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1.
Protist ; 170(5): 125680, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31563792

RESUMO

Marine unarmored dinoflagellates in the family Kareniaceae are known to possess chloroplasts of haptophyte origin, which contain fucoxanthin and its derivatives as major carotenoids, and lack peridinin. In the present study, the first species with the peridinin-type chloroplast in this family, Gertia stigmatica gen. et sp. nov., is described on the basis of ultrastructure, photosynthetic pigment composition, and molecular phylogeny inferred from nucleus- and chloroplast-encoded genes. Cells of G. stigmatica were small and harboring a chloroplast with an eyespot and two pyrenoids. The apical structure complex was straight, similar to Karenia and Karlodinium. Under transmission electron microscopy, the chloroplast was surrounded by two membranes, and the eyespot was composed of a single layer of osmiophilic globules (eyespot type A); this was never previously reported from the Kareniaceae. High performance liquid chromatography demonstrated the chloroplast contains peridinin, and neither fucoxanthin nor 19'-acyloxyfucoxanthins was identified. A phylogeny based on nucleus-encoded rDNAs suggested a position of G. stigmatica in the Kareniaceae, but not clustered within the previously described genera, i.e., Karenia, Karlodinium and Takayama. A phylogeny of chloroplast-encoded psbA, psbC and psbD indicated the chloroplast is of peridinin-type typical of dinoflagellates, but the most related species remains unclear.


Assuntos
Organismos Aquáticos , Carotenoides , Cloroplastos , Dinoflagelados/classificação , Organismos Aquáticos/classificação , Organismos Aquáticos/citologia , Organismos Aquáticos/metabolismo , Carotenoides/metabolismo , Cloroplastos/classificação , Cloroplastos/metabolismo , Dinoflagelados/citologia , Dinoflagelados/metabolismo , Especificidade da Espécie
2.
Biol Bull ; 236(2): 88-96, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30933641

RESUMO

Sacoglossan sea slugs feed by suctorially consuming siphonaceous green algae. Most sacoglossan species are feeding specialists, but the Caribbean coral reef-dwelling Elysia crispata is polyphagous and sequesters chloroplasts from multiple algal species into cells lining its digestive diverticulum for use in photosynthesis. We have used sequences of the chloroplast-encoded rbcL gene to compare the chloroplast donor algae in five populations of E. crispata from various Caribbean locations. We found that E. crispata utilizes more algal species than was previously known, including some algae previously not reported as present in the region. In addition, slugs from each location had unique chloroplast arrays with little overlap, except that all locations had slugs feeding on algae within the genus Bryopsis. This variation in diet between locations suggests that the slugs may be exhibiting local adaptation in their dietary choices, and it highlights ecological differences between the Caribbean-wide reef-dwelling ecotypes and the mangrove lagoon ecotypes found in the Florida Keys.


Assuntos
Clorófitas/classificação , Cloroplastos/classificação , Gastrópodes/fisiologia , Animais , Região do Caribe , Clorófitas/genética , Cloroplastos/genética , Dieta , Ecossistema , Fotossíntese , Análise de Sequência de DNA
3.
PLoS One ; 14(2): e0211340, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30716116

RESUMO

Artemisia selengenesis is not only a health food, but also a well-known traditional Chinese medicine. Only a fraction of the chloroplast (cp) genome data of Artemisia has been reported and chloroplast genomic materials have been widely used in genomic evolution studies, molecular marker development, and phylogenetic analysis of the genus Artemisia, which makes evolutionary studies, genetic improvement, and phylogenetic identification very difficult. In this study, the complete chloroplast genome of A. selengensis was compared with that of other species within Artemisia and phylogenetic analyses was conducted with other genera in the Asteraceae family. The results showed that A. selengensis is an AT-rich species and has a typical quadripartite structure that is 151,215 bp in length. Comparative genome analyses demonstrated that the available chloroplast genomes of species of Artemisia were well conserved in terms of genomic length, GC contents, and gene organization and order. However, some differences, which may indicate evolutionary events, were found, such as a re-inversion event within the Artemisia genus, an unequal duplicate phenomenon of the ycf1 gene because of the expansion and contraction of the IR region, and the fast-evolving regions. Repeated sequences analysis showed that Artemisia chloroplast genomes presented a highly similar pattern of SSR or LDR distribution. A total of 257 SSRs and 42 LDRs were identified in the A. selengensis chloroplast genome. The phylogenetic analysis showed that A. selengensis was sister to A. gmelinii. The findings of this study will be valuable in further studies to understand the genetic diversity and evolutionary history of Asteraceae.


Assuntos
Artemisia/genética , Cloroplastos/genética , Genoma de Cloroplastos , Artemisia/classificação , Asteraceae/genética , Composição de Bases , Cloroplastos/classificação , Hibridização Genômica Comparativa , DNA de Cloroplastos/química , DNA de Cloroplastos/isolamento & purificação , DNA de Cloroplastos/metabolismo , Repetições de Microssatélites/genética , Filogenia , Plantas Medicinais/genética , Análise de Sequência de DNA
4.
Mol Phylogenet Evol ; 127: 248-255, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-29885933

RESUMO

Phylogenetic relationships within the green algal phylum Chlorophyta have proven difficult to resolve. The core Chlorophyta include Chlorophyceae, Ulvophyceae, Trebouxiophyceae, Pedinophyceae and Chlorodendrophyceae, but the relationships among these classes remain unresolved and the monophyly of Ulvophyceae and Trebouxiophyceae are highly controversial. We analyzed a dataset of 101 green algal species and 73 protein-coding genes sampled from complete and partial chloroplast genomes, including six newly sequenced ulvophyte genomes (Blidingia minima NIES-1837, Ulothrix zonata, Halochlorococcum sp. NIES-1838, Scotinosphaera sp. NIES-154, Caulerpa brownii and Cephaleuros sp. HZ-2017). We applied the Tree Certainty (TC) score to quantify the level of incongruence between phylogenetic trees in chloroplast genomic datasets, and show that the conflicting phylogenetic trees of core Chlorophyta stem from the most GC-heterogeneous sites. With removing the most GC-heterogeneous sites, our chloroplast phylogenomic analyses using heterogeneous models consistently support monophyly of the Chlorophyceae and of the Trebouxiophyceae, but the Ulvophyceae was resolved as polyphyletic. Our analytical framework provides an efficient approach to reconstruct the optimal phylogenetic relationships by minimizing conflicting signals.


Assuntos
Clorófitas/genética , Cloroplastos/classificação , Cloroplastos/genética , Modelos Genéticos , Filogenia , Sequência de Bases , Teorema de Bayes , DNA de Cloroplastos/genética , Genoma de Cloroplastos , Funções Verossimilhança
5.
PLoS One ; 13(4): e0196473, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29694421

RESUMO

Cerasus humilis is endemic to China and is a new fruit tree species with economic and environmental benefits, with potential developmental and utilization applications. We report the first complete chloroplast genome sequence of C. humilis. Its genome is 158,084 bp in size, and the overall GC content is 36.8%. An inverted repeats (IR) of 52,672 bp in size is separated by a large single-copy (LSC) region of 86,374 bp and a small single-copy (SSC) region of 19,038 bp. The chloroplast genome of C. humilis contains 131 genes including 90 protein-coding genes, 33 transfer RNA genes, and 8 ribosomal RNA genes. The genome has a total 510 simple sequence repeats (SSRs). Of these, 306, 149, and 55 were found in the LSC, IR, and SSC regions, respectively. In addition, a comparison of the boundaries of the LSC, SSC, and IR regions of ten other Prunus species exhibited an overall high degree of sequence similarity, with slight variations in the IR boundary region which included gene deletions, insertions, expansions, and contractions. C. humilis lost the ycf1 gene at the IRA/SSC border and it has the largest ycf1 gene at the IRB/SSC border among these Prunus species, whereas the rps19 gene was inserted at the IRB/LSC junction. Furthermore, phylogenetic reconstruction using 61 conserved coding-protein genes clustered C. humilis with Prunus tomentosa. Thus, the complete chloroplast genome sequence of C. humilis provides a rich source of genetic information for studies on Prunus taxonomy, phylogeny, and evolution, as well as lays the foundation for further development and utilization of C. humilis.


Assuntos
Cloroplastos/genética , Genoma de Cloroplastos , Prunus/genética , Cloroplastos/classificação , Hibridização Genômica Comparativa , DNA de Plantas/química , DNA de Plantas/isolamento & purificação , DNA de Plantas/metabolismo , Repetições de Microssatélites/genética , Filogenia , Prunus/classificação , Análise de Sequência de DNA
6.
Mol Phylogenet Evol ; 114: 415-425, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-28606445

RESUMO

The number of species recognized in section Asperae of the flowering plant genus Hydrangea differs widely between subsequent revisions. This variation is largely centered around the H. aspera species complex, with numbers of recognized species varying from one to nearly a dozen. Despite indications of molecular variation in this complex, no sequence-based species delimitation methods have been employed to evaluate the primarily morphology-based species boundaries. In the present study, a multi-locus coalescent-based approach to species delimitation is employed in order to identify separate evolutionary lines within H. sect. Asperae, using four chloroplast and four nuclear molecular markers. Eight lineages were recovered within the focal group, of which five correspond with named morphotypes. The other three lineages illustrate types of conflict between molecular species delimitation and traditional morphology-based taxonomy. One molecular lineage comprises two named morphotypes, which possibly diverged recently enough to not have developed sufficient molecular divergence. A second conflict is found in H. strigosa. This morphotype is recovered as a separate lineage when occurring in geographic isolation, but when occurring in sympatry with two other morphotypes (H. aspera and H. robusta), the coalescent species delimitation lumps these taxa into a single putative species.


Assuntos
Hydrangea/classificação , Teorema de Bayes , Cloroplastos/classificação , Cloroplastos/genética , DNA de Plantas/química , DNA de Plantas/isolamento & purificação , DNA de Plantas/metabolismo , Hydrangea/anatomia & histologia , Hydrangea/genética , Microscopia Eletrônica de Varredura , Filogenia , Folhas de Planta/anatomia & histologia , Folhas de Planta/química , Quinona Redutases/classificação , Quinona Redutases/genética , RNA de Transferência de Valina/classificação , RNA de Transferência de Valina/genética
7.
Mol Phylogenet Evol ; 114: 93-110, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-28603037

RESUMO

Understanding the source of phenotypic variability is a challenge in the biological sciences. Variation in phenotypes is the result of variation in the genetics and environment the organism experiences, but elucidating the relative contribution of these two parameters can pose problems, especially in the field of systematics. Systematists are challenged to classify biological diversity into groups that share common ancestry. Phenotypic variation can be useful to demonstrate common ancestry, but only when the primary contributor to the variation is under strong genetic control, and thus heritable. Cusick's milkvetch (Astragalus cusickii) is a perennial forb endemic to the northwestern intermountain region of the United States. The species currently comprises four varieties based on subtle morphological dissimilarities, such as leaf size and density, and the size and shape of the seed pods. The taxonomic organization of the varieties of A. cusickii and related species of Astragalus were reexamined through phylogenetic analysis of low copy nuclear, nuclear-ribosomal, and chloroplast gene regions. Maximum parsimony, maximum likelihood, Bayesian inference, the genealogical sorting index, and an approximately unbiased test were used to determine appropriate species boundaries under the phylogenetic species concept. The results support reclassification of A. cusickii var. packardiae and A. cusickii var. sterilis as separate species. Additionally, evidence suggests a chloroplast capture event may have occurred in one population of A. cusickii var. packardiae.


Assuntos
Fabaceae/classificação , Teorema de Bayes , Cloroplastos/classificação , Cloroplastos/genética , DNA de Plantas/química , DNA de Plantas/isolamento & purificação , DNA de Plantas/metabolismo , Fabaceae/genética , Filogenia , Análise de Sequência de DNA
8.
Mol Phylogenet Evol ; 114: 63-72, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-28578201

RESUMO

The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684bp to 201,723 for Annonoideae and minimal 152,357 to 170,985bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega (dN/dS)-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods.


Assuntos
Annonaceae/classificação , Evolução Molecular , Annonaceae/genética , Composição de Bases , Teorema de Bayes , Cloroplastos/classificação , Cloroplastos/genética , DNA de Plantas/química , DNA de Plantas/isolamento & purificação , DNA de Plantas/metabolismo , DNA Ribossômico/classificação , DNA Ribossômico/genética , Genes de Plantas , Filogenia , Análise de Sequência de DNA
9.
Mol Phylogenet Evol ; 101: 216-223, 2016 08.
Artigo em Inglês | MEDLINE | ID: mdl-27138293

RESUMO

Vitales is well-known for including the economically important fruit crop, the wine grape (Vitis vinifera). However, the position of the Vitales in the higher eudicots has been a subject of much debate. It has been variously reported to be sister to the Saxifragales and together as sister to the rest of rosids, or sister to the fabids-malvids clade, or sister to the Santalales, or sister to the fabids-malvids-Saxifragales clade. However, in all of these scenarios, the support values for the relationship of Vitales on the phylogenies were only low to moderate. Additionally, all previous studies sampled only Vitis vinifera as the representative of the Vitales. We herein expanded the sampling of the Vitales to include representatives of all major clades of the order, as well as representatives of other key lineages including Saxifragales, Dilleniales, and Santalales. Extensive likelihood and Bayesian analyses were conducted to test the position of Vitales, using different numbers of genes, a variety of partitioning strategies, and both nucleotide and amino acid sequences. With the expanded sampling strategy, almost all analyses supported the relationship of Vitales as sister to Saxifragales. This relationship was supported in a 72-gene data set with a bootstrap value of 91%, the highest support value reported to date. Based on this topology, we discuss possible morphological synapomorphies shared between Vitales and Saxifragales. Furthermore, a hypothesis of reticulate evolution was postulated as an explanation for the incongruence of Vitales' position when comparing plastid and nuclear gene phylogenies.


Assuntos
Vitis/classificação , Teorema de Bayes , Cloroplastos/classificação , Cloroplastos/genética , DNA de Plantas/química , DNA de Plantas/isolamento & purificação , DNA de Plantas/metabolismo , Filogenia , Plastídeos/genética , Análise de Sequência de DNA , Vitis/genética
10.
Syst Biol ; 65(1): 51-65, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26430060

RESUMO

Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provide valuable information on evolutionary processes such as chloroplast capture following hybridization, incomplete lineage sorting, and horizontal gene transfer. Statistical tools that to date have been used in cophylogenetic studies only also have the potential to test for the degree of topological congruence between organellar and nuclear data sets and reliably detect outlier associations. Two distance-based methods, namely ParaFit and Procrustean Approach to Cophylogeny (PACo), were used in conjunction to detect those outliers contributing to conflicting phylogenies independently derived from chloroplast and nuclear sequence data. We explored their efficiency of retrieving outlier associations, and the impact of input data (unit branch length and additive trees) between data sets, by using several simulation approaches. To test their performance using real data sets, we additionally inferred the phylogenetic relationships within Neotropical Catasetinae (Epidendroideae, Orchidaceae), which is a suitable group to investigate phylogenetic incongruence because of hybridization processes between some of its constituent species. A comparison between trees derived from chloroplast and nuclear sequence data reflected strong, well-supported incongruence within Catasetum, Cycnoches, and Mormodes. As a result, outliers among chloroplast and nuclear data sets, and in experimental simulations, were successfully detected by PACo when using patristic distance matrices obtained from phylograms, but not from unit branch length trees. The performance of ParaFit was overall inferior compared to PACo, using either phylograms or unit branch lengths as input data. Because workflows for applying cophylogenetic analyses are not standardized yet, we provide a pipeline for executing PACo and ParaFit as well as displaying outlier associations in plots and trees by using the software R. The pipeline renders a method to identify outliers with high reliability and to assess the combinability of the independently derived data sets by means of statistical analyses.


Assuntos
Evolução Biológica , Cloroplastos/classificação , Cloroplastos/genética , Classificação/métodos , Orchidaceae/classificação , Orchidaceae/genética , Simbiose/genética , DNA de Cloroplastos/genética , DNA de Plantas/genética , Filogenia , Software
11.
J Proteome Res ; 14(5): 2090-108, 2015 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-25772754

RESUMO

Kranz C4 species strictly depend on separation of primary and secondary carbon fixation reactions in different cell types. In contrast, the single-cell C4 (SCC4) species Bienertia sinuspersici utilizes intracellular compartmentation including two physiologically and biochemically different chloroplast types; however, information on identity, localization, and induction of proteins required for this SCC4 system is currently very limited. In this study, we determined the distribution of photosynthesis-related proteins and the induction of the C4 system during development by label-free proteomics of subcellular fractions and leaves of different developmental stages. This was enabled by inferring a protein sequence database from 454 sequencing of Bienertia cDNAs. Large-scale proteome rearrangements were observed as C4 photosynthesis developed during leaf maturation. The proteomes of the two chloroplasts are different with differential accumulation of linear and cyclic electron transport components, primary and secondary carbon fixation reactions, and a triose-phosphate shuttle that is shared between the two chloroplast types. This differential protein distribution pattern suggests the presence of a mRNA or protein-sorting mechanism for nuclear-encoded, chloroplast-targeted proteins in SCC4 species. The combined information was used to provide a comprehensive model for NAD-ME type carbon fixation in SCC4 species.


Assuntos
Amaranthaceae/metabolismo , Cloroplastos/metabolismo , DNA Complementar/metabolismo , Regulação da Expressão Gênica de Plantas , Fotossíntese/genética , Amaranthaceae/genética , Dióxido de Carbono/metabolismo , Compartimento Celular , Cloroplastos/classificação , Cloroplastos/genética , DNA Complementar/genética , DNA de Plantas/genética , DNA de Plantas/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Células Vegetais/metabolismo , Folhas de Planta/citologia , Folhas de Planta/metabolismo , Proteômica
12.
Gene ; 530(2): 229-35, 2013 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-23973725

RESUMO

The sequence of the chloroplast genome, which is inherited maternally, contains useful information for many scientific fields such as plant systematics, biogeography and biotechnology because its characteristics are highly conserved among species. There is an increase in chloroplast genomes of angiosperms that have been sequenced in recent years. In this study, the nucleotide sequence of the chloroplast genome (cpDNA) of Veratrum patulum Loes. (Melanthiaceae, Liliales) was analyzed completely. The circular double-stranded DNA of 153,699 bp consists of two inverted repeat (IR) regions of 26,360 bp each, a large single copy of 83,372 bp, and a small single copy of 17,607 bp. This plastome contains 81 protein-coding genes, 30 distinct tRNA and four genes of rRNA. In addition, there are six hypothetical coding regions (ycf1, ycf2, ycf3, ycf4, ycf15 and ycf68) and two open reading frames (ORF42 and ORF56), which are also found in the chloroplast genomes of the other species. The gene orders and gene contents of the V. patulum plastid genome are similar to that of Smilax china, Lilium longiflorum and Alstroemeria aurea, members of the Smilacaceae, Liliaceae and Alstroemeriaceae (Liliales), respectively. However, the loss rps16 exon 2 in V. patulum results in the difference in the large single copy regions in comparison with other species. The base substitution rate is quite similar among genes of these species. Additionally, the base substitution rate of inverted repeat region was smaller than that of single copy regions in all observed species of Liliales. The IR regions were expanded to trnH_GUG in V. patulum, a part of rps19 in L. longiflorum and A. aurea, and whole sequence of rps19 in S. china. Furthermore, the IGS lengths of rbcL-accD-psaI region were variable among Liliales species, suggesting that this region might be a hotspot of indel events and the informative site for phylogenetic studies in Liliales. In general, the whole chloroplast genome of V. patulum, a potential medicinal plant, will contribute to research on the genetic applications of this genus.


Assuntos
Cloroplastos/genética , Genoma de Cloroplastos , Genômica , Filogenia , RNA de Plantas/genética , Veratrum/genética , Cloroplastos/classificação , Mapeamento Cromossômico , DNA Circular , Sequências Repetidas Invertidas , Liliaceae/classificação , Liliaceae/genética , RNA de Plantas/classificação , RNA Ribossômico/classificação , RNA Ribossômico/genética , RNA de Transferência/classificação , RNA de Transferência/genética , Smilacaceae/classificação , Smilacaceae/genética , Veratrum/classificação
13.
Protist ; 162(3): 394-404, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21130034

RESUMO

Kleptoplastidy is the ability of heterotrophic organisms to preserve chloroplasts of algal preys they eat and partially digest. As the sequestered chloroplasts stay functional for months, the "host" becomes photosynthetically active. Although remaining a marginal process, kleptoplastidy was observed in different protist lineages, including foraminifera. Previous studies showed at least eight species of the foraminiferal genera Haynesina and Elphidium grazing on diatoms and husbanding their chloroplasts. In order to characterize more precisely the origin of kleptochloroplasts in these genera, we obtained 1027 chloroplastic 16S rDNA sequences from 13 specimens of two Haynesina and five Elphidium species. We identified the foraminiferal kleptochloroplasts using a reference phylogeny made of 87 chloroplastic sequences of known species of diatoms and brown algae. All the analyzed specimens were performing kleptoplastidy and according to our phylogenetic analyses they seem to retain exclusively chloroplasts of diatom origin. There is no apparent specificity for the type of diatom from which chloroplasts originated, however some foraminiferal species seem to accept a wider range of diatoms than others. Possibly the diversity of kleptochloroplasts depends on the type of diatoms the foraminiferans feed on.


Assuntos
Cloroplastos/classificação , Diatomáceas/genética , Foraminíferos/classificação , Foraminíferos/microbiologia , Sequência de Bases , Cloroplastos/genética , DNA de Cloroplastos/química , DNA de Cloroplastos/genética , DNA de Protozoário/química , DNA de Protozoário/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Diatomáceas/classificação , Evolução Molecular , Foraminíferos/genética , Processos Heterotróficos , Dados de Sequência Molecular , Fotossíntese , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
14.
Photosynth Res ; 107(1): 1-6, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21190136

RESUMO

The integrated functioning of two photosystems (I and II) whether in cyanobacteria or in chloroplasts is the outstanding sign of a common ancestral origin. Many variations on the basic theme are currently evident in oxygenic photosynthetic organisms whether they are prokaryotes, unicellular, or multicellular. By conservative estimates, oxygenic photosynthesis has been around for at least ca. 2.2-2.7 billions years, consistent with cyanobacteria-type microfossils, biomarkers, and an atmospheric rise in oxygen to less than 1.0% of the present concentration. The presumptions of chloroplast formation by the cyanobacterial uptake into a eukaryote prior to 1.6 BYa ago are confounded by assumptions of host type(s) and potential tolerance of oxygen toxicity. The attempted dating and interrelationships of particular chloroplasts in various plant or animal lineages has relied heavily on phylogenomic analysis and evaluations that have been difficult to confirm separately. Many variations occur in algal groups, involving the type and number of accessory pigments, and the number(s) of membranes (2-4) enclosing a chloroplast, which can both help and complicate inferences made about early or late origins of chloroplasts. Integration of updated phylogenomics with physiological and cytological observations remains a special challenge, but could lead to more accurate assumptions of initial and extant endosymbiotic event(s) leading toward stable chloroplast associations.


Assuntos
Evolução Biológica , Cloroplastos/metabolismo , Cianobactérias/metabolismo , Oxigênio/metabolismo , Fotossíntese , Clorófitas/metabolismo , Cloroplastos/classificação , Cloroplastos/genética , Glaucófitas/metabolismo , Modelos Biológicos , Fotossíntese/genética , Complexo de Proteína do Fotossistema I/genética , Complexo de Proteína do Fotossistema II/genética , Rodófitas/metabolismo , Simbiose , Fatores de Tempo
15.
PLoS One ; 6(12): e29398, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-22242118

RESUMO

The Dinophysis genus is an ecologically and evolutionarily important group of marine dinoflagellates, yet their molecular phylogenetic positions and ecological characteristics such as trophic modes remain poorly understood. Here, a population of Dinophysis miles var. indica was sampled from South China Sea in March 2010. Nuclear ribosomal RNA gene (rDNA) SSU, ITS1-5.8S-ITS2 and LSU, mitochondrial genes encoding cytochrome B (cob) and cytochrome C oxidase subunit I (cox1), and plastid rDNA SSU were PCR amplified and sequenced. Phylogenetic analyses based on cob, cox1, and the nuclear rRNA regions showed that D. miles was closely related to D. tripos and D. caudata while distinct from D. acuminata. Along with morphology the LSU and ITS1-5.8S-ITS2 molecular data confirmed that this population was D. miles var. indica. Furthermore, the result demonstrated that ITS1-5.8S-ITS2 fragment was the most effective region to distinguish D. miles from other Dinophysis species. Three distinct types of plastid rDNA sequences were detected, belonging to plastids of a cryptophyte, a haptophyte, and a cyanobacterium, respectively. This is the first documentation of three photosynthetic entities associated with a Dinophysis species. While the cyanobacterial sequence likely represented an ectosymbiont of the D. miles cells, the detection of the cryptophyte and haptophyte plastid sequences indicates that the natural assemblage of D. miles likely retain more than one type of plastids from its prey algae for temporary use in photosynthesis. The result, together with recent findings of plastid types in other Dinophysis species, suggests that more systematic research is required to understand the complex nutritional physiology of this genus of dinoflagellates.


Assuntos
Núcleo Celular/genética , Cloroplastos/classificação , Cloroplastos/genética , Dinoflagelados/genética , Genes de Cloroplastos/genética , Genes Mitocondriais/genética , Filogenia , DNA Ribossômico/genética , DNA Espaçador Ribossômico/genética , Dinoflagelados/citologia , Dados de Sequência Molecular , Subunidades Ribossômicas Maiores/genética , Subunidades Ribossômicas Menores/genética , Especificidade da Espécie , Simbiose/genética
16.
Mol Biol Evol ; 28(4): 1491-503, 2011 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-21172830

RESUMO

Rubisco, the primary photosynthetic carboxylase, evolved 3-4 billion years ago in an anaerobic, high CO(2) atmosphere. The combined effect of low CO(2) and high O(2) levels in the modern atmosphere, and the inability of Rubisco to distinguish completely between CO(2) and O(2), leads to the occurrence of an oxygenation reaction that reduces the efficiency of photosynthesis. Among land plants, C(4) photosynthesis largely solves this problem by facilitating a high CO(2)/O(2) ratio at the site of Rubisco that resembles the atmosphere in which the ancestral enzyme evolved. The prediction that such conditions favor Rubiscos with higher kcat(CO2) and lower CO(2)/O(2) specificity (S(C/O)) is well supported, but the structural basis for the differences between C(3) and C(4) Rubiscos is not clear. Flaveria (Asteraceae) includes C(3), C(3)-C(4) intermediate, and C(4) species with kinetically distinct Rubiscos, providing a powerful system in which to study the biochemical transition of Rubisco during the evolution from C(3) to C(4) photosynthesis. We analyzed the molecular evolution of chloroplast rbcL and nuclear rbcS genes encoding the large subunit (LSu) and small subunit (SSu) of Rubisco from 15 Flaveria species. We demonstrate positive selection on both subunits, although selection is much stronger on the LSu. In Flaveria, two positively selected LSu amino acid substitutions, M309I and D149A, distinguish C(4) Rubiscos from the ancestral C(3) species and statistically account for much of the kinetic difference between the two groups. However, although Flaveria lacks a characteristic "C(4)" SSu, our data suggest that specific residue substitutions in the SSu are correlated with the kinetic properties of Rubisco in this genus.


Assuntos
Evolução Biológica , Flaveria/enzimologia , Fotossíntese/fisiologia , Ribulose-Bifosfato Carboxilase/genética , Ribulose-Bifosfato Carboxilase/metabolismo , Cloroplastos/classificação , Cloroplastos/enzimologia , Cloroplastos/genética , Flaveria/genética , Modelos Moleculares , Dados de Sequência Molecular , Filogenia , Estrutura Terciária de Proteína , Ribulose-Bifosfato Carboxilase/química
17.
ISME J ; 4(6): 777-83, 2010 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-20200567

RESUMO

Cyanobacteria have had a pivotal role in the history of life on Earth being the first organisms to perform oxygenic photosynthesis, which changed the atmospheric chemistry and allowed the evolution of aerobic Eukarya. Chloroplasts are the cellular organelles of photoautotrophic eukaryotes in which most portions of photosynthesis occur. Although the initial suggestion that cyanobacteria are the ancestors of chloroplasts was greeted with skepticism, the idea is now widely accepted. Here we attempt to resolve and date the cyanobacterial ancestry of the chloroplast using phylogenetic analysis and molecular clocks. We found that chloroplasts form a monophyletic lineage, are most closely related to subsection-I, N(2)-fixing unicellular cyanobacteria (Order Chroococcales), and heterocyst-forming Order Nostocales cyanobacteria are their sister group. Nostocales and Chroococcales appeared during the Paleoproterozoic and chloroplasts appeared in the mid-Proterozoic. The capability of N(2) fixation in cyanobacteria may have appeared only once during the late Archaean and early Proterozoic eons. Furthermore, we found that oxygen-evolving cyanobacteria could have appeared in the Archaean. Our results suggest that a free-living cyanobacterium with the capacity to store starch through oxygenic CO(2) fixation, and to fix atmospheric N(2), would be a very important intracellular acquisition, which, as can be recounted today from several lines of evidence, would have become the chloroplast by endosymbiosis.


Assuntos
Evolução Biológica , Cloroplastos/genética , Cianobactérias/genética , Filogenia , Cloroplastos/classificação , Cianobactérias/classificação , Fixação de Nitrogênio , Fotossíntese , RNA Ribossômico 16S/genética
18.
Mol Biol Evol ; 25(9): 2019-30, 2008 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-18614526

RESUMO

A unique combination of genetic features and a rich stock of information make the flowering plant genus Oenothera an appealing model to explore the molecular basis of speciation processes including nucleus-organelle coevolution. From representative species, we have recently reported complete nucleotide sequences of the 5 basic and genetically distinguishable plastid chromosomes of subsection Oenothera (I-V). In nature, Oenothera plastid genomes are associated with 6 distinct, either homozygous or heterozygous, diploid nuclear genotypes of the 3 basic genomes A, B, or C. Artificially produced plastome-genome combinations that do not occur naturally often display interspecific plastome-genome incompatibility (PGI). In this study, we compare formal genetic data available from all 30 plastome-genome combinations with sequence differences between the plastomes to uncover potential determinants for interspecific PGI. Consistent with an active role in speciation, a remarkable number of genes have high Ka/Ks ratios. Different from the Solanacean cybrid model Atropa/tobacco, RNA editing seems not to be relevant for PGIs in Oenothera. However, predominantly sequence polymorphisms in intergenic segments are proposed as possible sources for PGI. A single locus, the bidirectional promoter region between psbB and clpP, is suggested to contribute to compartmental PGI in the interspecific AB hybrid containing plastome I (AB-I), consistent with its perturbed photosystem II activity.


Assuntos
Cloroplastos/genética , Oenothera/genética , Sequência de Bases , Cloroplastos/classificação , Mapeamento Cromossômico , DNA Intergênico , DNA de Plantas , Evolução Molecular , Etiquetas de Sequências Expressas , Especiação Genética , Genoma de Planta , Genótipo , Oenothera/classificação , Oenothera/ultraestrutura , Edição de RNA , Seleção Genética
20.
Microbiology ; 142 ( Pt 1): 17-32, 1996 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-8581162

RESUMO

Sequences of the three integral membrane subunits (subunits a, b and c) of the F0 sector of the proton-translocating F-type (F0F1-) ATPases of bacteria, chloroplasts and mitochondria have been analysed. All homologous-sequenced proteins of these subunits, comprising three distinct families, have been identified by database searches, and the homologous protein sequences have been aligned and analysed for phylogenetic relatedness. The results serve to define the relationships of the members of each of these three families of proteins, to identify regions of relative conservation, and to define relative rates of evolutionary divergence. Of these three subunits, c-subunits exhibited the slowest rate of evolutionary divergence, b-subunits exhibited the most rapid rate of evolutionary divergence, and a-subunits exhibited an intermediate rate of evolutionary divergence. The results allow definition of the relative times of occurrence of specific events during evolutionary history, such as the intragenic duplication event that gave rise to large c-subunits in eukaryotic vacuolar-type ATPases after eukaryotes diverged from archaea, and the extragenic duplication of F-type ATPase b-subunits that occurred in blue-green bacteria before the advent of chloroplasts. The results generally show that the three F0 subunits evolved as a unit from a primordial set of genes without appreciable horizontal transmission of the encoding genetic information although a few possible exceptions were noted.


Assuntos
Bactérias/genética , Cloroplastos/genética , Mitocôndrias/genética , Filogenia , ATPases Translocadoras de Prótons/genética , Sequência de Aminoácidos , Bactérias/classificação , Bactérias/enzimologia , Cloroplastos/classificação , Cloroplastos/enzimologia , Substâncias Macromoleculares , Mitocôndrias/classificação , Mitocôndrias/enzimologia , Dados de Sequência Molecular , Conformação Proteica , ATPases Translocadoras de Prótons/classificação , Alinhamento de Sequência/métodos , Homologia de Sequência de Aminoácidos
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