Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

Verbruggen, Heroen; Maggs, Christine A.; Saunders, Gary W.; Gall, Line Le; Yoon, Hwan Su; Clerck, Olivier De

doi:10.1186/1471-2148-10-16

Cited by 106 publications

(128 citation statements)

References 91 publications

(83 reference statements)

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“…The final matrix contained 51 ITS rDNA, 36 rbcL and 33 coxI sequences. A suitable partitioning strategy and partition-specific substitution models were selected in a multistep process (Verbruggen et al, 2010). Initially, a guide tree was obtained by carrying out a second-level maximum likelihood (ML) search on the unpartitioned dataset with a HKY + Γ8 model using TreeFinder (Jobb et al, 2004).…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Morphological delineation and distribution patterns of four newly described species within theSynura peterseniispecies complex (Chrysophyceae, Stramenopiles)

Škaloud

Škaloudová

Procházková

et al. 2014

European Journal of Phycology

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The Synura petersenii species complex represents a common, cosmopolitan and highly diverse taxon of autotrophic freshwater flagellates. In this paper, we describe and characterize four new species (S. borealis, S. heteropora, S. hibernica and S. laticarina) that have been identified during our extensive sampling of freshwater habitats in 15 European countries. Morphometric analyses of siliceous scales led to the significant phenotypic differentiation of all four newly described species, and their separation from other related species of the S. petersenii complex. Two of these newly described species (S. hibernica and S. borealis) can be clearly distinguished by characteristic large colonies consisting of elongated, lanceolate-shaped cells. Development of strongly elongated, narrow cells in S. hibernica could be explained by the adaptation of this species to oligotrophic conditions. Though morphologically distinct, S. borealis possesses an exceptionally high degree of genetic diversity, possibly indicating recent speciation and evolutionary diversification within this taxon. Three of the four newly described species exhibit restricted biogeographic distribution. The evolutionarily related S. borealis and S. laticarina occur only in Northern Europe, and seem to be adapted to colder areas. The most remarkable distribution pattern was observed for S. hibernica, which has a geographic distribution that is restricted to western Ireland.

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Section: Phylogenetic Analysesmentioning

confidence: 99%

Morphological delineation and distribution patterns of four newly described species within theSynura peterseniispecies complex (Chrysophyceae, Stramenopiles)

Škaloud

Škaloudová

Procházková

et al. 2014

European Journal of Phycology

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“…1) [11]. The accepted evolutionary paradigm proposes that adelphoparasitism is the initial state, followed by parasite diversification, which leads to the development of alloparasites (Fig.…”

Section: Introductionmentioning

confidence: 99%

Are all red algal parasites cut from the same cloth?

Salomaki

Lane

2014

Acta Soc Bot Pol

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Parasitism is a common life strategy throughout the eukaryotic tree of life. Many devastating human pathogens, including the causative agents of malaria and toxoplasmosis, have evolved from a photosynthetic ancestor. However, how an organism transitions from a photosynthetic to a parasitic life history strategy remains mostly unknown. This is largely because few systems present the opportunity to make meaningful comparisons between a parasite and a close free-living relative. Parasites have independently evolved dozens of times throughout the Florideophyceae (Rhodophyta), and often infect close relatives. The accepted evolutionary paradigm proposes that red algal parasites arise by first infecting a close relative and over time diversify and infect more distantly related species. This provides a natural evolutionary gradient of relationships between hosts and parasites that share a photosynthetic common ancestor. Elegant microscopic work in the late 20th century provided detailed insight into the infection cycle of red algal parasites and the cellular interactions between parasites and their hosts. Those studies led to the use of molecular work to further investigate the origins of the parasite organelles and reveal the evolutionary relationships between hosts and their parasites. Here we synthesize the research detailing the infection methods and cellular interactions between red algal parasites and their hosts. We offer an alternative hypothesis to the current dogma of red algal parasite evolution and propose that red algae can adopt a parasitic life strategy through multiple evolutionary pathways, including direct infection of distant relatives. Furthermore, we highlight potential directions for future research to further evaluate parasite evolution in red algae.

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“…have not yet been resolved with confidence, but at least some phylogenies (e.g., [45]) do support the existence of the putative clade mentioned above.…”

Section: Rab Gene Duplications Have Been Very Unevenly Distributed Acmentioning

confidence: 99%

“…Dashed lines indicate two branches that are uncertain. The clade comprising the red algal classes Porphyridiophyceae, Stylonematophyceae, and Compsopogonophyceae was suggested by some phylogenetic analyses [45], but statistical support was lacking. The monophyly of the green algal class Trebouxiophyceae, including Coccomyxa subellipsoidea and Chlorella variabilis, is generally accepted in the literature, but recent phylogenetic analyses based on plastid genome data cast doubt on this assumption [62].…”

Section: The Expanded Sampling For the First Time Documents The Presementioning

confidence: 99%

Contrasting patterns in the evolution of the Rab GTPase family in Archaeplastida

Petrželková

Eliáš

2014

Acta Soc Bot Pol

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Rab GTPases are a vast group of proteins serving a role of master regulators in membrane trafficking in eukaryotes. Previous studies delineated some 23 Rab and Rab-like paralogs ancestral for eukaryotes and mapped their current phylogenetic distribution, but the analyses relied on a limited sampling of the eukaryotic diversity. Taking advantage of the recent growth of genome and transcriptome resources for phylogenetically diverse plants and algae, we reanalyzed the evolution of the Rab family in eukaryotes with the primary plastid, collectively constituting the presumably monophyletic supergroup Archaeplastida. Our most important novel findings are as follows: (i) the ancestral set of Rabs in Archaeplastida included not only the paralogs Rab1, Rab2, Rab5, Rab6, Rab7, Rab8, Rab11, Rab18, Rab23, Rab24, Rab28, IFT27, and RTW (=Rabl2), as suggested previously, but also Rab14 and Rab34, because Rab14 exists in glaucophytes and Rab34 is present in glaucophytes and some green algae; (ii) except in embryophytes, Rab gene duplications have been rare in Archaeplastida. Most notable is the independent emergence of divergent, possibly functionally novel, in-paralogs of Rab1 and Rab11 in several archaeplastidial lineages; (iii) recurrent gene losses have been a significant factor shaping Rab gene complements in archaeplastidial species; for example, the Rab21 paralog was lost at least six times independently within Archaeplastida, once in the lineage leading to the "core" eudicots; (iv) while the glaucophyte Cyanophora paradoxa has retained the highest number of ancestral Rab paralogs among all archaeplastidial species studied so far, rhodophytes underwent an extreme reduction of the Rab gene set along their stem lineage, resulting in only six paralogs (Rab1, Rab2, Rab6, Rab7, Rab11, and Rab18) present in modern red algae. Especially notable is the absence of Rab5, a virtually universal paralog essential for the endocytic pathway, suggesting that endocytosis has been highly reduced or rewired in rhodophytes.

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Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

Cited by 106 publications

References 91 publications

Morphological delineation and distribution patterns of four newly described species within theSynura peterseniispecies complex (Chrysophyceae, Stramenopiles)

Morphological delineation and distribution patterns of four newly described species within theSynura peterseniispecies complex (Chrysophyceae, Stramenopiles)

Are all red algal parasites cut from the same cloth?

Contrasting patterns in the evolution of the Rab GTPase family in Archaeplastida

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