Abstract
BackgroundThe chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined.ResultsThe chloroplast genome of Gracilaria firma maps as a circular molecule of 187,001 bp and contains 252 genes, which are distributed on both strands and consist of 35 RNA genes (3 rRNAs, 30 tRNAs, tmRNA and a ribonuclease P RNA component) and 217 protein-coding genes, including the unidentified open reading frames. The chloroplast genome of G. firma is by far the largest reported for Gracilariaceae, featuring a unique intergenic region of about 7000 bp with discontinuous vestiges of red algal plasmid DNA sequences interspersed between the nblA and cpeB genes. This chloroplast genome shows similar gene content and order to other Florideophycean taxa. Phylogenomic analyses based on the concatenated amino acid sequences of 146 protein-coding genes confirmed the monophyly of the classes Bangiophyceae and Florideophyceae with full nodal support. Relationships within the subclass Rhodymeniophycidae in Florideophyceae received moderate to strong nodal support, and the monotypic family of Gracilariales were resolved with maximum support.ConclusionsChloroplast genomes hold substantial information that can be tapped for resolving the phylogenetic relationships of difficult regions in the Rhodymeniophycidae, which are perceived to have experienced rapid radiation and thus received low nodal support, as exemplified in this study. The present study shows that chloroplast genome of G. firma could serve as a key link to the full resolution of Gracilaria sensu lato complex and recognition of Hydropuntia as a genus distinct from Gracilaria sensu stricto.
Highlights
The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications
Gracilaria firma has the largest chloroplast genome reported within the order Gracilariales far, with the chloroplast genomes of G. salicornia, G. chilensis, G. tenuistipitata var. liui and Gracilariopsis lemaneiformis each reporting the size of 179, 185, 183 and 183 kb
Despite the rather large variation in genome size, the chloroplast genome of G. firma demonstrated an extensive conservation of synteny to other members of Gracilariales, as evidenced by the single locally collinear blocks (LCBs) resulted from the chloroplast genome alignment (Fig. 3)
Summary
The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. The Florideophyceae which accommodates more than 6700 species of red algae [3] has only chloroplast genomes of 15 species published to date. Gracilaria firma Chang et Xia is an agar-producing seaweed distributed in the tropical and subtropical regions in the western Pacific [7,8,9]. It is an economically important marine crop that has been cultivated on commercial scale in several countries including Taiwan [10], Vietnam [11] and the Philippines [12]. Some regional abalone farms preferred using G. firma as the natural feed [10]
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