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Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/45864

Title: Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta): an update on the use of chloroplast phylogenomics to resolve the Florideophyceae
Authors: Poh-Kheng Ng
Showe-Mei Lin
Phaik-Eem Lim
Li-Chia Liu
Chien-Ming Chen
Tun-Wen Pai
Contributors: 國立臺灣海洋大學:海洋生物研究所
Keywords: Red algal plasmid remnants
Gracilaria firma
Chloroplast genome
Gracilariaceae
Conserved synteny
Phylogenomic analyses
Date: 2017
Issue Date: 2018-04-16T02:03:15Z
Publisher: BMC Genomics.
Abstract: Abstract:Background
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.

Results
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.

Conclusions
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.
Relation: 18(40)
URI: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/45864
Appears in Collections:[海洋生物研究所] 期刊論文

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