Mobile DNAs: the poacher turned gamekeeper

The selfish DNA hypothesis imagines the genome as an ecological community, a collection of interacting DNA sequences with differing evolutionary origins and potentially different interests. We are now finding out more about the ways in which host sequences can enlist the help of formerly parasitic DNAs.     

What tangled web: barriers to rampant horizontal gene transfer

Dawkins in his The Selfish Gene(1) quite aptly applies the term "selfish" to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza(2) as well as Orgel and Crick(3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick(3) associated parasitic DNA with a potential to outgrow their host genomes by propagating both vertically via conventional genome replication as well as infectiously by horizontal gene transfer (HGT) to other genomes. Still later, Doolittle(4) speculated that unchecked HGT between unrelated genomes so complicates phylogeny that the conventional representation of a tree of life would have to be replaced by a thicket or a web of life.(4) In contrast, considerable data now show that reconstructions based on whole genome sequences are consistent with the conventional "tree of life".(5-10) Here, we identify natural barriers that protect modern genome populations from the inroads of rampant HGT.     

From pathogen genomes to host plant processes: the power of plant parasitic oomycetes

Recent pathogenomic research on plant parasitic oomycete effector function and plant host responses has resulted in major conceptual advances in plant pathology, which has been possible thanks to the availability of genome sequences.     

A slowly evolving host moves first in symbiotic interactions

Symbiotic relationships, both parasitic and mutualistic, are ubiquitous in nature. Understanding how these symbioses evolve, from bacteria and their phages to humans and our gut microflora, is crucial in understanding how life operates. Often, symbioses consist of a slowly evolving host species with each host only interacting with its own subpopulation of symbionts. The Red Queen hypothesis describes coevolutionary relationships as constant arms races with each species rushing to evolve an advantage over the other, suggesting that faster evolution is favored. Here, we use a simple game theoretic model of host-symbiont coevolution that includes population structure to show that if the symbionts evolve much faster than the host, the equilibrium distribution is the same as it would be if it were a sequential game where the host moves first against its symbionts. For the slowly evolving host, this will prove to be advantageous in mutualisms and a handicap in antagonisms. The result follows from rapid symbiont adaptation to its host and is robust to changes in the parameters, even generalizing to continuous and multiplayer games. Our findings provide insight into a wide range of symbiotic phenomena and help to unify the field of coevolutionary theory.     

Phylogenetic analysis of nuclear and mitochondrial genes supports species groups for Columbicola (Insecta: Phthiraptera)

The dove louse genus Columbicola has become a model system for studying the interface between microevolutionary processes and macroevolutionary patterns. This genus of parasitic louse (Phthiraptera) contains 80 described species placed into 24 species groups. Samples of Columbicola representing 49 species from 78 species of hosts were obtained and sequenced for mitochondrial (COI and 12S) and nuclear (EF-1alpha) genes. We included multiple representatives from most host species for a total of 154 individual Columbicola, the largest molecular phylogenetic study of a genus of parasitic louse to date. These sequences revealed considerable divergence within several widespread species of lice, and in some cases these species were paraphyletic. These divergences correlated with host association, indicating the potential for cryptic species in several of these widespread louse species. Both parsimony and Bayesian maximum likelihood phylogenetic analyses of these sequences support monophyly for nearly all the non-monotypic species groups included in this study. These trees also revealed considerable structure with respect to biogeographic region and host clade association. These patterns indicated that switching of parasites between host clades is limited by biogeographic proximity.     

A FIELD GUIDE TO THE RECORDING OF PARASITIC INFESTATION OF GAME ANIMALS

The importance of a survey of parasites in various game areas in East Africa is outlined both from the point of view of understanding the ecosystem and of exploiting its productivity. The commonly-encountered parasites are described and their normal locations in the host are given. Standard ways of classifying and assessing the degree of infestation by these major parasites are suggested, and the most appropriate manner of preserving specimens for subsequent examination is noted. A check-sheet for the recording of parasites in a post-mortem examination of game animals is included. Such a check-sheet, completed as suggested, together with adequate well-labelled collections, should be of great value in building up a general picture of the incidence and degree of parasitic infestation of various host animals in East African game areas.     

Evaluating the protein coding potential of exonized transposable element sequences

Background  

Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS) and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons.     

Niche metabolism in parasitic protozoa

Complete or partial genome sequences have recently become available for several medically and evolutionarily important parasitic protozoa. Through the application of bioinformatics complete metabolic repertoires for these parasites can be predicted. For experimentally intractable parasites insight provided by metabolic maps generated in silico has been startling. At its more extreme end, such bioinformatics reckoning facilitated the discovery in some parasites of mitochondria remodelled beyond previous recognition, and the identification of a non-photosynthetic chloroplast relic in malarial parasites. However, for experimentally tractable parasites, mapping of the general metabolic terrain is only a first step in understanding how the parasite modulates its streamlined, yet still often puzzlingly complex, metabolism in order to complete life cycles within host, vector, or environment. This review provides a comparative overview and discussion of metabolic strategies used by several different parasitic protozoa in order to subvert and survive host defences, and illustrates how genomic data contribute to the elucidation of parasite metabolism.     

Identification of novel Mycoplasma hyorhinis gene fragments by differential display analysis of co-cultures

Mycoplasmas are a diverse group of wall-less prokaryotes that have evolved an unusually small genome by adopting a parasitic mode of life. Recently, intense efforts have been made to sequence mycoplasma genomes and to define a minimal genome using mycoplasma as a model. Due to their parasitic nature, mycoplasma species are often difficult to cultivate, making it challenging to identify and sequence mycoplasma genes. In this report, we describe a method for identifying mycoplasma gene fragments from co-cultures using differential display analysis. Using this technique, we have identified fragments of seven putative genes from Mycoplasma hyorhinis. Sequence similarities suggest that four of these genes are members of the proposed minimal mycoplasma genome. The application of differential display analysis to co-cultures should be useful in the identification of genes from a variety of pathogenic organisms that are difficult to cultivate without a host.     

Interactions between bacteria and plant-parasitic nematodes: now and then

Based on genome-to-genome analyses of gene sequences obtained from plant-parasitic, root-knot nematodes (Meloidogyne spp.), it seems likely that certain genes have been derived from bacteria by horizontal gene transfer. Strikingly, a common theme underpinning the function of these genes is their apparent direct relationship to the nematodes' parasitic lifestyle. Phylogenetic analyses implicate rhizobacteria as the predominant group of 'gene donor' bacteria. Root-knot nematodes and rhizobia occupy similar niches in the soil and in roots, and thus the opportunity for genetic exchange may be omnipresent. Further, both organisms establish intimate developmental interactions with host plants, and mounting evidence suggests that the mechanisms for these interactions are shared too. We propose that the origin of parasitism in Meloidogyne may have been facilitated by acquisition of genetic material from soil bacteria through horizontal transfer, and that such events represented key steps in speciation of plant-parasitic nematodes. To further understand the mechanisms of horizontal gene transfer, and also to provide experimental tools to manipulate this promising bio-control agent, we have initiated a genomic sequence of the bacterial hyper-parasite of plant parasitic nematodes, Pasteuria penetrans. Initial data have established that P. penetrans is closely related to Bacillus spp., to the extent that considerable genome synteny is apparent. Hence, Bacillus serves as a model for Pasteuria, and vice versa.     

The first steps of transposable elements invasion: parasitic strategy vs. genetic drift

Transposable elements are often considered as selfish DNA sequences able to invade the genome of their host species. Their evolutive dynamics are complex, due to the interaction between their intrinsic amplification capacity, selection at the host level, transposition regulation, and genetic drift. Here, we propose modeling the first steps of TE invasion, i.e., just after a horizontal transfer, when a single copy is present in the genome of one individual. If the element has a constant transposition rate, it will disappear in most cases: the elements with low-transposition rate are frequently lost through genetic drift, while those with high-transposition rate may amplify, leading to the sterility of their host. Elements whose transposition rate is regulated are able to successfully invade the populations, thanks to an initial transposition burst followed by a strong limitation of their activity. Self-regulation or hybrid dysgenesis may thus represent some genome-invasion parasitic strategies.     

Molecular diversity of bacterial endosymbionts associated with dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) reveals a high degree of phylogenetic congruence with their host

Bacterial endosymbionts have been detected in some groups of plant‐parasitic nematodes, but few cases have been reported compared to other groups in the phylum Nematoda, such as animal‐parasitic or free‐living nematodes. This study was performed on a wide variety of plant‐parasitic nematode families and species from different host plants and nematode populations. A total of 124 nematode populations (previously identified morphologically and molecularly) were screened for the presence of potential bacterial endosymbionts using the partial 16S rRNA gene and fluorescence in situ hybridization (FISH) and confocal microscopy. Potential bacterial endosymbionts were only detected in nematode species belonging to the genus Xiphinema and specifically in the X. americanum group. Fifty‐seven partial 16S rRNA sequences were obtained from bacterial endosymbionts in this study. One group of sequences was closely related to the genus ‘Candidatus Xiphinematobacter’ (19 bacterial endosymbiont sequences were associated with seven nematode host species, including two that have already been described and three unknown bacterial endosymbionts). The second bacterial endosymbiont group (38 bacterial endosymbiont sequences associated with six nematode species) was related to the family Burkholderiaceae, which includes fungal and soil–plant bacterial endosymbionts. These endosymbionts were reported for the first time in the phylum Nematoda. Our findings suggest that there is a highly specific symbiotic relationship between nematode host and bacterial endosymbionts. Overall, these results were corroborated by a phylogeny of nematode host and bacterial endosymbionts that suggested that there was a high degree of phylogenetic congruence and long‐term evolutionary persistence between hosts and endosymbionts.     

Horizontal gene transfer of a plastid gene in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae)

Plastid sequences are among the most widely used in phylogenetic and phylogeographic studies in flowering plants, where they are usually assumed to evolve like non-recombining, uniparentally transmitted, single-copy genes. Among others, this assumption can be violated by intracellular gene transfer (IGT) within cells or by the exchange of genes across mating barriers (horizontal gene transfer, HGT). We report on HGT of a plastid region including rps2, trnL-F, and rbcL in a group of non-photosynthetic flowering plants. Species of the parasitic broomrape genus Phelipanche harbor two copies of rps2, a plastid ribosomal gene, one corresponding to the phylogenetic position of the respective species, the other being horizontally acquired from the related broomrape genus Orobanche. While the vertically transmitted copies probably reside within the plastid genome, the localization of the horizontally acquired copies is not known. With both donor and recipient being parasitic plants, a possible pathway for the exchange of genetic material is via a commonly attacked host.     

Rearrangement of duplicated DNA in specialized cells of Neurospora

Introduction of DNA into Neurospora crassa can lead to sequence instability in the sexual phase of the life cycle. Sequence instability was investigated by using a set of strains transformed with single copies of a plasmid including host sequences, Neurospora sequences deleted from the host genome, and foreign sequences. The sequences already represented in the host were rearranged at high frequency in a cross. In general, both elements of the duplication, that from the plasmid and that from the host, became rearranged, whether or not they were linked. Unique sequences were left unaltered. Cytosine residues in the rearranged sequences typically became methylated de novo. Results from tetrad analyses indicated that the rearrangements occur before meiosis, during a stage between fertilization and karyogamy. We suggest that this previously unrecognized genetic process, RIP (rearrangement induced premeiotically), may contribute diversity for evolution and also maintain the gross organization of the genome.     

Mutualists and parasites: how to paint yourself into a (metabolic) corner.

Eukaryotes have developed an elaborate series of interactions with bacteria that enter their bodies and/or cells. Genome evolution of symbiotic and parasitic bacteria multiplying inside eukaryotic cells results in both convergent and divergent changes. The genome sequences of the symbiotic bacteria of aphids, Buchnera aphidicola, and the parasitic bacteria of body louse and humans, Rickettsia prowazekii, provide insights into these processes. Convergent genome characteristics include reduction in genome sizes and lowered G+C content values. Divergent evolution was recorded for amino acid and cell wall biosynthetic genes. The presence of pseudogenes in both genomes provides examples of recent gene inactivation events and offers clues to the process of genome deterioration and host-cell adaptation.