Tracking the ancestry of a deeply conserved eumetazoan SINE domain

Transposable elements (TEs), such as short interspersed elements (SINEs), evolve rapidly and are generally restricted to specific lineages. Here, we demonstrate that a central core of the previously described Deu-domain located within DeuSINEs (Nishihara et al. 2006) is widely distributed throughout the Metazoa. We characterize five new SINEs with this core sequence from the genomes of cnidarians, molluscs, annelids, and arthropods. Because this domain can be traced back to the cnidarian-bilaterian split >600 Ma, we propose naming it the "Nin" domain (the meaning of the Japanese character "Nin" is to endure and hide). Given that conserved noncoding DNA, such as that derived from the activity of SINEs, can be functionally relevant for the host genome (Sasaki et al. 2008), our findings highlight the need to understand these functions and the roles they may have played in supporting the evolution of multicellular genomes.     

Translation initiation in Archaea: conserved and domain-specific features

Initiation is a critical step in translation, during which the ribosome lands on the start codon and sets the correct reading frame for mRNA decoding. The rate and efficiency of translation are largely determined by initiation, which is therefore the preferred target of translation regulation mechanisms. Initiation has incurred an extensive evolutionary divergence among the primary domains of cell descent. The Archaea, albeit prokaryotes, have an initiation mechanism and apparatus more complex than those of the Bacteria; the molecular details of archaeal initiation are just beginning to be unravelled. The most notable aspects of archaeal initiation are the presence of two, perhaps three, distinct mechanisms for mRNA-ribosome interaction and the presence of a relatively large set of IFs (initiation factors), several of which are shared exclusively with the Eukarya. Among these, the protein termed a/eIF2 (archaeal/eukaryotic IF2) and aIF6 (archaeal IF6) are of special interest, since they appear to play key regulatory roles in the Eukarya. Studies of the function of these factors in Archaea have uncovered new features that will help to elucidate their conserved and domain-specific functions.     

Comparative structural analysis of haemagglutinin proteins from type A influenza viruses: conserved and variable features

Background

Genome variation is very high in influenza A viruses. However, viral evolution and spreading is strongly influenced by immunogenic features and capacity to bind host cells, depending in turn on the two major capsidic proteins. Therefore, such viruses are classified based on haemagglutinin and neuraminidase types, e.g. H5N1. Current analyses of viral evolution are based on serological and primary sequence comparison; however, comparative structural analysis of capsidic proteins can provide functional insights on surface regions possibly crucial to antigenicity and cell binding.

Results

We performed extensive structural comparison of influenza virus haemagglutinins and of their domains and subregions to investigate type- and/or domain-specific variation. We found that structural closeness and primary sequence similarity are not always tightly related; moreover, type-specific features could be inferred when comparing surface properties of haemagglutinin subregions, monomers and trimers, in terms of electrostatics and hydropathy. Focusing on H5N1, we found that variation at the receptor binding domain surface intriguingly relates to branching of still circulating clades from those ones that are no longer circulating.

Conclusions

Evidence from this work suggests that integrating phylogenetic and serological analyses by extensive structural comparison can help in understanding the ‘functional evolution’ of viral surface determinants. In particular, variation in electrostatic and hydropathy patches can provide molecular evolution markers: intriguing surface charge redistribution characterizing the haemagglutinin receptor binding domains from circulating H5N1 clades 2 and 7 might have contributed to antigenic escape hence to their evolutionary success and spreading.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0363-5) contains supplementary material, which is available to authorized users.     

Phylogenetic detection of conserved gene clusters in microbial genomes

Background  

Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional selection. Thus, identification of conserved gene clusters that are under functional selection provides an effective channel for gene annotation, microarray screening, and pathway reconstruction. The problem of devising a robust method to identify these conserved gene clusters and to evaluate the significance of the conservation in multiple genomes has a number of implications for comparative, evolutionary and functional genomics as well as synthetic biology.     

Phylogenetic diversity and ecological features in the Egyptian flora

Until fairly recently, regional-scale ecological and evolutionarypatterns have tended to be ignored as conservation efforts have been concernedwith species and their habitats. Here we compare frequencies in the Egyptianflora of particular rank sizes (order, family and genus) with patterns ofspecies abundance (classified as very rare, rare, common, or very common) and anarray of life-history attributes. The angiosperm flora of Egypt is representedby 2446 taxa (2088 species), including taxa in 10 subclasses, 51 orders, 120families, and 742 genera. A high degree of monotypism was observed: four ordersare monotypic (each existing as single species), and have very rare overallabundances; 30 families are monotypic (17 of which are very rare or rare); and 354genera are monotypic (over 70% of which are very rare or rare). Fourteenfamilies (in particular the Resedaceae and Zygophyllaceae) have at leastone-fifth of their global species represented in the Egyptian flora. Introducedspecies in general, and tree, aquatic herb and liana life forms all are especially well represented among monotypic genera. Native taxa are highlyrepresented among rare and very rare abundance classes, while introduced taxadid not differ significantly in their abundance patterns, compared to overallflora values. Few large genera (>20 spp.) occur in the flora, with mostspecies concentrated in genera containing 8–19 species per genus.Similarly, few families were highly speciose. Annual and herbaceous species weresignificantly over-represented, mainly among large, speciose genera andfamilies. However, perennials, trees, shrubs, aquatic herbs, lianas and parasiticspecies were found mainly in families and genera having very few taxa.Life-history attributes may have important implications to speciation rates.Taxonomically based results, involving abundances and life-history attributes,are discussed in the context of biodiversity and conservation.     

Phylogenetic analysis of the Cnidaria

The recent members of the phylum Cnidaria were analyzed with phylogenetic methodology and the help of the PAUP Computer program. The Cnidaria are established as a monophylum by their cnidocysts, planula larva, and a polyp stage. The Ctenophora were seen as the most probable sister group of the Cnidaria. Arguments for the monophyly of the cnidarian classes Anthozoa, Scyphozoa, Cubozoa, and Hydrozoa were providea. For the ground plan of the Cnidaria the following characters were postulated: triphasic life cycle consisting of a planula larva, a benthic polyp stage, and a sexually propagating medusa like stage. For the polyp a radial symmetry, lack of septae, and hollow tentacles were assumed. The original medusa probably was tetraradial and developed from the polyp stage by a total metamorphosis. Twelve polarized characters were used to generate cladograms. The most parsimonious one showed the Anthozoa as the first offshoot of the tree with the united Scyphozoa, Cubozoa and Hydrozoa forming its sister group. Within this sister group the Scyphozoa and Cubozoa were seen as sistergroups to each other. Both groups united are then the sistergroup of the Hydrozoa. A bootstrap analysis yielded the same tree with high probabilities for the internal nodes. Despite assuming a planktonic origin of the Cnidaria in this investigation, the resulting cladogram is also compatible with an evolution of the medusa stage within the Cnidaria after the splitting-off of the Anthozoa. The possible loss of the medusa stage in the Anthozoa is discussed.     

Unique genes in plants: specificities and conserved features throughout evolution

Background  

Plant genomes contain a high proportion of duplicated genes as a result of numerous whole, segmental and local duplications. These duplications lead up to the formation of gene families, which are the usual material for many evolutionary studies. However, all characterized genomes include single-copy (unique) genes that have not received much attention. Unlike gene duplication, gene loss is not an unspecific mechanism but is rather influenced by a functional selection. In this context, we have established and used stringent criteria in order to identify suitable sets of unique genes present in plant proteomes. Comparisons of unique genes in the green phylum were used to characterize the gene and protein features exhibited by both conserved and species-specific unique genes.     

Phylogenetic significance of stylar features in genus Vicia (Leguminosae): an analysis with molecular phylogeny

Tribe Fabeae consists of five genera, Lathyrus (160 spp.), Lens (4–6 spp.), Pisum (2–3 spp.), Vavilovia (monotypic), and Vicia (160 spp.), and shows a diversity in stylar features. At least six different stylar types are known in the tribe. In order to reclassify the tribe at the rank of genus, we tried to discover apomorphies in stylar features using a molecular phylogenetic study. We surveyed internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA of representative species, selected from each group having different types of styles in the tribe. We paid particular attention in sampling to members of Vicia section Vicilla, as stylar features are heterogeneous within this section. Consequently, our sample set included 15 species of section Vicilla, 23 species of other Fabeae, and two species of Trifolieae, which were used as a sister group of Fabeae. Based on our analysis, we found that a laterally compressed style and an abaxially tufted hairy style would be advanced against a dorsiventrally compressed style and an evenly hairy style, respectively, in genus Vicia. The species group, which shares the latter apomorphy, is composed of 56 species and was dispersed into 11 sections of two subgenera in the recent system of genus Vicia. We consider future revision of Fabeae should treat this species group as a single higher taxon.     

Phylogenetic analysis of upland cotton MATE gene family reveals a conserved subfamily involved in transport of proanthocyanidins

Molecular Biology Reports - The multidrug and toxic compound extrusion (MATE) protein belongs to a secondary transporter family, which plays a role in transporting different kinds of substrates...     

Comparative genomic analysis of a neurotoxigenic Clostridium species using partial genome sequence: Phylogenetic analysis of a few conserved proteins involved in cellular processes and metabolism

Clostridial organisms produce neurotoxins, which are generally regarded as the most potent toxic substances of biological origin and potential biological warfare agents. Clostridium tetani produces tetanus neurotoxin and is responsible for the fatal tetanus disease. In spite of the extensive immunization regimen, the disease is an important cause of death especially among neonates. Strains of C. tetani have not been genetically characterized except the complete genome sequencing of strain E88. The present study reports the genetic makeup and phylogenetic affiliations of an environmental strain of this bacterium with respect to C. tetani E88 and other clostridia. A shot gun library was constructed from the genomic DNA of C. tetani drde, isolated from decaying fish sample. Unique clones were sequenced and sequences compared with its closest relative C. tetani E88.A total of 275 clones were obtained and 32,457 bases of non-redundant sequence were generated. A total of 150 base changes were observed over the entire length of sequence obtained, including, additions, deletions and base substitutions. Of the total 120 ORFs detected, 48 exhibited closest similarity to E88 proteins of which three are hypothetical proteins. Eight of the ORFs exhibited similarity with hypothetical proteins from other organisms and 10 aligned with other proteins from unrelated organisms. There is an overall conservation of protein sequences among the two strains of C. tetani and. Selected ORFs involved in cellular processes and metabolism were subjected to phylogenetic analysis.     

SynBlast: Assisting the analysis of conserved synteny information

Motivation  

In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information.     

Unique and conserved features of floral evocation in legumes

Legumes, with their unique ability to fix atmospheric nitrogen, play a vital role in ensuring future food security and mitigating the effects of climate change because they use less fossil energy and produce less greenhouse gases compared with N-fertilized systems. Grain legumes are second only to cereal crops as a source of human and animal food, and they contribute approximately one third of the protein consumed by the human population. The productivity of seed crops, such as grain legumes, is dependent on flowering. Despite the genetic variation and importance of flowering in legume production, studies of the molecular pathways that control flowering in legumes are limited.Recent advances in genomics have revealed that legume flowering pathways are divergent from those of such model species as Arabidopsis thaliana. Here, we discuss the current understanding of flowering time regulation in legumes and highlight the unique and conserved features of floral evocation in legumes.     

Phylogenetic affinity of a Giardia lamblia cysteine desulfurase conforms to canonical pattern of mitochondrial ancestry

Among a few potential archezoan groups, only the Metamonada (diplomonads, retortamonads, and oxymonads) still retain the status of amitochondriate protists that diverged before the acquisition or retention of mitochondria. Indeed, finding that diplomonad genomes harbor a gene encoding a mitochondrial type chaperonin 60, the most compelling evidence for their secondarily amitochondriate nature, may be interpreted as an acquisition of this important general chaperone during some transient alpha-proteobacterial endosymbiosis. Recently published data on the cysteine desulfurase IscS demonstrated an alpha-proteobacterial origin of mitochondrial enzymes including a diplomonad Giardia lamblia homolog. An extended phylogenetic analysis of IscS is reported here that revealed a full canonical pattern of mitochondrial ancestry for the giardial enzyme. The above canonical pattern, a sister group relationship of mitochondria and rickettsiae exclusive of free-living alpha-proteobacteria, was robustly confirmed by a comprehensive analysis of Cob and Cox1 subunits of the respiratory chain encoded by resident mitochondrial genes. Given that Fe-S cluster assembly involving IscS represents an essential mitochondrial function, these data strongly suggest that diplomonads once harbored bona fide mitochondria.     

Phylogenetic analysis of the spirochetes.

The 16S rRNA sequences were determined for species of Spirochaeta, Treponema, Borrelia, Leptospira, Leptonema, and Serpula, using a modified Sanger method of direct RNA sequencing. Analysis of aligned 16S rRNA sequences indicated that the spirochetes form a coherent taxon composed of six major clusters or groups. The first group, termed the treponemes, was divided into two subgroups. The first treponeme subgroup consisted of Treponema pallidum, Treponema phagedenis, Treponema denticola, a thermophilic spirochete strain, and two species of Spirochaeta, Spirochaeta zuelzerae and Spirochaeta stenostrepta, with an average interspecies similarity of 89.9%. The second treponeme subgroup contained Treponema bryantii, Treponema pectinovorum, Treponema saccharophilum, Treponema succinifaciens, and rumen strain CA, with an average interspecies similarity of 86.2%. The average interspecies similarity between the two treponeme subgroups was 84.2%. The division of the treponemes into two subgroups was verified by single-base signature analysis. The second spirochete group contained Spirochaeta aurantia, Spirochaeta halophila, Spirochaeta bajacaliforniensis, Spirochaeta litoralis, and Spirochaeta isovalerica, with an average similarity of 87.4%. The Spirochaeta group was related to the treponeme group, with an average similarity of 81.9%. The third spirochete group contained borrelias, including Borrelia burgdorferi, Borrelia anserina, Borrelia hermsii, and a rabbit tick strain. The borrelias formed a tight phylogenetic cluster, with average similarity of 97%. THe borrelia group shared a common branch with the Spirochaeta group and was closer to this group than to the treponemes. A single spirochete strain isolated fromt the shew constituted the fourth group. The fifth group was composed of strains of Serpula (Treponema) hyodysenteriae and Serpula (Treponema) innocens. The two species of this group were closely related, with a similarity of greater than 99%. Leptonema illini, Leptospira biflexa, and Leptospira interrogans formed the sixth and most deeply branching group. The average similarity within this group was 83.2%. This study represents the first demonstration that pathogenic and saprophytic Leptospira species are phylogenetically related. The division of the spirochetes into six major phylogenetic clusters was defined also by sequence signature elements. These signature analyses supported the conclusion that the spirochetes represent a monophylectic bacterial phylum.     

Phylogenetic analysis ofUlmaceae

A phylogenetic analysis of theUlmaceae, Cannabaceae, Barbeyaceae, andBroussonetia of theMoraceae produced nine equally parsimonious trees with 127 steps. TheUlmoideae (Ulmaceae, sensuGrudzinskaya) are a monophyletic group and distinct from theCeltidoideae. The genusAmpelocera occupies an isolated taxonomic position among the celtidoids. The similarity ofAmpelocera to the fossil celtidoid flowerEoceltis of North America suggests thatAmpelocera posesses an archaic suite of characters, and occupies a primitive position among the celtidoids, theCannabaceae and theMoraceae. The relationships among the other celtidoid taxa,Cannabaceae, andBroussonetia are problematic. TheCannabaceae andBroussonetia of theMoraceae are nested within the celtidoids suggesting that this is a paraphyletic group. The close, but unresolved, relationship of the celtidoids to theMoraceae andCannabaceae observed in this analysis, and the appearance of the celtidoids in the fossil record prior to the ulmoids suggests that the evolutionary relationship of the ulmoids and celtidoids may be more distant than current taxonomic treatments reflect.     

Evolution of the MAGUK protein gene family in premetazoan lineages

Background  

Cell-to-cell communication is a key process in multicellular organisms. In multicellular animals, scaffolding proteins belonging to the family of membrane-associated guanylate kinases (MAGUK) are involved in the regulation and formation of cell junctions. These MAGUK proteins were believed to be exclusive to Metazoa. However, a MAGUK gene was recently identified in an EST survey of Capsaspora owczarzaki, an unicellular organism that branches off near the metazoan clade. To further investigate the evolutionary history of MAGUK, we have undertook a broader search for this gene family using available genomic sequences of different opisthokont taxa.     

Devonian features in Ludlovian graptolites — no guide to ancestry

A diverse group of Ludlovian Monograptus species is characterized by the retarded growth of thecal hoods, either proximally [ M. colonus (Barrande), M. chimaera (Barrande) and M. haupti Kühne] or throughout the rhabdosome [M. micropoma (Jaekel)]. In all these species the hoods are secondary structures, i.e. later growth additions to the thecae. By contrast, in the Devonian Monograptus species the thecal hoods are primary structures, i.e. the outward extension of the dorsal thecal wall. and are formed by undelayed growth that typically is completed before growth of the succeeding theca begins. It is among Ludlovian ( M. uncinatus Tullberg) and Pridolian ( M. simih Přibyl) forms with homologous hoods that the roots of the majority of the Devonian Monograptus species might be found. The Ludlovian M. micropoma and M. haupti should not be affiliated to the group of Monograptus vomerinus (Nicholson), which is highly characteristic of, and restricted to, the late Llandovery and Wenlock graptolite faunas.