The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae

The Chlorophyceae, an advanced class of chlorophyte green algae, comprises five lineages that form two major clades (Chlamydomonadales + Sphaeropleales and Oedogoniales + Chaetopeltidales + Chaetophorales). The four complete chloroplast DNA (cpDNA) sequences currently available for chlorophyceans uncovered an extraordinarily fluid genome architecture as well as many structural features distinguishing this group from other green algae. We report here the 521,168-bp cpDNA sequence from a member of the Chaetopeltidales (Floydiella terrestris), the sole chlorophycean lineage not previously sampled for chloroplast genome analysis. This genome, which contains 97 conserved genes and 26 introns (19 group I and 7 group II introns), is the largest chloroplast genome ever sequenced. Intergenic regions account for 77.8% of the genome size and are populated by short repeats. Numerous genomic features are shared with the cpDNA of the chaetophoralean Stigeoclonium helveticum, notably the absence of a large inverted repeat and the presence of unique gene clusters and trans-spliced group II introns. Although only one of the Floydiella group I introns encodes a homing endonuclease gene, our finding of five free-standing reading frames having similarity with such genes suggests that chloroplast group I introns endowed with mobility were once more abundant in the Floydiella lineage. Parsimony analysis of structural genomic features and phylogenetic analysis of chloroplast sequence data unambiguously resolved the Oedogoniales as sister to the Chaetopeltidales and Chaetophorales. An evolutionary scenario of the molecular events that shaped the chloroplast genome in the Chlorophyceae is presented

Saisonnalité du transport de carbone organique dissous dans le ruisseau de l'Hermine, un bassin versant de tête de réseau du Bouclier Canadien

Nous avons étudié la variabilité saisonnière de la relation entre les fluctuations des concentrations en carbone organique dissous (COD) dans le ruisseau de l'Hermine (Québec, Canada) et les changements du débit (Q). Un total de 93 événements hydrologiques échantillonnés de 1994 à 2003 et regroupés sur une base saisonnière (hiver-printemps, été, automne) a été analysé. Le modèle de régression linéaire est utilisé afin de déterminer, pour chaque événement, la pente de la relation entre la concentration en COD dans le ruisseau et le débit. Ces pentes sont regroupées par saison et selon un seuil arbitraire de un qui permet de contraster les conditions hydrologiques et climatiques initiales des événements répertoriés. Les résultats du test de Kruskal-Wallis, visant la comparaison entre les événements de pentes supérieures et inférieures à un, montrent clairement la saisonnalité de la relation entre le COD et le débit. La saisonnalité de la relation COD/Q est ensuite mise en relation avec des variables climatiques et hydrologiques susceptibles de conditionner le transport du COD dans le bassin de l'Hermine. Les résultats montrent que les changements saisonniers des conditions climatiques et hydrologiques dans le bassin versant ont un impact significatif sur la relation entre le COD et le débit. Ainsi, le volume de précipitation tombé durant l'événement, la température moyenne de l'air et la température du sol régissent significativement (p =0,041; 0,001 et 0,009 respectivement) le transport du COD pour la période hiver-printemps. Les basses températures du sol et l'apport élevé en eau via les précipitations et la fonte favorisent le lessivage intense du COD soluble déjà limité par les basses températures. Au cours de l'été, l'état initial d'humidité du bassin est le principal facteur contrôlant l'évolution des concentrations de COD lors d'une crue; les fortes relations avec le pourcentage d'humidité des sols et le débit total 24 h avant l'événement le prouvent (p =0,039 et 0,0003 respectivement). Les changements les plus prononcés du COD surviennent, au cours de l'été, suite à une période prolongée de sécheresse. À l'automne, le transport du COD est influencé par le volume de précipitation tombé durant l'événement (p =0,031) et la température du sol (p =0,042). La modélisation de la relation COD/Q par les variables hydro-climatiques montre que 40% de la relation COD/Q s'explique par la température du sol durant la période d'hiver-printemps. Durant l'été, les conditions initiales d'humidité du bassin, traduites par le débit 24 h avant l'événement, expliquent à 51% la relation COD/Q. À l'automne, la relation COD/Q est gouvernée à 50% à la fois par le volume de précipitation tombé durant l'événement et la température du sol. L'analyse de ces données établit clairement la saisonnalité de la relation COD/Q et que des variables climatiques et hydrologiques permettent de quantifier ces fluctuations saisonnières.The terrestrial organic carbon (C) pool, estimated to 1.5 x 1015 kg C for the first meter of soil (Amundson, 2001), represents a major terrestrial elemental stock for which the recycling rate and the response to perturbations are still unknown. Under the present changing climatic conditions, C fluxes in terrestrial ecosystems could be significantly disturbed during the next decades. Indeed, the multi-annual changes in temperature and precipitation are likely to have a major impact on the net primary production and on organic matter decomposition in soils. This situation influences the production of the dissolved organic carbon (DOC) in soils, its transport to surface waters and hence, water quality. In this context, a better knowledge of the climatic and hydrologic factors influencing seasonal variations in DOC export is crucial to improve our understanding of the potential transformation of carbon stocks and fluxes in terrestrial ecosystems.The objectives of the present study were 1) to evaluate the seasonality in the relationship between dissolved organic carbon (DOC) concentrations in the stream and streamflow (Q) and 2) to quantify the impact of seasonal changes in climatic and hydrological conditions in the watershed on the DOC/Q relationship.The Hermine catchment is located about 80 km north of Montréal, Québec, Canada. An intermittent first-order stream drains the 5.1 ha catchment. Soils are Orthic and Gleyed Humo-Ferric and Ferro-Humic Podzols. The stream water was sampled daily, from 1994 to 2003, with an automatic sampler. The stream discharge was calculated from the water level above a 90º V-notch weir using a Global level sensor bubbler. Soil organic C content was analysed by the modified Walkley-Black method. Because of the high cost of DOC analysis for numerous samples, the DOC content was estimated by the relationship obtained between eight stream water samples analysed with a Shimadzu TOC analyser (Shimadzu, Kyoto, Japan) and the corresponding absorbance measured at 254 nm. From the initial year of the project, 1994, the regression used was Y=-0.05 + 32.60 X with an r2 value of 0.58 and a precision of 0.05 mg·L-1.The relationship between the DOC concentration and Q at the Hermine was positive and significant (p < 0.01) when all data were considered (n=1960). Because of the weakness of this relation (r2 =0.12), the stream samples, from 1994 to 2003, were seasonally split into 93 distinct hydrological events: 33 for winter-spring, 34 for summer and 26 for fall. A linear regression model was used to determine, for each event, the slope of the relationship between the DOC concentrations in the stream and Q. To contrast the antecedent conditions of the Hermine watershed, the events from a given season were divided into two groups. The Kruskal-Wallis test was then used to establish the link between the slope of the DOC/Q relationships on the one hand, and the environmental watershed conditions on the other hand: the climatic variables (volume of precipitation during event, mean air and soil temperatures) and the hydrological variables (stream discharge 24 h before the event, soil moisture, and ground water level).The DOC concentrations in the stream varied on an annual, a seasonal and an event basis. For the period 1994 to 2003, the annual mean concentrations, calculated from daily samples, varied from 2.0 to 2.5 mg DOC·L-1. On a seasonal basis, mean daily DOC was higher during the summer and the fall (2.9 and 2.8 mg DOC·L-1 respectively), and lower in the winter-spring (2.1 mg DOC·L-1). The relation between DOC concentrations and Q fluctuated as a function of the seasonal evolution of climatic and hydrological conditions in the Hermine catchment. For winter-spring events, 79% of the events had a DOC/Q slope lower than one. This period was characterised by high streamflow levels and high total DOC fluxes even though the daily mean DOC concentrations were low (2.1 mg DOC·L-1). The volume of precipitation during the event (p =0.041), the mean air temperature (p =0.001) and the soil temperature (p =0.009) were significantly related to the difference between events with slopes lower and higher than one. Indeed the slope of the relation increases when soil temperatures are elevated. When the temperatures are higher, DOC export increases and subsurface flow in soil horizon is enriched in DOC. Under colder temperature, the DOC production is limited and the soluble organic substances stored in soils are leached out the catchment with the high volume of precipitation and with the water coming from the snowmelt. For the summer period, there were 20 events with slopes greater than one against 14 with slopes lower than one. The soil humidity (p =0.039) and the total streamflow 24 h before the event (p=0.0003), were the two variables that significantly distinguished both slope groups. Rapid changes in DOC concentration occur during hydrological events following a long drought period. Under dry conditions, the subsurface flow in soil horizons rich in organic matter, the re-hydration of bed sediments and the hydrophobic behaviour of soil particles can all contribute to the export of very high DOC concentrations, even during small events. The relationships between DOC and Q, for the fall season, were significantly influenced by the volume of precipitation during the event (p =0.031) and the mean soil temperature (p =0.042). The events with the lower slopes showed the highest volume of precipitation during event and the lowest soil temperature. For these events occurring under wet conditions, the water originates essentially from the B and C horizons, and DOC fluctuations are then limited because of the low concentrations of the DOC in these horizons (anionic sorption of soluble organic substances by iron oxides).Best-fit from multiple regressions indicated that 40% of the link between DOC and Q was explained by the soil temperature during the winter-spring period (p =0.0001). For summer, the streamflow 24 h before events accounted for 51% of the variation in DOC/Q relationships (p =0.00001). For the fall period, the volume of precipitation during event and the soil temperature both contributed equally to the DOC/Q relationships (p =0.001). From these results, obtained from a multi-year project, it is clear that the relation between DOC and Q is a function of the variability in the climatic and hydrological watershed conditions. In a context of global warming, it is possible that warmer air temperatures have an effect on soil temperature. Thus, during winter-spring and fall periods, the duration and the intensity of the DOC production in soils will increase and the export of DOC from the watershed to other surface water system could become more important under equivalent or higher streamflow. Higher air temperature also means higher evapotranspiration by the forest during the summer period, and consequently dryer watershed conditions. A low streamflow and a low soil humidity level could be expected and then, brief rain events will sporadically flush the soluble organic carbon accumulated in the soil. The DOC export would be insignificant for that period, but the DOC would reach the highest annual level. The new knowledge on the DOC/Q relationships, at the hydrological event scale, will be added to the accumulated data on the possible effects of global warming on the carbon cycle in forested ecosystems

A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies

BACKGROUND: The Viridiplantae comprise two major phyla: the Streptophyta, containing the charophycean green algae and all land plants, and the Chlorophyta, containing the remaining green algae. Despite recent progress in unravelling phylogenetic relationships among major green plant lineages, problematic nodes still remain in the green tree of life. One of the major issues concerns the scaly biflagellate Mesostigma viride, which is either regarded as representing the earliest divergence of the Streptophyta or a separate lineage that diverged before the Chlorophyta and Streptophyta. Phylogenies based on chloroplast and mitochondrial genomes support the latter view. Because some green plant lineages are not represented in these phylogenies, sparse taxon sampling has been suspected to yield misleading topologies. Here, we describe the complete chloroplast DNA (cpDNA) sequence of the early-diverging charophycean alga Chlorokybus atmophyticus and present chloroplast genome-based phylogenies with an expanded taxon sampling. RESULTS: The 152,254 bp Chlorokybus cpDNA closely resembles its Mesostigma homologue at the gene content and gene order levels. Using various methods of phylogenetic inference, we analyzed amino acid and nucleotide data sets that were derived from 45 protein-coding genes common to the cpDNAs of 37 green algal/land plant taxa and eight non-green algae. Unexpectedly, all best trees recovered a robust clade uniting Chlorokybus and Mesostigma. In protein trees, this clade was sister to all streptophytes and chlorophytes and this placement received moderate support. In contrast, gene trees provided unequivocal support to the notion that the Mesostigma + Chlorokybus clade represents the earliest-diverging branch of the Streptophyta. Independent analyses of structural data (gene content and/or gene order) and of subsets of amino acid data progressively enriched in slow-evolving sites led us to conclude that the latter topology reflects the true organismal relationships. CONCLUSION: In disclosing a sister relationship between the Mesostigmatales and Chlorokybales, our study resolves the long-standing debate about the nature of the unicellular flagellated ancestors of land plants and alters significantly our concepts regarding the evolution of streptophyte algae. Moreover, in predicting a richer chloroplast gene repertoire than previously inferred for the common ancestor of all streptophytes, our study has contributed to a better understanding of chloroplast genome evolution in the Viridiplantae

Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution

Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.

The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity, and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic, and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov

Electronic Structure of Dinuclear Gold(I) Complexes

Cyclic voltammetry (CV) experiments on LL(AuSR∗)2 complexes [LL = diphenylphosphinomethane (dppm), diphenylphosphinopentane (dpppn); R* = p-SC6H4CH3] show anodic sweeps that broaden by about 25 mV on going from the longer (dpppn) to the shorter (dppm) bidentate phosphine ligand. Changing concentrations had no effect on the shape of the waveform. The result suggests a weak intramolecular metal-metal interaction in dppm(AuSR∗)2 that correlates well with rate acceleration occurring in the reaction of dppm(AuSR∗)2 with organic disulfides. Quantum yields for cis-dppee(AuX)2 [dppee = 1,2-bis(diphenylphosphino)ethylene; X = Cl, Br, I] complexes, (disappearance) Φ , are significantly higher in complexes with a softer X ligand, a trend that correlates well with aurophilicity. This result also suggests that electronic perturbation caused by Au(I)-Au(I) interactions is important in explaining the reactivity of some dinuclear gold(I) complexes. The crystal structure for cis-dppee(Aul)2 shows short intramolecular Au(I)-Au(I) interactions of 2.9526 (6) A°, while the structure of trans-dppee(AuI)2 , shows intermolecular Au(I)-Au(I) interactions of 3.2292 (9) A°. The substitution of .As for P results in a ligand, cis-diphenylarsinoethylene (cis-dpaee), that is photochemically active, in contrast to the cis-dppee ligand. The complexes, cis-dpaee(AuX)2, are also photochemically active but with lower quantum yields than the cis-dppee(AuX)2 complexes

Broad Phylogenomic Sampling and the Sister Lineage of Land Plants

The tremendous diversity of land plants all descended from a single charophyte green alga that colonized the land somewhere between 430 and 470 million years ago. Six orders of charophyte green algae, in addition to embryophytes, comprise the Streptophyta s.l. Previous studies have focused on reconstructing the phylogeny of organisms tied to this key colonization event, but wildly conflicting results have sparked a contentious debate over which lineage gave rise to land plants. The dominant view has been that ‘stoneworts,’ or Charales, are the sister lineage, but an alternative hypothesis supports the Zygnematales (often referred to as “pond scum”) as the sister lineage. In this paper, we provide a well-supported, 160-nuclear-gene phylogenomic analysis supporting the Zygnematales as the closest living relative to land plants. Our study makes two key contributions to the field: 1) the use of an unbiased method to collect a large set of orthologs from deeply diverging species and 2) the use of these data in determining the sister lineage to land plants. We anticipate this updated phylogeny not only will hugely impact lesson plans in introductory biology courses, but also will provide a solid phylogenetic tree for future green-lineage research, whether it be related to plants or green algae

Interorganellar DNA transfer in wheat: dynamics and phylogenetic origin

A homology search of wheat chloroplast (ct) and mitochondrial (mt) genomes identified 54 ctDNA segments that have homology with 66 mtDNA segments. The mtDNA segments were classified according to their origin: orthologs (prokaryotic origin), xenologs (interorganellar DNA transfer origin) and paralogs (intraorganellar DNA amplification origin). The 66 mtDNA sequences with homology to ctDNA segments included 14 paralogs, 18 orthologs and 34 xenologs. Analysis of the xenologs indicated that the DNA transfer occurred unidirectionally from the ct genome to the mt genome. The evolutionary timing of each interorganellar DNA transfer that generated a xenolog was estimated. This analysis showed that 2 xenologs originated early in green plant evolution, 4 in angiosperm evolution, 3 in monocotyledon evolution, 9 during cereal diversification and 8 in the evolution of wheat. Six other xenologs showed recurrent transfer from the ct to mt genomes in more than one taxon. The two remaining xenologs were uninformative on the evolutionary timing of their transfer. The wheat mt nad9 gene was found to be chimeric, consisting of the cereal nad9 gene and its 291 bp 5′-flanking region that included a 58 bp xenolog of the ct-ndhC origin