The Experts below are selected from a list of 219 Experts worldwide ranked by ideXlab platform
Fabiano L Thompson - One of the best experts on this subject based on the ideXlab platform.
-
new insights on the terpenome of the red seaweed laurencia dendroidea Florideophyceae rhodophyta
Marine Drugs, 2015Co-Authors: Louisi De Oliveira, Leonardo T Salgado, Renato Crespo Pereira, Diogo A Tschoeke, Aline Santos De Oliveira, Lilian Jorge Hill, Wladimir C Paradas, Cristiane C Thompson, Fabiano L ThompsonAbstract:The red seaweeds belonging to the genus Laurencia are well known as halogenated secondary metabolites producers, mainly terpenoids and acetogennins. Several of these chemicals exhibit important ecological roles and biotechnological applications. However, knowledge regarding the genes involved in the biosynthesis of these compounds is still very limited. We detected 20 different genes involved in the biosynthesis of terpenoid precursors, and 21 different genes coding for terpene synthases that are responsible for the chemical modifications of the terpenoid precursors, resulting in a high diversity of carbon chemical skeletons. In addition, we demonstrate through molecular and cytochemical approaches the occurrence of the mevalonate pathway involved in the biosynthesis of terpenes in L. dendroidea. This is the first report on terpene synthase genes in seaweeds, enabling further studies on possible heterologous biosynthesis of terpenes from L. dendroidea exhibiting ecological or biotechnological interest.
-
transcriptomic analysis of the red seaweed laurencia dendroidea Florideophyceae rhodophyta and its microbiome
BMC Genomics, 2012Co-Authors: Louisi De Oliveira, Gustavo B Gregoracci, Genivaldo G Z Silva, Leonardo T Salgado, Gilberto Amado Rodrigues Da Cunha Filho, Marcio Alvesferreira, Renato Crespo Pereira, Fabiano L ThompsonAbstract:Seaweeds of the Laurencia genus have a broad geographic distribution and are largely recognized as important sources of secondary metabolites, mainly halogenated compounds exhibiting diverse potential pharmacological activities and relevant ecological role as anti-epibiosis. Host-microbe interaction is a driving force for co-evolution in the marine environment, but molecular studies of seaweed-associated microbial communities are still rare. Despite the large amount of research describing the chemical compositions of Laurencia species, the genetic knowledge regarding this genus is currently restricted to taxonomic markers and general genome features. In this work we analyze the transcriptomic profile of L. dendroidea J. Agardh, unveil the genes involved on the biosynthesis of terpenoid compounds in this seaweed and explore the interactions between this host and its associated microbiome. A total of 6 transcriptomes were obtained from specimens of L. dendroidea sampled in three different coastal locations of the Rio de Janeiro state. Functional annotations revealed predominantly basic cellular metabolic pathways. Bacteria was the dominant active group in the microbiome of L. dendroidea, standing out nitrogen fixing Cyanobacteria and aerobic heterotrophic Proteobacteria. The analysis of the relative contribution of each domain highlighted bacterial features related to glycolysis, lipid and polysaccharide breakdown, and also recognition of seaweed surface and establishment of biofilm. Eukaryotic transcripts, on the other hand, were associated with photosynthesis, synthesis of carbohydrate reserves, and defense mechanisms, including the biosynthesis of terpenoids through the mevalonate-independent pathway. This work describes the first transcriptomic profile of the red seaweed L. dendroidea, increasing the knowledge about ESTs from the Florideophyceae algal class. Our data suggest an important role for L. dendroidea in the primary production of the holobiont and the role of Bacteria as consumers of organic matter and possibly also as nitrogen source. Furthermore, this seaweed expressed sequences related to terpene biosynthesis, including the complete mevalonate-independent pathway, which offers new possibilities for biotechnological applications using secondary metabolites from L. dendroidea.
Gary W. Saunders - One of the best experts on this subject based on the ideXlab platform.
-
molecular analysis of parasites in the choreocolacaceae rhodophyta reveals a reduced harveyella mirabilis plastid genome and supports the transfer of genera to the rhodomelaceae rhodophyta
bioRxiv, 2017Co-Authors: Eric D Salomaki, Gary W. Saunders, Christopher E LaneAbstract:Parasitism is a life strategy that has repeatedly evolved within the Florideophyceae. Until recently, the accepted paradigm of red algal parasite evolution was that parasites arise by first infecting a close relative and, either through host jumping or diversification, adapt to infect more distant relatives. The terms adelphoparasite and alloparasite have been used to distinguish parasites that are closely related to their hosts from those more distantly related to their hosts, respectively. Phylogenetic studies have cast doubt on the utility of these terms as data show that even alloparasites predominately infect with the same family. All adelphoparasites that have been investigated have lost a native plastid and instead hijack and incorporate a copy of their hosts plastid when packaging spores. In contrast, a highly reduced plastid that has lost all genes involved with photosynthesis was sequenced from the alloparasite Choreocolax polysiphoniae, which indicates that it did not pass through an adelphoparasite stage. In this study we investigate whether other species in the Choreocolacaceae, a family of alloparasites, also retains its native plastid, as well as test the hypothesis that alloparasites can arise and subsequently speciate to form monophyletic clades that infect a range of hosts. We present the plastid genome for Harveyella mirabilis which, similar to that of C. polysiphoniae, has lost genes involved in photosynthesis. The H. mirabilis plastid shares more synteny with free-living red algal plastids than that of C. polysiphoniae Phylogenetic analysis identifies a well-supported monophyletic clade of parasites in the Choreocolacaceae, which retain their own plastid genomes, within the Rhodomelaceae. We therefore transfer genera in the Choreocolacaceae to the Rhodomelaceae.
-
Divergence time estimates and the evolution of major lineages in the florideophyte red algae
Scientific Reports, 2016Co-Authors: Eun Chan Yang, Debashish Bhattacharya, Suzanne Fredericq, Gary W. Saunders, Sung Min Boo, Andrew H. Knoll, Louis Graf, Hwan Su YoonAbstract:The Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox 1, and plastid rbc L, psa A and psb A genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817–1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681–879) Ma], Nemaliophycidae [ca. 661 (597–736) Ma], Corallinophycidae [ca. 579 (543–617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442–580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae.
-
acquiring dna sequence data from dried archival red algae Florideophyceae for the purpose of applying available names to contemporary genetic species a critical assessment
Botany, 2012Co-Authors: Gary W. Saunders, Daniel C McdevitAbstract:Two DNA extraction protocols and nine variations of advocated DNA barcode markers (nuclear LSU D2/D3, ITS1, ITS2, mitochondrial COI-5P, plastid rbcL, UPA) were assessed for their abilities to yield...
-
a comparison of two dna barcode markers for species discrimination in the red algal family kallymeniaceae gigartinales Florideophyceae with a description of euthora timburtonii sp nov
Botany, 2010Co-Authors: Bridgette E Clarkston, Gary W. SaundersAbstract:Accurate identification of many red algae to the species level using only morphological characters can be diffi- cult. The emerging field of ''molecular-assisted alpha taxonomy'' can greatly alleviate this issue. In this approach, a large number of specimens are sequenced for a standard DNA marker as a first step to genetic species assignment, followed by detailed morphological observations. Regions of both the mitochondrial cytochromec oxidase I gene (COI-5P) and the plastid 23S rRNA gene (UPA) have been proposed as DNA barcode markers to accomplish this task. We compared the utility of each marker as a species identification tool using members of the marine red algal family Kallymeniaceae from British Columbia, Canada. Our results indicate that COI-5P is a more sensitive marker for delimiting species, but that it can be difficult to acquire clean amplification products for many isolates of Kallymeniaceae, owing to biological contami- nation. This problem can be overcome by using specific primers. UPA, on the other hand, has universal primers that work in diverse lineages (e.g., red, brown, and green algae), but lower interspecific sequence variation, which has the potential to underestimate species diversity, although this was not observed in our study. During our survey, we uncovered a new species of the Kallymeniaceae, Euthora timburtonii Clarkston et G.W. Saunders sp. nov., which we describe here.
-
a nuclear phylogeny of the Florideophyceae rhodophyta inferred from combined ef2 small subunit and large subunit ribosomal dna establishing the new red algal subclass corallinophycidae
Molecular Phylogenetics and Evolution, 2007Co-Authors: Line Le Gall, Gary W. SaundersAbstract:Previous studies have indicated that resolution of supraordinal relationships in the red algal class Florideophyceae will require additional characters, improved taxon sampling and optimized methods of phylogenetic analysis. To this end, we have generated data to introduce a novel nuclear marker to red algal systematics, elongation factor 2, as well as expanded ribosomal DNA alignments (SSU and LSU) to include 62 ingroup and 4 outgroup taxa. Both single gene and combined data sets were considered. Our analyses resulted in better resolution of both deep as well as more recent divergences, with higher support realized at many nodes. Distance, parsimony and bayesian analyses of the single gene and combined data sets indicated that the subclasses Hildenbrandiophycidae, Ahnfeltiophycidae and Rhodymeniophycidae were monophyletic, whereas the Nemaliophycidae was polyphyletic: one lineage containing the Rhodogorgonales and Corallinales (CR complex); and the other containing the Acrochaetiales, Balbianiales, Balliales, Batrachospermales, Colaconematales, Nemaliales, Palmariales, and Thoreales (APB complex). Based on these results a new subclass of the Florideophyceae, the Corallinophycidae subclassis nov., is proposed to accommodate the Corallinales and Rhodogorgonales. In addition to resolving supraordinal relationships, the present analyses resolved some novel ordinal affinities within the Nemaliophycidae and Rhodymeniophycidae, which are discussed here.
Louisi De Oliveira - One of the best experts on this subject based on the ideXlab platform.
-
new insights on the terpenome of the red seaweed laurencia dendroidea Florideophyceae rhodophyta
Marine Drugs, 2015Co-Authors: Louisi De Oliveira, Leonardo T Salgado, Renato Crespo Pereira, Diogo A Tschoeke, Aline Santos De Oliveira, Lilian Jorge Hill, Wladimir C Paradas, Cristiane C Thompson, Fabiano L ThompsonAbstract:The red seaweeds belonging to the genus Laurencia are well known as halogenated secondary metabolites producers, mainly terpenoids and acetogennins. Several of these chemicals exhibit important ecological roles and biotechnological applications. However, knowledge regarding the genes involved in the biosynthesis of these compounds is still very limited. We detected 20 different genes involved in the biosynthesis of terpenoid precursors, and 21 different genes coding for terpene synthases that are responsible for the chemical modifications of the terpenoid precursors, resulting in a high diversity of carbon chemical skeletons. In addition, we demonstrate through molecular and cytochemical approaches the occurrence of the mevalonate pathway involved in the biosynthesis of terpenes in L. dendroidea. This is the first report on terpene synthase genes in seaweeds, enabling further studies on possible heterologous biosynthesis of terpenes from L. dendroidea exhibiting ecological or biotechnological interest.
-
transcriptomic analysis of the red seaweed laurencia dendroidea Florideophyceae rhodophyta and its microbiome
BMC Genomics, 2012Co-Authors: Louisi De Oliveira, Gustavo B Gregoracci, Genivaldo G Z Silva, Leonardo T Salgado, Gilberto Amado Rodrigues Da Cunha Filho, Marcio Alvesferreira, Renato Crespo Pereira, Fabiano L ThompsonAbstract:Seaweeds of the Laurencia genus have a broad geographic distribution and are largely recognized as important sources of secondary metabolites, mainly halogenated compounds exhibiting diverse potential pharmacological activities and relevant ecological role as anti-epibiosis. Host-microbe interaction is a driving force for co-evolution in the marine environment, but molecular studies of seaweed-associated microbial communities are still rare. Despite the large amount of research describing the chemical compositions of Laurencia species, the genetic knowledge regarding this genus is currently restricted to taxonomic markers and general genome features. In this work we analyze the transcriptomic profile of L. dendroidea J. Agardh, unveil the genes involved on the biosynthesis of terpenoid compounds in this seaweed and explore the interactions between this host and its associated microbiome. A total of 6 transcriptomes were obtained from specimens of L. dendroidea sampled in three different coastal locations of the Rio de Janeiro state. Functional annotations revealed predominantly basic cellular metabolic pathways. Bacteria was the dominant active group in the microbiome of L. dendroidea, standing out nitrogen fixing Cyanobacteria and aerobic heterotrophic Proteobacteria. The analysis of the relative contribution of each domain highlighted bacterial features related to glycolysis, lipid and polysaccharide breakdown, and also recognition of seaweed surface and establishment of biofilm. Eukaryotic transcripts, on the other hand, were associated with photosynthesis, synthesis of carbohydrate reserves, and defense mechanisms, including the biosynthesis of terpenoids through the mevalonate-independent pathway. This work describes the first transcriptomic profile of the red seaweed L. dendroidea, increasing the knowledge about ESTs from the Florideophyceae algal class. Our data suggest an important role for L. dendroidea in the primary production of the holobiont and the role of Bacteria as consumers of organic matter and possibly also as nitrogen source. Furthermore, this seaweed expressed sequences related to terpene biosynthesis, including the complete mevalonate-independent pathway, which offers new possibilities for biotechnological applications using secondary metabolites from L. dendroidea.
Hwan Su Yoon - One of the best experts on this subject based on the ideXlab platform.
-
Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants
BMC Biology, 2016Co-Authors: Junmo Lee, John A. West, Debashish Bhattacharya, Chung Hyun Cho, Seung In Park, Ji Won Choi, Hyun Suk Song, Hwan Su YoonAbstract:The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms. Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages.
-
Divergence time estimates and the evolution of major lineages in the florideophyte red algae
Scientific Reports, 2016Co-Authors: Eun Chan Yang, Debashish Bhattacharya, Suzanne Fredericq, Gary W. Saunders, Sung Min Boo, Andrew H. Knoll, Louis Graf, Hwan Su YoonAbstract:The Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox 1, and plastid rbc L, psa A and psb A genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817–1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681–879) Ma], Nemaliophycidae [ca. 661 (597–736) Ma], Corallinophycidae [ca. 579 (543–617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442–580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae.
-
DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA)1
Journal of Phycology, 2006Co-Authors: Hwan Su Yoon, Kirsten M. Müller, Robert G. Sheath, Debashish BhattacharyaAbstract:Previous phylogenetic studies of the Rhodophyta have provided a framework for understanding red algal phylogeny, but there still exists the need for a comprehensive analysis using a broad sampling of taxa and sufficient phylogenetic information to clearly define the major lineages. In this study, we determined 48 sequences of the PSI P700 chl a apoprotein A1 (psaA) and rbcL coding regions and established a robust red algal phylogeny to identify the major clades. The tree included most of the lineages of the Bangiophyceae (25 genera, 48 taxa). Seven well-supported lineages were identified with this analysis with the Cyanidiales having the earliest divergence and being distinct from the remaining taxa; i.e. the Porphyridiales 1‐3, Bangiales, Florideophyceae, and Compsopogonales. We also analyzed data sets with fewer taxa but using seven proteins or the DNA sequence from nine genes to resolve inter-clade relationships. Based on all of these analyses, we propose that the Rhodophyta contains two new subphyla, the Cyanidiophytina with a single class, the Cyanidiophyceae, and the Rhodophytina with six classes, the Bangiophyceae, Compsopogonophyceae, Florideophyceae, Porphyridiophyceae classis nov. (which contains Porphyridium, Flintiella ,a ndErythrolobus), Rhodellophyceae, and Stylonematophyceae classis nov. (which contains Stylonema, Bangiopsis, Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora ,a ndRufusia). We also describe a new order, Rhodellales, and a new family, Rhodellaceae (with Rhodella, Dixoniella, and Glaucosphaera). Key index words: Bangiophyceae; Compsopogonophyceae; Cyanidiophyceae; Florideophyceae; Porphyridiophycae; red algal lineages; Rhodellophyceae; Rhodophyta; Stylonematophyceae Abbreviations: BPP, Bayesian posterior probabilities; ML, maximum likelihood; MP, maximum parsimony; PsaA, PSI P700 chlorophyll a apoprotein A1; PsaB, PSI P700 chlorophyll a apoprotein A2; PsbA, PSII reaction center protein D1; PsbC, PSII 44 KD apoprotein; PsbD, PSII D2 reaction center protein; TBR, tree bisection-reconnection
Leonardo T Salgado - One of the best experts on this subject based on the ideXlab platform.
-
new insights on the terpenome of the red seaweed laurencia dendroidea Florideophyceae rhodophyta
Marine Drugs, 2015Co-Authors: Louisi De Oliveira, Leonardo T Salgado, Renato Crespo Pereira, Diogo A Tschoeke, Aline Santos De Oliveira, Lilian Jorge Hill, Wladimir C Paradas, Cristiane C Thompson, Fabiano L ThompsonAbstract:The red seaweeds belonging to the genus Laurencia are well known as halogenated secondary metabolites producers, mainly terpenoids and acetogennins. Several of these chemicals exhibit important ecological roles and biotechnological applications. However, knowledge regarding the genes involved in the biosynthesis of these compounds is still very limited. We detected 20 different genes involved in the biosynthesis of terpenoid precursors, and 21 different genes coding for terpene synthases that are responsible for the chemical modifications of the terpenoid precursors, resulting in a high diversity of carbon chemical skeletons. In addition, we demonstrate through molecular and cytochemical approaches the occurrence of the mevalonate pathway involved in the biosynthesis of terpenes in L. dendroidea. This is the first report on terpene synthase genes in seaweeds, enabling further studies on possible heterologous biosynthesis of terpenes from L. dendroidea exhibiting ecological or biotechnological interest.
-
transcriptomic analysis of the red seaweed laurencia dendroidea Florideophyceae rhodophyta and its microbiome
BMC Genomics, 2012Co-Authors: Louisi De Oliveira, Gustavo B Gregoracci, Genivaldo G Z Silva, Leonardo T Salgado, Gilberto Amado Rodrigues Da Cunha Filho, Marcio Alvesferreira, Renato Crespo Pereira, Fabiano L ThompsonAbstract:Seaweeds of the Laurencia genus have a broad geographic distribution and are largely recognized as important sources of secondary metabolites, mainly halogenated compounds exhibiting diverse potential pharmacological activities and relevant ecological role as anti-epibiosis. Host-microbe interaction is a driving force for co-evolution in the marine environment, but molecular studies of seaweed-associated microbial communities are still rare. Despite the large amount of research describing the chemical compositions of Laurencia species, the genetic knowledge regarding this genus is currently restricted to taxonomic markers and general genome features. In this work we analyze the transcriptomic profile of L. dendroidea J. Agardh, unveil the genes involved on the biosynthesis of terpenoid compounds in this seaweed and explore the interactions between this host and its associated microbiome. A total of 6 transcriptomes were obtained from specimens of L. dendroidea sampled in three different coastal locations of the Rio de Janeiro state. Functional annotations revealed predominantly basic cellular metabolic pathways. Bacteria was the dominant active group in the microbiome of L. dendroidea, standing out nitrogen fixing Cyanobacteria and aerobic heterotrophic Proteobacteria. The analysis of the relative contribution of each domain highlighted bacterial features related to glycolysis, lipid and polysaccharide breakdown, and also recognition of seaweed surface and establishment of biofilm. Eukaryotic transcripts, on the other hand, were associated with photosynthesis, synthesis of carbohydrate reserves, and defense mechanisms, including the biosynthesis of terpenoids through the mevalonate-independent pathway. This work describes the first transcriptomic profile of the red seaweed L. dendroidea, increasing the knowledge about ESTs from the Florideophyceae algal class. Our data suggest an important role for L. dendroidea in the primary production of the holobiont and the role of Bacteria as consumers of organic matter and possibly also as nitrogen source. Furthermore, this seaweed expressed sequences related to terpene biosynthesis, including the complete mevalonate-independent pathway, which offers new possibilities for biotechnological applications using secondary metabolites from L. dendroidea.