Horizontal gene transfer and the unusual genomic architecture of bdelloid rotifers

Bdelloid rotifers are microscopic aquatic animals, notable for their ancient asexuality and their extreme desiccation tolerance. In the absence of sexual reproduction, bdelloids have persisted for over 40 million years, diverging into >450 morphologically distinct species. Despite the two-fold cost of sex, asexual lineages tend to be short-lived and species poor. Many theories exist to explain the success of sexual reproduction, and in the light of these, ancient asexual lineages are an evolutionary paradox. Understanding the persistence and speciation of ancient asexuals may provide clues to factors underlying the success of sexual reproduction. Bdelloid rotifers have unusual genomic features that may have provided some compensation for their long-term absence of sexual reproduction. Here I focus on two: multiple gene copies and horizontal gene transfer (HGT). Bdelloids have multiple copies of many genes, and are considered degenerate tetraploids. In genomes influenced by the opposing forces of gene conversion and divergence of former alleles, I examine the relationships between, and biochemical implications of divergence of a multi-gene family of alpha tubulin. Horizontally acquired genes were initially identified in sub-telomeric regions of two species of bdelloid rotifer. In order to understand what role foreign genes might have played in bdelloid evolution we need to examine the extent, frequency and mechanism of HGT. Here I develop a bioinformatics pipeline for identifying horizontally acquired genes in transcriptomes. By comparing HGT in a number of bdelloid species I demonstrate that the majority of transcribed foreign genes were acquired before the divergence of extant bdelloid species, but the presence of more recently acquired genes implies that HGT is ongoing. By comparing the extent of HGT in closely related species with different desiccation frequencies I provide initial support for the hypothesis that bdelloid HGT is facilitated by DNA breakage and repair during cycles of desiccation and rehydration.Open Acces

Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers.

BACKGROUND: Bdelloid rotifers are microscopic animals that have apparently survived without sex for millions of years and are able to survive desiccation at all life stages through a process called anhydrobiosis. Both of these characteristics are believed to have played a role in shaping several unusual features of bdelloid genomes discovered in recent years. Studies into the impact of asexuality and anhydrobiosis on bdelloid genomes have focused on understanding gene copy number. Here we investigate copy number and sequence divergence in alpha tubulin. Alpha tubulin is conserved and normally present in low copy numbers in animals, but multiplication of alpha tubulin copies has occurred in animals adapted to extreme environments, such as cold-adapted Antarctic fish. Using cloning and sequencing we compared alpha tubulin copy variation in four species of bdelloid rotifers and four species of monogonont rotifers, which are facultatively sexual and cannot survive desiccation as adults. Results were verified using transcriptome data from one bdelloid species, Adineta ricciae. RESULTS: In common with the typical pattern for animals, monogonont rotifers contain either one or two copies of alpha tubulin, but bdelloid species contain between 11 and 13 different copies, distributed across five classes. Approximately half of the copies form a highly conserved group that vary by only 1.1% amino acid pairwise divergence with each other and with the monogonont copies. The other copies have divergent amino acid sequences that evolved significantly faster between classes than within them, relative to synonymous changes, and vary in predicted biochemical properties. Copies of each class were expressed under the laboratory conditions used to construct the transcriptome. CONCLUSIONS: Our findings are consistent with recent evidence that bdelloids are degenerate tetraploids and that functional divergence of ancestral copies of genes has occurred, but show how further duplication events in the ancestor of bdelloids led to proliferation in both conserved and functionally divergent copies of this gene.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Structure of a glycosylphosphatidylinositol-anchored domain from a trypanosome variant surface glycoprotein.

The cell surface of African trypanosomes is covered by a densely packed monolayer of a single protein, the variant surface glycoprotein (VSG). The VSG protects the trypanosome cell surface from effector molecules of the host immune system and is the mediator of antigenic variation. The sequence divergence between VSGs that is necessary for antigenic variation can only occur within the constraints imposed by the structural features necessary to form the monolayer barrier. Here, the structures of the two domains that together comprise the C-terminal di-domain of VSG ILTat1.24 have been determined. The first domain has a structure similar to the single C-terminal domain of VSG MITat1.2 and provides proof of structural conservation in VSG C-terminal domains complementing the conservation of structure present in the N-terminal domain. The second domain, although based on the same fold, is a minimized version missing several structural features. The structure of the second domain contains the C-terminal residue that in the native VSG is attached to a glycosylphosphatidylinositol (GPI) anchor that retains the VSG on the external face of the plasma membrane. The solution structures of this domain and a VSG GPI glycan have been combined to produce the first structure-based model of a GPI-anchored protein. The model suggests that the core glycan of the GPI anchor lies in a groove on the surface of the domain and that there is a close association between the GPI glycan and protein. More widely, the GPI glycan may be an integral part of the structure of other GPI-anchored proteins

Differential gene expression according to race and host plant in the pea aphid

Host-race formation in phytophagous insects is thought to provide the opportunity for local adaptation and subsequent ecological speciation. Studying gene expression differences among host-races may help to identify phenotypes under (or resulting from) divergent selection and their genetic, molecular and physiological bases. The pea aphid (Acyrthosiphon pisum) comprises host-races specialising on numerous plants in the Fabaceae, and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. In this study, we examine transcriptome-wide gene expression both in response to environment and across pea aphid races selected to cover the range of genetic divergence reported in this species complex. We identify changes in expression in response to host-plant, indicating the importance of gene expression in aphid-plant interactions. Races can be distinguished on the basis of gene expression, and higher numbers of differentially expressed genes are apparent between more divergent races; these expression differences between host-races may result from genetic drift and reproductive isolation, and possibly divergent selection. Expression differences related to plant adaptation include a sub-set of chemosensory and salivary genes. Genes showing expression changes in response to host plant do not make up a large portion of between-race expression differences, providing confirmation of previous studies’ findings that genes involved in expression differences between diverging populations or species are not necessarily those showing initial plasticity in the face of environmental change

The Genetics of Host Plant Acceptance in Pea Aphids

The evolution of host-associated sympatric populations in phytophagous insects (so called “host races”) connects adaptive divergence to barriers to gene flow. Pea aphid (Acyrthosiphon pisum) host races specialise on legume species, and because host plant choice leads to assortative mating, the genetic basis of host plant acceptance is key to understanding speciation. Aphids use smell and taste in their host plant selection. While chemosensory genes frequently emerge as “outliers” in genome scans, their link to plant acceptance behaviour remains unclear. We examined the genetic basis of host-associated phenotypes using an F2 cross between two pea aphid host-associated races (specialised on alfalfa—Medicago sativa- and pea—Pisum sativum), assaying behaviour on both host plants and conducting QTL and regional heritability analyses based on a high-resolution linkage map. We identified five regions of moderate effect associated with acceptance of alfalfa, two with pea acceptance and two with survival on alfalfa. Two QTLs, one for alfalfa and one for pea acceptance, are located within a large rearranged region on chromosome 1, while other QTLs linked to alfalfa acceptance and survival are in the same region on chromosome 3—linking host plant choice to fitness. These findings highlight the polygenic basis of acceptance behaviour and the role of gene clustering and chromosomal rearrangements in promoting coupling among barrier loci. We identified 60 chemosensory genes within regions connected to acceptance, 24 of which were divergent among pea aphid races in previous genome scan or gene expression analyses. Evidence linking these genes to acceptance phenotypes supports their role in determining host plant specificity and as barrier loci contributing to pea aphid speciation

The evolution of strong reproductive isolation between sympatric intertidal snails

The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'

The past and future of experimental speciation

Speciation is the result of evolutionary processes that generate barriers to gene flow between populations, facilitating reproductive isolation. Speciation is typically studied via theoretical models and “snap-shot” tests in natural populations. Experimental speciation enables real-time direct tests of speciation theory and has been long-touted as a critical complement to other approaches. We argue that, despite its promise to elucidate the evolution of reproductive isolation, experimental speciation has been underutilised and lags behind other contributions to speciation research. We review recent experiments and outline a framework for how experimental speciation can be implemented to address current outstanding questions that are otherwise challenging to answer. Greater uptake of this approach is necessary to rapidly advance understanding of speciation

Cryptic diversity in the genus Adineta Hudson & Gosse, 1886 (Rotifera: Bdelloidea: Adinetidae): a DNA taxonomy approach

12th International Rotifer Symposium (ROTIFERA) -- AUG 16-21, 2009 -- Humboldt Univ, Berlin, GERMANYWOS: 000284960500005Cryptic species are continuously discovered in rotifers using different methods to delineate these units of diversity. DNA taxonomy is the most effective method taxonomists have to untie potential cryptic taxa. Here, we estimate hidden diversity in a genus of bdelloid rotifers, Adineta. We analyse cryptic diversity using a coalescent approach to infer evolutionarily significant units from a phylogenetic tree obtained from cytochrome oxidase I sequences. Cryptic diversity was measured for eight traditional species and from several additional undetermined populations. Taxonomic inflation of up to 36 taxa was found in A. vaga from DNA taxonomy. As observed in other microscopic organisms, cryptic taxa within each traditional species were not geographically isolated, but had significantly narrower ecological niches than expected by chance alone.Leibniz Inst Freshwater Ecol & Inland Fisheries (IGB)Natural Environment Research Council [NE/G013179/1

Klf4 reverts developmentally programmed restriction of ground state pluripotency

Mouse embryonic stem (ES) cells derived from pluripotent early epiblast contribute functionally differentiated progeny to all foetal lineages of chimaeras. By contrast, epistem cell (EpiSC) lines from post-implantation epithelialised epiblast are unable to colonise the embryo even though they express the core pluripotency genes Oct4, Sox2 and Nanog. We examined interconversion between these two cell types. ES cells can readily become EpiSCs in response to growth factor cues. By contrast, EpiSCs do not change into ES cells. We exploited PiggyBac transposition to introduce a single reprogramming factor, Klf4, into EpiSCs. No effect was apparent in EpiSC culture conditions, but in ground state ES cell conditions a fraction of cells formed undifferentiated colonies. These EpiSC-derived induced pluripotent stem (Epi-iPS) cells activated expression of ES cell-specific transcripts including endogenous Klf4, and downregulated markers of lineage specification. X chromosome silencing in female cells, a feature of the EpiSC state, was erased in Epi-iPS cells. They produced high-contribution chimaeras that yielded germline transmission. These properties were maintained after Cre-mediated deletion of the Klf4 transgene, formally demonstrating complete and stable reprogramming of developmental phenotype. Thus, re-expression of Klf4 in an appropriate environment can regenerate the naïve ground state from EpiSCs. Reprogramming is dependent on suppression of extrinsic growth factor stimuli and proceeds to completion in less than 1% of cells. This substantiates the argument that EpiSCs are developmentally, epigenetically and functionally differentiated from ES cells. However, because a single transgene is the minimum requirement to attain the ground state, EpiSCs offer an attractive opportunity for screening for unknown components of the reprogramming process