ArticleBMC evolutionary biology2016
Chloroplast genomes as a tool to resolve red algal phylogenies: a case study in the Nemaliales.
Article in BMC evolutionary biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 51 citations in OpenAlex.
- Mitogenome structure and phylogenomics of the order Thoreales (Nemaliophycidae, Rhodophyta).Journal of phycology · 2026Article
- Plastid genome structure and phylogenomics of the freshwater red algal order Batrachospermales (Rhodophyta).Journal of phycology · 2026Article
- ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.Molecular ecology resources · 2026Article
- Complete chloroplast genome sequence and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2026Article
- Phylogenetic relationships among seven freshwater red algal genera in the Batrachospermaceae (Batrachospermales, Rhodophyta) using complete chloroplast genome data.Journal of phycology · 2025Article
- Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alga Dasyclonium.Molecular ecology resources · 2025Article
- The versatility of algae in addressing the global sustainability challenges.Frontiers in bioengineering and biotechnology · 2025Review
- Complete chloroplast genome of the marine red algaMicrobiology resource announcements · 2024Article
- Description ofPhytoKeys · 2024Article
- Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution.Frontiers in plant science · 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
- Relative expression analysis of light-harvesting genes in the freshwater alga Lympha mucosa (Batrachospermales, Rhodophyta).Journal of phycology · 2020Article
- Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era.Ecology and evolution · 2020Article
- The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species.Molecules (Basel, Switzerland) · 2019Article
- Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats.PloS one · 2018Article
- Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence.Scientific reports · 2017Article
- Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora.Genetics and molecular biologyArticle
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Authors and funding
5 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundObtaining strongly supported phylogenies that permit confident taxonomic and evolutionary interpretations has been a challenge in algal biology. High-throughput sequencing has improved the capacity to generate data and yields more informative datasets. We sequenced and analysed the chloroplast genomes of 22 species of the order Nemaliales as a case study in the use of phylogenomics as an approach to achieve well-supported phylogenies of red algae.
resultsChloroplast genomes of the order Nemaliales are highly conserved, gene-dense and completely syntenic with very few cases of gene loss. Our ML estimation based on 195 genes recovered a completely supported phylogeny, permitting re-classification of the order at various taxonomic levels. Six families are recognised and the placement of several previously contradictory clades is resolved. Two new sub-orders are described, Galaxaurineae and Nemaliineae, based on the early-branching nature and monophyly of the groups, and presence or absence of a pericarp. Analyses of subsets of the data showed that >90 % bootstrap support can be achieved with datasets as small as 2500 nt and that fast and medium evolving genes perform much better when it comes to resolving phylogenetic relationships.
conclusionsIn this study we show that phylogenomics is an efficient and effective approach to investigate phylogenetic relationships. The six currently circumscribed Nemaliales families are clustered into two evolutionary lineages with strong statistical support based on chloroplast phylogenomic analyses. The conserved nature of red algal chloroplast genomes is a convenient and accessible source of data to resolve their ancient relationships.
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