Chloroplast genomes as a tool to resolve red algal phylogenies: a case study in the Nemaliales

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0772-3) contains supplementary material, which is available to authorized users.

Molecular Assisted Identification Reveals Hidden Red Algae Diversity from the Burica Peninsula, Pacific Panama

“…Divergences between H. borowitzkae specimens and sequences available from other Hommersandiophycus species ranged from 3.9-9.1%. been recorded previously from both the Caribbean and Pacific coasts of Central America e.g., [5,38,39]. This is the first report of the species from Pacific Panama.…”

“…However, the level of sequence variation between the Punta Burica specimens and other specimens in this clade are greater than the intraspecific values that have been found in many studies i.e., [36,37], and although T. cylindrica is assigned to the Punta Burica specimens here, a world-wide reassessment of the species is needed to determine its true distribution. Tricleocarpa cylindrica has been recorded previously from both the Caribbean and Pacific coasts of Central America e.g., [5,38,39]. This is the first report of the species from Pacific Panama.…”

“…Two of these species, are known only from Taiwan. Izziella orientalis has been recorded in both the Indian and Pacific Oceans, while I. formosana, originally described from Taiwan, was also recently reported from Pacific Costa Rica [39]. This is the first report of an Izziella species from Pacific Panama.…”

“…Neoizziella currently includes only two species, N. asiatica and N. divaricata [42,46]. A recent Costa Rica record of Neoizziella asiatica was the first from outside of the Indo-Pacific region [39]. This is the first report of the species from Pacific Panama.…”

Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta)

“…However, red algae are still underrepresented in genome datasets, despite promising results whenever they have been applied to phylogenetic studies (Costa et al. , Lee et al. ).…”