the anti-inflammatory effect (Kim et al. 2018). It also was found effective on the germination, growth, and yield of some vegetable crops which can be used as fertilizer. In addition, a quantitative differential gene expression analyses of some G. textorii genes indicated this species could be applicable to marine environment monitoring (Woo et al. 2008). However, until recently, no genomic studies on G. textorii have been reported.
The determination of the complete G. textorii plastid genome sequence by next-generation sequencing methods was conducted. The specimen was collected from north China (Taigong Island, Rizhao, Shandong Province, 35°27′54′′ N, 119°35′58′′ E) and stored at the Culture Collection of Seaweed at the Ocean University of China (accession number: 2017050065). Total DNA was extracted using the modified CTAB method (Doyle and Doyle 1990). Paired-end reads (150 bp) were sequenced by using Illumina HiSeq system (Illumina, San Diego, CA, USA). tRNAscan-SE Search Server (Schattner et al. 2005) was used to identify the tRNA genes. The other plastid genomic regions were annotated with Geneious R10 (Biomatters Ltd, Auckland, New Zealand), using the Gracilaria chilensis (NC_029860) plastid genome as a reference.
The complete G. textorii plastid genome is a circular DNA molecule measuring 179,609 bp in length with the overall G + C content of 28.78% (GenBank accession number MN053320). The plastid genome contained 237 genes, including 203 protein-coding genes, 1 ribonuclease gene (rnpB), 3 rRNA genes, 30 tRNA genes, and 1 intron interrupting the trnM gene. The nucleotide composition was 35.73% A, 14.44% C, 14.34% G, and 35.49% T. The length of the coding region was 145,209 bp, corresponding to 80.85% of the total length. The plastid genome of G. textorii was compact, with 11 pairs of overlapping genes found with overlap lengths of 3–95 bp (trnT–ilvB, rnpB–syfB, ycf40–rps1, ycf29–trnH, psbD–psbC, carA–ycf53, trnR–chlI, atpF–atpD, rps18–rpl33, rpl23–rpl4, and rpl14–rps17).
82 shared plastid protein sequences from 17 red algae including G. textorii were used to conduct phylogenetic analysis by using MrBayes 3.1.2 software (Ronquist and Huelsenbeck 2003). Cyanidioschyzon merolae (NC_004799) was served as the outgroup. Poorly aligned regions were removed by using the Gblocks server. Florideophyceae, Bangiophyceae and Cyanidiophyceae species formed separate branches (Figure 1). G. textorii showed a closer relationship with Gracilaria salicornia in Gracilaria. This complete plastid genome analysis of G. textorii helps us better understand the evolutionary process of Gracilaria.
Figure 1.
Phylogenetic tree (Bayesian method) based on the complete plastid genome sequence of red algae as shown below: Gracilaria textorii (MN053320), Gracilaria salicornia (NC_023785), Gracilaria tenuistipitata var. liui (AY673996), Gracilaria chilensis (NC_029860), Gracilariopsis chorda (NC_031149), Gracilariopsis lemaneiformis (KP330491), Grateloupia taiwanensis (KC894740), Schizymenia dubyi (NC_031169), Chondrus crispus (NC_020795), Ceramium japonicum (NC_031174), Nemalion sp. (LT622871), Ahnfeltia plicata (NC_031145), Palmaria palmata (NC_031147), Pyropia yezoensis (KC517072), Porphyra purpurea (U38804), Galdieria sulphuraria (KJ700459), and Cyanidioschyzon merolae (NC_004799). The asterisks after species names indicate newly determined plastid genomes.
Disclosure statement
No conflict of interest for all the authors including the implementation of research experiments and writing this article was reported.
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