Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

International audienceHigh-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey–predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction

Prasinoviruses of the Marine Green Alga Ostreococcus tauri Are Mainly Species Specific

ABSTRACT Prasinoviruses infecting unicellular green algae in the order Mamiellales (class Mamiellophyceae) are commonly found in coastal marine waters where their host species frequently abound. We tested 40 Ostreococcus tauri viruses on 13 independently isolated wild-type O. tauri strains, 4 wild-type O. lucimarinus strains, 1 Ostreococcus sp. (“ Ostreococcus mediterraneus ”) clade D strain, and 1 representative species of each of two other related species of Mamiellales, Bathycoccus prasinos and Micromonas pusilla . Thirty-four out of 40 viruses infected only O. tauri , 5 could infect one other species of the Ostreococcus genus, and 1 infected two other Ostreococcus spp., but none of them infected the other genera. We observed that the overall susceptibility pattern of Ostreococcus strains to viruses was related to the size of two host chromosomes known to show intraspecific size variations, that genetically related viruses tended to infect the same host strains, and that viruses carrying inteins were strictly strain specific. Comparison of two complete O. tauri virus proteomes revealed at least three predicted proteins to be candidate viral specificity determinants. </jats:p

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts

Mating system drives negative associations between morphological features in Schistosomatidae

<p>Abstract</p> <p>Background</p> <p>Sexual morphological features are known to be associated with the mating systems of several animal groups. However, it has been suggested that morphological features other than sexual characteristics could also be constrained by the mating system as a consequence of negative associations. <it>Schistosomatidae </it>are parasitic organisms that vary in mating system and can thus be used to explore links between the mating system and negative associations with morphological features.</p> <p>Results</p> <p>A comparative analysis of <it>Schistosomatidae </it>morphological features revealed an association between the mating system (monogamous <it>versus </it>polygynandrous) and morphological characteristics of reproduction, nutrition, and locomotion.</p> <p>Conclusions</p> <p>The mating system drives negative associations between somatic and sexual morphological features. In monogamous species, males display a lower investment in sexual tissues and a higher commitment of resources to tissues involved in female transport, protection, and feeding assistance. In contrast, males of polygynandrous species invest to a greater extent in sexual tissues at the cost of reduced commitment to female care.</p

Molecular evolution of the crustacean hyperglycemic hormone family in ecdysozoans

<p>Abstract</p> <p>Background</p> <p>Crustacean Hyperglycemic Hormone (CHH) family peptides are neurohormones known to regulate several important functions in decapod crustaceans such as ionic and energetic metabolism, molting and reproduction. The structural conservation of these peptides, together with the variety of functions they display, led us to investigate their evolutionary history. CHH family peptides exist in insects (Ion Transport Peptides) and may be present in all ecdysozoans as well. In order to extend the evolutionary study to the entire family, CHH family peptides were thus searched in taxa outside decapods, where they have been, to date, poorly investigated.</p> <p>Results</p> <p>CHH family peptides were characterized by molecular cloning in a branchiopod crustacean, <it>Daphnia magna</it>, and in a collembolan, <it>Folsomia candida</it>. Genes encoding such peptides were also rebuilt <it>in silico </it>from genomic sequences of another branchiopod, a chelicerate and two nematodes. These sequences were included in updated datasets to build phylogenies of the CHH family in pancrustaceans. These phylogenies suggest that peptides found in Branchiopoda and Collembola are more closely related to insect ITPs than to crustacean CHHs. Datasets were also used to support a phylogenetic hypothesis about pancrustacean relationships, which, in addition to gene structures, allowed us to propose two evolutionary scenarios of this multigenic family in ecdysozoans.</p> <p>Conclusions</p> <p>Evolutionary scenarios suggest that CHH family genes of ecdysozoans originate from an ancestral two-exon gene, and genes of arthropods from a three-exon one. In malacostracans, the evolution of the CHH family has involved several duplication, insertion or deletion events, leading to neuropeptides with a wide variety of functions, as observed in decapods. This family could thus constitute a promising model to investigate the links between gene duplications and functional divergence.</p

Picoeukaryotic sequences in the Sargasso Sea metagenome

Many sequences from picoeukaryotes were found in DNA sequence data assembled from Sargasso seawater

Phenotypic plasticity in haptoral structures of Ligophorus cephali (Monogenea: Dactylogyridae) on the flathead mullet (Mugil cephalus): A Geometric Morphometric Approach

Evaluating phenotypic plasticity in attachment organs of parasites can provide information on the capacity to colonise new hosts and illuminate evolutionary processes driving host specificity. We analysed the variability in shape and size of the dorsal and ventral anchors of Ligophorus cephali from Mugil cephalus by means of geometric morphometrics and multivariate statistics. We also assessed the morphological integration between anchors and between the roots and points in order to gain insight into their functional morphology. Dorsal and ventral anchors showed a similar gradient of overall shape variation, but the amount of localised changes was much higher in the former. Statistical models describing variations in shape and size revealed clear differences between anchors. The dorsal anchor/bar complex seems more mobile than the ventral one in Ligophorus, and these differences may reflect different functional roles in attachment to the gills. The lower residual variation associated with the ventral anchor models suggests a tighter control of their shape and size, perhaps because these anchors seem to be responsible for firmer attachment and their size and shape would allow more effective responses to characteristics of the microenvironment within the individual host. Despite these putative functional differences, the high level of morphological integration indicates a concerted action between anchors. In addition, we found a slight, although significant, morphological integration between roots and points in both anchors, which suggests that a large fraction of the observed phenotypic variation does not compromise the functional role of anchors as levers. Given the low level of genetic variation in our sample, it is likely that much of the morphological variation reflects host-driven plastic responses. This supports the hypothesis of monogenean specificity through host-switching and rapid speciation. The present study demonstrates the potential of geometric morphometrics to provide new and previously unexplored insights into the functional morphology of attachment and evolutionary processes of host¿parasite coevolution

Monogeneans of West African Cichlid Fish: Evolution and Cophylogenetic Interactions

The goals of this paper were to investigate phylogenetic and evolutionary patterns of cichlid fish from West Africa and their Cichlidogyrus and Scutogyrus monogenean parasites, to uncover the presence of host-parasite cospeciation and to assess the level of morphological adaptation in parasites. This required the following steps, each one representing specific objectives of this paper: (1) to build phylogenetic trees for Cichlidogyrus and Scutogyrus species based on ribosomal DNA sequences, (2) to investigate phylogenetic relationships within West African cichlid fish based on the analysis of mitochondrial cytochrome b DNA sequences, (3) to investigate host-parasite cophylogenetic history to gain clues on parasite speciation process, and (4) to investigate the link between the morphology of the attachment apparatus and parasite phylogeny. Phylogenetic analyses supported the monophyletic origin of the Cichlidogyrus/Scutogyrus group, and suggested that Cichlidogyrus is polyphyletic and that Scutogyrus is monophyletic. The phylogeny of Cichlidae supported the separation of mouthbrooders and substrate-brooders and is consistent with the hypothesis that the mouthbrooding behavior of Oreochromis and Sarotherodon evolved from substrate-brooding behavior. The mapping of morphological characters of the haptor onto the parasite phylogenetic tree suggests that the attachment organ has evolved from a very simple form to a more complex one. The cophylogenetic analyses indicated a significant fit between trees using distance-based tests, but no significant cospeciation signal using tree-based tests, suggesting the presence of parasite duplications and host switches on related host species. This shed some light on the diversification process of Cichlidogyrus species parasitizing West African cichlids

Review of the phylogenetic reconstruction of the diatoms using molecular tools with an analysis of a seven gene data set using multiple outgroups and morphological data for a total evidence approach

Medlin tested multiple outgroups with 18S rRNA dataset and found that haptophytes, ciliates, prasinophytes and chlorophytes recovered monophyletic Coscinodiscophyceae, Mediophyceae, Bacillariophyceae with strong BT support. Theriot et al. added six plastid genes to the diatom dataset but with only one outgroup, Bolidomonas and omitted most of the V4 region of that gene and bases beyond position 1200. They recovered a grade of clades from radial into polar centrics, into araphid pennates into the monophyletic raphid pennates. Their structural gradation hypothesis (SGH) contrasts to the CMB hypothesis of Medlin and Kaczmarska. We selected only those species with all seven genes from their dataset and added the entire 18S RNA gene to make a new dataset to which we sequentially added heterokont, haptophyte, and prasinophyte/chlorophyte outgroups. We analysed it using 1) evolutionary models with parameters relaxed across genes and codon positions for coding sequences (codon partition analysis scheme = CP) and 2) no partitions or evolutionary models as applied to each gene, using only optimised models of evolution for the entire dataset (NCP). CP recovered a monophyletic mediophycean and bacillariophycean clade and three coscinodiscophycean clades. Sequentially adding more outgroups did not change clade topology but dramatically increased BT support. NCP recovered a monophyletic Coscinodiscophyceae and Bacillariophyceae and three Mediophyceae clades, each with strong bootstrap support. Morphological data was added and analyzed similarly. NCP recovered three monophyletic classes and CP recovered the Bacillariophyceae arising from within the Mediophyceae, making the subphylum monophyletic but the class was paraphyletic. Each analysis was tested with SH tests in PAUP and IQTree. Plastid inheritance in the diatoms is not homogenous and thus their phylogenies may not be homologous. If so, then our application of gene models may be overparametrising the data. The application of no partitioning models with morphological data supported the CMB hypothesis

L'justice en Espagne au Dix-huitème siècle

Extrait de la Revue des Pyrinées-Année 189