Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae

BMC Genomics

Research Article

Tun-Wen Pai¹  Chien-Ming Chen¹  Showe-Mei Lin²  Li-Chia Liu²  Poh-Kheng Ng²  Phaik-Eem Lim³ 

[1] Department of Computer Science and Engineering, National Taiwan Ocean University, 20244, Keelung, Taiwan;Institute of Marine Biology, National Taiwan Ocean University, 20244, Keelung, Taiwan;Institute of Ocean and Earth Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia;

关键词: Chloroplast genome;    Gracilaria firma;    Gracilariaceae;    Conserved synteny;    Phylogenomic analyses;    Red algal plasmid remnants;   

DOI  :  10.1186/s12864-016-3453-0

 received in 2016-10-18, accepted in 2016-12-22,  发布年份 2017

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2017