Multigene phylogeny of the red algal subclass Nemaliophycidae

Lam, Daryl W.; Verbruggen, Heroen; Saunders, Gary W.; Vis, Morgan L.

doi:10.1016/j.ympev.2015.10.015

Cited by 21 publications

(31 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…More recently, molecular data have been analyzed and great progress has been made in describing new genera and species (Cianciola et al 2010; Saunders and McDonald 2010; Le Gall and Saunders 2010). However, teasing apart the evolutionary histories of red algal orders has proven quite difficult even with the abundance of sequence data currently available (Verbruggen et al 2010; Lam et al 2016). Resolving the evolutionary relationships among florideophytes will provide a robust framework for asking a wide range of evolutionary questions including, but not limited to, transitions from marine to freshwater habitats, the evolution of the complex triphasic life-cycle found in many Florideophyceae orders, and the evolution of parasitism, a life strategy that has arisen many times among the Florideophyceae (Blouin and Lane 2012; Salomaki and Lane 2014; Blouin and Lane 2015; Lam et al 2016).…”

Section: Introductionmentioning

confidence: 99%

“…However, teasing apart the evolutionary histories of red algal orders has proven quite difficult even with the abundance of sequence data currently available (Verbruggen et al 2010; Lam et al 2016). Resolving the evolutionary relationships among florideophytes will provide a robust framework for asking a wide range of evolutionary questions including, but not limited to, transitions from marine to freshwater habitats, the evolution of the complex triphasic life-cycle found in many Florideophyceae orders, and the evolution of parasitism, a life strategy that has arisen many times among the Florideophyceae (Blouin and Lane 2012; Salomaki and Lane 2014; Blouin and Lane 2015; Lam et al 2016). The use of the maternally inherited mitochondrial genome to resolve evolutionary relationships among the Florideophyceae shows promise (Yang et al 2015).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Red Algal Mitochondrial Genomes are More Complete than Previously Reported

Salomaki

Lane²

2016

Genome Biol Evol

View full text Add to dashboard Cite

The enslavement of an alpha-proteobacterial endosymbiont by the last common eukaryotic ancestor resulted in large-scale gene transfer of endosymbiont genes to the host nucleus as the endosymbiont transitioned into the mitochondrion. Mitochondrial genomes have experienced widespread gene loss and genome reduction within eukaryotes and DNA sequencing has revealed that most of these gene losses occurred early in eukaryotic lineage diversification. On a broad scale, more recent modifications to organelle genomes appear to be conserved and phylogenetically informative. The first red algal mitochondrial genome was sequenced more than 20 years ago, and an additional 29 Florideophyceae mitochondria have been added over the past decade. A total of 32 genes have been described to have been missing or considered non-functional pseudogenes from these Florideophyceae mitochondria. These losses have been attributed to endosymbiotic gene transfer or the evolution of a parasitic life strategy. Here we sequenced the mitochondrial genomes from the red algal parasite Choreocolax polysiphoniae and its host Vertebrata lanosa and found them to be complete and conserved in structure with other Florideophyceae mitochondria. This result led us to resequence the previously published parasite Gracilariophila oryzoides and its host Gracilariopsis andersonii, as well as reevaluate reported gene losses from published Florideophyceae mitochondria. Multiple independent losses of rpl20 and a single loss of rps11 can be verified. However by reannotating published data and resequencing specimens when possible, we were able to identify the majority of genes that have been reported as lost or pseudogenes from Florideophyceae mitochondria.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Red Algal Mitochondrial Genomes are More Complete than Previously Reported

Salomaki

Lane²

2016

Genome Biol Evol

View full text Add to dashboard Cite

show abstract

“…Among the five subclasses of Florideophyceae, the Nemaliophycidae is the most taxonomically diverse, providing an ideal case study for red algal evolution (Lam et al. ). Freshwater red algae occur in early diverging members of the phyllum, for example, Compsopogon (Compsopogonophyceae), Bangia (Bangiophyceae), Chroodactylon and Chroothece (Stylonematophyceae), Kyliniella (Porphyridiophyceae), and in some Florideophyceae with mostly marine representatives, for example, Hildenbrandiophycidade ( Hildenbrandia ) and Rhodymeniophycidade ( Bostrychia , Caloglossa, and Polysiphonia ).…”

mentioning

confidence: 99%

“…These three orders have been shown to be relatively phylogenetically distant (Lam et al. , Yang et al. ).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta)

Paiano

Cortona

Costa

et al. 2017

Journal of Phycology

Self Cite

View full text Add to dashboard Cite

Little is known about genome organization in members of the order Batrachospermales, and the infra‐ordinal relationship remains unresolved. Plastid (cp) genomes of seven members of the freshwater red algal order Batrachospermales were sequenced, with the following aims: (i) to describe the characteristics of cp genomes and compare these with other red algal groups; (ii) to infer the phylogenetic relationships among these members to better understand the infra‐ordinal classification. Cp genomes of Batrachospermales are large, with several cases of gene loss, they are gene‐dense (high gene content for the genome size and short intergenic regions) and have highly conserved gene order. Phylogenetic analyses based on concatenated nucleotide genome data roughly supports the current taxonomic system for the order. Comparative analyses confirm data for members of the class Florideophyceae that cp genomes in Batrachospermales is highly conserved, with little variation in gene composition. However, relevant new features were revealed in our study: genome sizes in members of Batrachospermales are close to the lowest values reported for Florideophyceae; differences in cp genome size within the order are large in comparison with other orders (Ceramiales, Gelidiales, Gracilariales, Hildenbrandiales, and Nemaliales); and members of Batrachospermales have the lowest number of protein‐coding genes among the Florideophyceae. In terms of gene loss, apcF, which encodes the allophycocyanin beta subunit, is absent in all sequenced taxa of Batrachospermales. We reinforce that the interordinal relationships between the freshwater orders Batrachospermales and Thoreales within the Nemaliophycidae is not well resolved due to limited taxon sampling.

show abstract

Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era

Zhan

Shih

Liu

2020

Ecology and Evolution

View full text Add to dashboard Cite

Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). In this proof‐of‐concept study, we leveraged this resource by developing and applying a phylogenomic strategy to seek candidate plastid markers suitable for phylogenetic community analysis. We ranked the core genes of 107 published plastid genomes based on various sequence‐derived properties and their tree distance to plastid genome phylogenies. The resulting ranking revealed that the most widely used marker, rbcL, is not necessarily the optimal marker, while other promising markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of them, rpoC1, in a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for investigating the biodiversity and community ecology of the red algae.

show abstract

Multigene phylogeny of the red algal subclass Nemaliophycidae

Cited by 21 publications

References 34 publications

Red Algal Mitochondrial Genomes are More Complete than Previously Reported

Red Algal Mitochondrial Genomes are More Complete than Previously Reported

Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta)

Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era

Contact Info

Product

Resources

About