title: Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae.
abstract: The 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.
  
  
  
  The 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.
  
  
  
  Chloroplast 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.
authors.affiliation: Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244, Taiwan.
authors.forename: Poh-Kheng
authors.initials: PK
authors.lastname: Ng
authors.affiliation: Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244, Taiwan. linsm@ntou.edu.tw.
authors.forename: Showe-Mei
authors.initials: SM
authors.lastname: Lin
authors.affiliation: Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, 50603, Malaysia. phaikeem@um.edu.my.
authors.forename: Phaik-Eem
authors.initials: PE
authors.lastname: Lim
authors.affiliation: Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244, Taiwan.
authors.forename: Li-Chia
authors.initials: LC
authors.lastname: Liu
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 20244, Taiwan.
authors.forename: Chien-Ming
authors.initials: CM
authors.lastname: Chen
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 20244, Taiwan.
authors.forename: Tun-Wen
authors.initials: TW
authors.lastname: Pai
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D054628:Genome, Chloroplast / Q000235:genetics*; D023281:Genomics; D044724:Gracilaria / Q000145:classification / Q000166:cytology* / Q000235:genetics*; D010802:Phylogeny
keywords: Chloroplast genome; Conserved synteny; Gracilaria firma; Gracilariaceae; Phylogenomic analyses; Red algal plasmid remnants