The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the ...study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task.
To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the Phylogeny.fr platform.
BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://www.phylogeny.fr.
Virophages are recently discovered double-stranded DNA virus satellites that prey on giant viruses (nucleocytoplasmic large DNA viruses; NCLDVs), which are themselves parasites of unicellular ...eukaryotes. This coupled parasitism can result in the indirect control of eukaryotic cell mortality by virophages. However, the details of such tripartite relationships remain largely unexplored. We have discovered ∼300 predicted genes of putative virophage origin in the nuclear genome of the unicellular algaBigelowiella natans. Physical clustering of these genes indicates that virophage genomes are integrated into theB. natansgenome. Virophage inserts show high levels of similarity and synteny between each other, indicating that they are closely related. Virophage genes are transcribed not only in the sequencedB. natansstrain but also in otherBigelowiellaisolates, suggesting that transcriptionally active virophage inserts are widespread inBigelowiellapopulations. Evidence thatB. natansis also a host to NCLDV members is provided by the identification of NCLDV inserts in its genome. These putative large DNA viruses may be infected byB. natansvirophages. We also identify four repeated elements sharing structural and genetic similarities with transpovirons—a class of mobile elements first discovered in giant viruses—that were probably independently inserted in theB. natansgenome. We argue that endogenized provirophages may be beneficial to both the virophage andB. natansby (i) increasing the chances for the virophage to coinfect the host cell with an NCLDV prey and (ii) defending the host cell against fatal NCLDV infections.
In June 2016, in the northern highlands of Ethiopia, the Simien Mountains National Park guards have evicted the 2500 inhabitants of Gich, the most populated village of the park, and resettled them ...thirty kilometers further west, in the small town of Debark. For Ethiopian authorities, this operation seeks to put a stop to the degradation of nature, and by doing so to meet the recommendations formulated by the Unesco experts, who have been advocating for fifty years both this objective of safeguarding a degraded nature, and this mean of resettling its inhabitants. Then, while the resettled inhabitants end up socially uprooted and economically impoverished, those who still live within the borders of the national park continue to be sanctioned by fines or short terms of imprisonment for farming, grazing, inhabiting the land or hunting animals. This article is rooted in the African environmental history which analyses the institutional, ideal and scientific mechanisms of such an invention of a “pristine” nature. In order to contribute to further strengthening this sub-field of environmental history, special attention will be devoted to raise one question: why global conservation politics today seem doomed to produce social injustice, that is to make peoples that live within nature enduring political discrimination (being deprived of rights still available to Others) and moral domination (being deprived of these rights in the name of an ethic defined by Others)? A range of interviews with guards, farmers, former and present inhabitants, tour guides and visitors of Simien suggests, on the one hand, the crucial role of the experts from the international conservation institutions in promoting a neo-Malthusian view of African environments and their use by Africans. On the other hand, these testimonies highlight the social weight of an authoritarian Ethiopian State which is committed to bring external recognition to the Ethiopian nation, in order to forcefully assert his influence on the inside. Finally, at the crossroads of these two scales of action, the anonymous but daily actors of conservation suggest that at the very heart of the social injustice surrounding the global politics of nature lies the lasting image of an African nature at once pristine and degraded, that means a nature that cannot exist, and thus cannot be saved.
It is often anticipated that many of today's diploid plant species are in fact paleopolyploids. Given that an ancient large-scale duplication will result in an excess of relatively old duplicated ...genes with similar ages, we analyzed the timing of duplication of pairs of paralogous genes in 14 model plant species. Using EST contigs (unigenes), we identified pairs of paralogous genes in each species and used the level of synonymous nucleotide substitution to estimate the relative ages of gene duplication. For nine of the investigated species (wheat Triticum aestivum, maize Zea mays, tetraploid cotton Gossypium hirsutum, diploid cotton G. arboretum, tomato Lycopersicon esculentum, potato Solanum tuberosum, soybean Glycine max, barrel medic Medicago truncatula, and Arabidopsis thaliana), the age distributions of duplicated genes contain peaks corresponding to short evolutionary periods during which large numbers of duplicated genes were accumulated. Large-scale duplications (polyploidy or aneuploidy) are strongly suspected to be the cause of these temporal peaks of gene duplication. However, the unusual age profile of tandem gene duplications in Arabidopsis indicates that other scenarios, such as variation in the rate at which duplicated genes are deleted, must also be considered.
To study the evolutionary effects of polyploidy on plant gene functions, we analyzed functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in ...Arabidopsis thaliana. Genes retained in duplicate are not distributed evenly among Gene Ontology or Munich Information Center for Protein Sequences functional categories, which indicates a nonrandom process of gene loss. Genes involved in signal transduction and transcription have been preferentially retained, and those involved in DNA repair have been preferentially lost. Although the two members of each gene pair must originally have had identical transcription profiles, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. We identified several cases where groups of duplicated gene pairs have diverged in concert, forming two parallel networks, each containing one member of each gene pair. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. We also find that the rate of protein sequence evolution has been significantly asymmetric in >20% of duplicate pairs. Together, these results suggest that functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids.
The discovery of Acanthamoeba polyphaga mimivirus in 2003 using the free-living amoeba
caused a paradigm shift in the virology field. Twelve years later, using another amoeba as a host, i.e.,
, novel ...isolates of giant viruses have been discovered. This amoeba-virus relationship led scientists to study the evolution of giant viruses and explore the origins of eukaryotes. The purpose of this article is to review all the giant viruses that have been isolated from
, compare their genomic features, and report the influence of these viruses on the cell cycle of their amoebal host. To date, viruses putatively belonging to eight different viral taxa have been described: 7 are lytic and 1 is non-lytic. The comparison of giant viruses infecting
has suggested three homogenous groups according to their size, the replication time inside the host cell, and the number of encoding tRNAs. This approach is an attempt at determining the evolutionary origins and trajectories of the virus; therefore, more giant viruses infecting
must be discovered and studied to create a comprehensive knowledge on these intriguing biological entities.
The Arabidopsis genome contains numerous large duplicated chromosomal segments, but the different approaches used in previous analyses led to different interpretations regarding the number and timing ...of ancestral large-scale duplication events. Here, using more appropriate methodology and a more recent version of the genome sequence annotation, we investigate the scale and timing of segmental duplications in Arabidopsis. We used protein sequence similarity searches to detect duplicated blocks in the genome, used the level of synonymous substitution between duplicated genes to estimate the relative ages of the blocks containing them, and analyzed the degree of overlap between adjacent duplicated blocks. We conclude that the Arabidopsis lineage underwent at least two distinct episodes of duplication. One was a polyploidy that occurred much more recently than estimated previously, before the Arabidopsis/Brassica rapa split and probably during the early emergence of the crucifer family (24-40 Mya). An older set of duplicated blocks was formed after the monocot/dicot divergence, and the relatively low level of overlap among these blocks indicates that at least some of them are remnants of a larger duplication such as a polyploidy or aneuploidy.
infects the amoeba
and has recently been described as a distant relative of the African swine fever virus. To characterize the diversity and evolution of this novel viral genus, we report here on the ...isolation and genome sequencing of a second strain of
, namely LCC10. Detailed analysis of the sequencing data suggested that its 362-Kb genome is linear with covalently closed hairpin termini, so that DNA forms a single continuous polynucleotide chain. Comparative genomic analysis indicated that although the two sequenced
strains share extensive gene collinearity, 180 predicted genes were either gained or lost in only one genome. As already observed in another distant relative, i.e.,
, which infects the same host, the center and extremities of the
genome exhibited a higher rate of sequence divergence and the major capsid protein gene was colonized by type-I introns. A possible role of the
host in the genesis of these evolutionary traits is hypothesized. The
genome exhibited a significant gene strand bias over the two-third of genome length, a feature not seen in the other members of the "extended
" clade. We suggest that this gene strand bias was induced by a putative single origin of DNA replication located near the genome extremity that imparted a selective force favoring the genes positioned on the leading strand.
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