Abstract
The complete Gracilaria bailiniae plastid genome was determined and analyzed in this work. It had a circular mapping molecular with the length of 185,129 bp and contained 231 genes including 193 protein-coding, 3 rRNA, 1 tmRNA, 29 tRNA genes, and 5 unidentified open reading frames. Phylogenetic analysis showed that G. bailiniae clustered together with Gracilaria chorda and Gracilariopsis lemaneiformis. The complete plastid genome provided in this work would be useful for elucidation of Gracilaria evolution.
Gracilaria bailiniae (J.F. Zhang & B.M. Xia) J.F. Zhang & B.M. Xia (Gracilariaceae, Rhodophyta) is a marine red alga. Gracilariopsis bailiniae J. Zhang & B.M. Xia is the basionym of Gracilaria bailiniae. As an agar-producing seaweed (Rabanal et al. Citation1997), efforts have been directed towards the development of culture techniques and the improvement of agar quality (Castaños and Buendia Citation1998). However, there has been no genomic studies on G. bailiniae.
Herein, we reported and characterized the complete G. bailiniae plastid genome (MF372957). One G. bailiniae individual (specimen number: 2016050140) was collected from Shantou, Guangdong Province of China (21°24′26′′ N, 111°13′7′′ E) and stored at −80 °C in the Culture Collection of Seaweed at the Ocean University of China for DNAs isolation. Paired-end reads were sequenced by using Illumina HiSeq × Ten system (Illumina, San Diego, CA). Approximately 9 Gb of paired-end (150 bp) sequence data were randomly extracted from the total sequencing output and used as input for NOVOPlasty (Dierckxsens et al. Citation2017) to assemble the plastid genome. The plastid genome of Gracilaria chorda (GenBank accession number: NC_031149) was used as the seed sequence. The tRNA genes were identified by using tRNAscan-SE Search Server (Schattner et al. Citation2005). Other regions were annotated from the G. chorda plastid genome by using Geneious R10 (Biomatters Ltd, Auckland, New Zealand). The nucleotide sequences were aligned by using MAFFT (Katoh et al. Citation2002). Concatenated alignments were generated and poorly aligned regions were removed by using the Gblocks server (http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=gblocks) (Castresana Citation2000). The phylogeny based on the complete plastid genome shared by Gracilariaceae species was inferred from the ML search and ML bootstrap analysis using RAxML (Stamatakis Citation2006); bootstrap probability values were calculated from 1000 replicates and Rhodymenia pseudopalmata (KC875852) served as the out-group.
The complete G. bailiniae plastid genome is a circular DNA molecule with the length of 185,129 bp. The overall AT content of the complete plastid genome was 62.1%. The plastid genome contained 231 genes, including 193 protein-coding, 3 rRNA, 1 tmRNA, 29 tRNA genes, and 5 unidentified open reading frames. Phylogenetic analysis showed that G. bailiniae clustered together with Gracilaria chorda and Gracilariopsis lemaneiformis () which indicated the phylogenesis classification of G. bailiniae. The determination of the complete plastid genome sequences provided new molecular data to illuminate the Gracilaria evolution.
Figure 1. Phylogenetic tree (maximum likelihood) based on the complete plastid genome sequence of Gracilariaceae. The numbers along the branches are RAxML bootstrap supports based on 1000 nreps (<70% support not shown). The asterisks after species names indicate newly determined mitochondrial genomes.
Disclosure statement
There are no conflicts of interest for all the authors including the implementation of research experiments and writing this article.
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References
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