ArticleBMC genomics2017
Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- First identification report for amino acid composition of red algaeBiotechnologia · 2024Article
- Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance.BMC genomics · 2023Article
- Phylogeny ofFrontiers in plant science · 2023Article
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- Towards the Well-Tempered Chloroplast DNA Sequences.Plants (Basel, Switzerland) · 2021Article
- Characterization of ACE Inhibitory Peptides Prepared fromMarine drugs · 2021Article
- Foliose Ulva Species Show Considerable Inter-Specific Genetic Diversity, Low Intra-Specific Genetic Variation, and the Rare Occurrence of Inter-Specific Hybrids in the Wild.Journal of phycology · 2021Article
- Identification of evolutionary relationships and DNA markers in the medicinally important genusPeerJ · 2021Article
- The complete chloroplast genome and characteristics analysis of Callistemon rigidus R.Br.Molecular biology reports · 2020Article
- In Silico Analysis of ACE Inhibitory Peptides from Chloroplast Proteins of Red Alga Grateloupia asiatica.Marine biotechnology (New York, N.Y.) · 2020Article
- Comparison of chloroplast genomes of Gynura species: sequence variation, genome rearrangement and divergence studies.BMC genomics · 2019Article
- The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species.Molecules (Basel, Switzerland) · 2019Article
- Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii.Molecules (Basel, Switzerland) · 2018Article
- The Complete Chloroplast Genomes ofFrontiers in plant science · 2018Article
- Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats.PloS one · 2018Article
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6 authors.
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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.
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