Publications

inside out: archaeal ectosymbionts suggest a second model of reduced-genome evolution.	reduced-genome symbionts and their organelle counterparts, which have even smaller genomes, are essential to the lives of many organisms. but how and why have these genomes become so small? endosymbiotic genome reduction is a product of isolation within the host, followed by massive pseudogenization and gene loss often including dna repair mechanisms. this phenomenon can be observed in insect endosymbionts such as the bacteria carsonella ruddii and buchnera aphidicola. yet endosymbionts are not ...	2017	28326078
symbiont diversity of aphis (toxoptera) citricidus (hemiptera: aphididae) as influenced by host plants.	aphids are well known for their association with endosymbiont bacteria. almost all aphids harbor buchnera aphidicola as an obligate symbiont and several other bacteria as facultative symbionts. associations of facultative symbionts and aphids are quite variable in terms of diversity and prevalence across aphid species. facultative symbionts can have a major impact on aphid bioecological traits. a number of factors shape the outcome of the facultative symbiont-aphid association, including aphid c ...	2017	27872949
drift barriers to quality control when genes are expressed at different levels.	gene expression is imperfect, sometimes leading to toxic products. solutions take two forms: globally reducing error rates, or ensuring that the consequences of erroneous expression are relatively harmless. the latter is optimal, but because it must evolve independently at so many loci, it is subject to a stringent "drift barrier"-a limit to how weak the effects of a deleterious mutation s can be, while still being effectively purged by selection, expressed in terms of the population size n of a ...	2017	27838629
buchnera has changed flatmate but the repeated replacement of co-obligate symbionts is not associated with the ecological expansions of their aphid hosts.	symbiotic associations with bacteria have facilitated important evolutionary transitions in insects and resulted in long-term obligate interactions. recent evidence suggests that these associations are not always evolutionarily stable and that symbiont replacement, and/or supplementation of an obligate symbiosis by an additional bacterium, has occurred during the history of many insect groups. yet, the factors favouring one symbiont over another in this evolutionary dynamic are not well understo ...	2016	27862540
host plant determines the population size of an obligate symbiont (buchnera aphidicola) in aphids.	buchnera aphidicolais an obligate endosymbiont that provides aphids with several essential nutrients. though much is known about aphid-buchnera interactions, the effect of the host plant on buchnera population size remains unclear. here we used quantitative pcr (qpcr) techniques to explore the effects of the host plant on buchnera densities in the cotton-melon aphid, aphis gossypii buchneratiters were significantly higher in populations that had been reared on cucumber for over 10 years than in ...	2016	26850304
holes in the hologenome: why host-microbe symbioses are not holobionts.	the advent of relatively inexpensive tools for characterizing microbial communities has led to an explosion of research exploring the diversity, ecology, and evolution of microbe-host systems. some now question whether existing conceptual frameworks are adequate to explain microbe-host systems. one popular paradigm is the "holobiont-hologenome," which argues that a host and its microbiome evolve as a single cooperative unit of selection (i.e., a superorganism). we argue that the hologenome is ba ...	2016	27034285
comparison of fitness traits and their plasticity on multiple plants for sitobion avenae infected and cured of a secondary endosymbiont.	regiella insecticola has been found to enhance the performance of host aphids on certain plants, but its functional role in adaptation of host aphids to plants is still controversial. here we evaluate the impacts of r. insecticola infections on vital life-history traits of sitobion avenae (fabricius), and their underlying genetic variation and phenotypic plasticity on three plants. it was shown that effects of r. insecticola on s. avenae's fitness (i.e., developmental time and fecundity) were ne ...	2016	26979151
recapitulating phylogenies using k-mers: from trees to networks.	ernst haeckel based his landmark tree of life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. much of this idea has since been discredited. today, phylogenies are often based on molecular sequences. a typical phylogenetic inference aims to capture and represent, in the form of a tree, the evolutionary history of a family of molecular s ...	2016	28105314
gene family expansions in aphids maintained by endosymbiotic and nonsymbiotic traits.	facilitating the evolution of new gene functions, gene duplication is a major mechanism driving evolutionary innovation. gene family expansions relevant to host/symbiont interactions are increasingly being discovered in eukaryotes that host endosymbiotic microbes. such discoveries entice speculation that gene duplication facilitates the evolution of novel, endosymbiotic relationships. here, using a comparative transcriptomic approach combined with differential gene expression analysis, we invest ...	2016	26878871
bacterial communities of the cotton aphid aphis gossypii associated with bt cotton in northern china.	aphids are infected with a wide variety of endosymbionts that can confer ecologically relevant traits. however, the bacterial communities of most aphid species are still poorly characterized. this study investigated the bacterial diversity of the cotton aphid aphis gossypii associated with bt cotton in northern china by targeting the v4 region of the 16s rdna using the illumina miseq platform. our sequencing data revealed that bacterial communities of a. gossypii were generally dominated by the ...	2016	27079679
direct flow cytometry measurements reveal a fine-tuning of symbiotic cell dynamics according to the host developmental needs in aphid symbiosis.	endosymbiotic associations constitute a driving force in the ecological and evolutionary diversification of metazoan organisms. little is known about whether and how symbiotic cells are coordinated according to host physiology. here, we use the nutritional symbiosis between the insect pest, acyrthosiphon pisum, and its obligate symbiont, buchnera aphidicola, as a model system. we have developed a novel approach for unculturable bacteria, based on flow cytometry, and used this method to estimate ...	2016	26822159
the role of mobile genetic elements in evolutionary longevity of heritable endobacteria.	the movement of mobile genetic elements (mges), including bacteriophages, insertion sequence (is) elements, and integrative and conjugative elements (ices) can have profound effects on bacterial evolution by introducing novel genes, or disrupting the existing ones. obligate endobacteria are a distinctive group of bacteria that reside within the intracellular compartments of their eukaryotic hosts. many obligate endobacteria are reproductively dependent on their hosts. vertical transmission, in a ...	2016	27066304
metabolic complementation in bacterial communities: necessary conditions and optimality.	bacterial communities may display metabolic complementation, in which different members of the association partially contribute to the same biosynthetic pathway. in this way, the end product of the pathway is synthesized by the community as a whole. however, the emergence and the benefits of such complementation are poorly understood. herein, we present a simple model to analyze the metabolic interactions among bacteria, including the host in the case of endosymbiotic bacteria. the model conside ...	2016	27774085
the role of mobile genetic elements in evolutionary longevity of heritable endobacteria.	the movement of mobile genetic elements (mges), including bacteriophages, insertion sequence (is) elements, and integrative and conjugative elements (ices) can have profound effects on bacterial evolution by introducing novel genes, or disrupting the existing ones. obligate endobacteria are a distinctive group of bacteria that reside within the intracellular compartments of their eukaryotic hosts. many obligate endobacteria are reproductively dependent on their hosts. vertical transmission, in a ...	2016	27066304
disruption of phenylalanine hydroxylase reduces adult lifespan and fecundity, and impairs embryonic development in parthenogenetic pea aphids.	phenylalanine hydroxylase (pah) is a key tyrosine-biosynthetic enzyme involved in neurological and melanin-associated physiological processes. despite extensive investigations in holometabolous insects, a pah contribution to insect embryonic development has never been demonstrated. here, we have characterized, for the first time, the pah gene in a hemimetabolous insect, the aphid acyrthosiphon pisum. phylogenetic and sequence analyses confirmed that appah is closely related to metazoan pah, exhi ...	2016	27694983
symbionts modify interactions between insects and natural enemies in the field.	eukaryotes commonly host communities of heritable symbiotic bacteria, many of which are not essential for their hosts' survival and reproduction. there is laboratory evidence that these facultative symbionts can provide useful adaptations, such as increased resistance to natural enemies. however, we do not know how symbionts affect host fitness when the latter are subject to attack by a natural suite of parasites and pathogens. here, we test whether two protective symbionts, regiella insecticola ...	2016	27561159
vat, an amazing gene conferring resistance to aphids and viruses they carry: from molecular structure to field effects.	we review half a century of research on cucumis melo resistance to aphis gossypii from molecular to field levels. the vat gene is unique in conferring resistance to both a. gossypii and the viruses it transmits. this double phenotype is aphid clone-dependent and has been observed in 25 melon accessions, mostly from asia. it is controlled by a cluster of genes including cc-nlr, which has been characterized in detail. copy-number polymorphisms (for the whole gene and for a domain that stands out i ...	2016	27725823
bacteriome-localized intracellular symbionts in pollen-feeding beetles of the genus dasytes (coleoptera, dasytidae).	several insect taxa are associated with intracellular symbionts that provision limiting nutrients to their hosts. such tightly integrated symbioses are especially common in insects feeding on nutritionally challenging diets like phloem sap or vertebrate blood, but also occur in seed-eating and omnivorous taxa. here, we characterize an intracellular symbiosis in pollen-feeding beetles of the genus dasytes (coleoptera, dasytidae). high-throughput tag-encoded 16s amplicon pyrosequencing of adult d. ...	2016	27713733
genome sequence of candidatus arsenophonus lipopteni, the exclusive symbiont of a blood sucking fly lipoptena cervi (diptera: hippoboscidae).	candidatus arsenophonus lipopteni (enterobacteriaceae, gammaproteobacteria) is an obligate intracellular symbiont of the blood feeding deer ked, lipoptena cervi (diptera: hippoboscidae). the bacteria reside in specialized cells derived from host gut epithelia (bacteriocytes) forming a compact symbiotic organ (bacteriome). compared to the closely related complex symbiotic system in the sheep ked, involving four bacterial species, lipoptena cervi appears to maintain its symbiosis exclusively with ...	2016	27660670
genome evolution in the obligate but environmentally active luminous symbionts of flashlight fish.	the luminous bacterial symbionts of anomalopid flashlight fish are thought to be obligately dependent on their hosts for growth and share several aspects of genome evolution with unrelated obligate symbionts, including genome reduction. however, in contrast to most obligate bacteria, anomalopid symbionts have an active environmental phase that may be important for symbiont transmission. here we investigated patterns of evolution between anomalopid symbionts compared with patterns in free-living ...	2016	27389687
seasonal changes in the endosymbiotic consortia of aphids from the genus cinara.	buchnera aphidicola is the primary endosymbiont of aphids with which it maintains an obligate mutualistic symbiotic relationship. insects also maintain facultative symbiotic relationships with secondary symbionts, and serratia symbiotica is the most common in aphids. the presence of both symbionts in aphids of the subfamily lachninae has been widely studied by our group. we examined two closely related aphids, cinara tujafilina and c. cedri in the present study. even though both b. aphidicola st ...	2016	27297891
reinventing the wheel and making it round again: evolutionary convergence in buchnera-serratia symbiotic consortia between the distantly related lachninae aphids tuberolachnus salignus and cinara cedri.	virtually all aphids (aphididae) harbor buchnera aphidicola as an obligate endosymbiont to compensate nutritional deficiencies arising from their phloem diet. many species within the lachninae subfamily seem to be consistently associated also with serratia symbiotica we have previously shown that both cinara (cinara) cedri and cinara (cupressobium) tujafilina (lachninae: eulachnini tribe) have indeed established co-obligate associations with both buchnera and s. symbiotica however, while buchner ...	2016	27190007
nitrogen hurdle of host alternation for a polyphagous aphid and the associated changes of endosymbionts.	low proportion of essential amino acids (eaas) is one of the barriers for animals to use phloem as a diet. endosymbionts with eaas synthesis functions are considered crucial for ameliorating the lack of eaas in insects' diets. in this study, we transferred the insects from a cabbage-reared myzus persicae population onto 3 new plant species including eggplant, tobacco and spinach. the performance on these plants was evaluated and the dynamics of endosymbionts in relation to this host alternation ...	2016	27094934
biology, pest status, microbiome and control of kudzu bug (hemiptera: heteroptera: plataspidae): a new invasive pest in the u.s.	soybean is an important food crop, and insect integrated pest management (ipm) is critical to the sustainability of this production system. in recent years, the introduction into the united states of the kudzu bug currently identified as megacopta cribraria (f.), poses a threat to soybean production. the kudzu bug was first discovered in the state of georgia, u.s. in 2009 and since then has spread to most of the southeastern states. because it was not found in the north american subcontinent bef ...	2016	27649166
draft genome sequence of the bactrocera oleae symbiont "candidatus erwinia dacicola".	"candidatus erwinia dacicola" is a gammaproteobacterium that forms a symbiotic association with the agricultural pest bactrocera oleae here, we present a 2.1-mb draft hybrid genome assembly for "ca. erwinia dacicola" generated from single-cell and metagenomic data.	2016	27634990
essential functions linked with structural disorder in organisms of minimal genome.	intrinsically disordered regions (idrs) of proteins fulfill important regulatory roles in most organisms. however, the proteins of certain endosymbiont and intracellular pathogenic bacteria with extremely reduced genomes contain disproportionately small amounts of idrs, consisting almost entirely of folded domains. as their genomes co-evolving with their hosts have been reduced in unrelated lineages, the proteomes of these bacteria represent independently evolved minimal protein sets. we systema ...	2016	27608806
cellular and molecular remodelling of a host cell for vertical transmission of bacterial symbionts.	various insects require intracellular bacteria that are restricted to specialized cells (bacteriocytes) and are transmitted vertically via the female ovary, but the transmission mechanisms are obscure. we hypothesized that, in the whitefly bemisia tabaci, where intact bacteriocytes (and not isolated bacteria) are transferred to oocytes, the transmission mechanism would be evident as cellular and molecular differences between the nymph (pre-adult) and adult bacteriocytes. we demonstrate dramatic ...	2016	27358364
defying muller's ratchet: ancient heritable endobacteria escape extinction through retention of recombination and genome plasticity.	heritable endobacteria, which are transmitted from one host generation to the next, are subjected to evolutionary forces that are different from those experienced by free-living bacteria. in particular, they suffer consequences of muller's ratchet, a mechanism that leads to extinction of small asexual populations due to fixation of slightly deleterious mutations combined with the random loss of the most-fit genotypes, which cannot be recreated without recombination. mycoplasma-related endobacter ...	2016	27329757
snapshots of a shrinking partner: genome reduction in serratia symbiotica.	genome reduction is pervasive among maternally-inherited endosymbiotic organisms, from bacteriocyte- to gut-associated ones. this genome erosion is a step-wise process in which once free-living organisms evolve to become obligate associates, thereby losing non-essential or redundant genes/functions. serratia symbiotica (gammaproteobacteria), a secondary endosymbiont present in many aphids (hemiptera: aphididae), displays various characteristics that make it a good model organism for studying gen ...	2016	27599759
insect symbionts in food webs.	recent research has shown that the bacterial endosymbionts of insects are abundant and diverse, and that they have numerous different effects on their hosts' biology. here we explore how insect endosymbionts might affect the structure and dynamics of insect communities. using the obligate and facultative symbionts of aphids as an example, we find that there are multiple ways that symbiont presence might affect food web structure. many symbionts are now known to help their hosts escape or resist ...	2016	27481779
symbiosis studies in microbial ecology.		2016	27682576
convergent evolution of trna gene targeting preferences in compact genomes.	in gene-dense genomes, mobile elements are confronted with highly selective pressure to amplify without causing excessive damage to the host. the targeting of trna genes as potentially safe integration sites has been developed by retrotransposons in various organisms such as the social amoeba dictyostelium discoideum and the yeast saccharomyces cerevisiae. in d. discoideum, trna gene-targeting retrotransposons have expanded to approximately 3 % of the genome. recently obtained genome sequences o ...	2016	27583033
small rna regulators of plant-hemipteran interactions: micromanagers with versatile roles.	non-coding small rnas (srnas) in plants have important roles in regulating biological processes, including development, reproduction, and stress responses. recent research indicates significant roles for srna-mediated gene silencing during plant-hemipteran interactions that involve all three of these biological processes. plant responses to hemipteran feeding are determined by changes in the host transcriptome that appear to be fine-tuned by srnas. the role of srna in plant defense responses is ...	2016	27625654
novel insights into insect-microbe interactions-role of epigenomics and small rnas.	it has become increasingly clear that microbes form close associations with the vast majority of animal species, especially insects. in fact, an array of diverse microbes is known to form shared metabolic pathways with their insect hosts. a growing area of research in insect-microbe interactions, notably for hemipteran insects and their mutualistic symbionts, is to elucidate the regulation of this inter-domain metabolism. this review examines two new emerging mechanisms of gene regulation and th ...	2016	27540386
heat sensitivity of wmel wolbachia during aedes aegypti development.	the wmel strain of wolbachia bacteria is known to prevent dengue and zika virus transmission in the mosquito vector aedes aegypti. accordingly, the release of wmel-infected a. aegypti in endemic regions has been recommended by the world health organization as a potential strategy for controlling dengue and zika outbreaks. however, the utility of this approach could be limited if high temperatures in the aquatic habitats where a. aegypti develop are detrimental to wolbachia. we exposed wmel-infec ...	2016	27459519
ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use.	genetic decoding is not 'frozen' as was earlier thought, but dynamic. one facet of this is frameshifting that often results in synthesis of a c-terminal region encoded by a new frame. ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational 'correction' of problem or 'savior' indels. utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. one class of re ...	2016	27436286
bacterial cell biology outside the streetlight.	as much as vertical transmission of microbial symbionts requires their deep integration into the host reproductive and developmental biology, symbiotic lifestyle might profoundly affect bacterial growth and proliferation. this review describes the reproductive oddities displayed by bacteria associated - more or less intimately - with multicellular eukaryotes.	2016	27306428
correction for traverse and ochman, conserved rates and patterns of transcription errors across bacterial growth states and lifestyles.		2016	27402746
comparative analysis of rnai-based methods to down-regulate expression of two genes expressed at different levels in myzus persicae.	with the increasing availability of aphid genomic data, it is necessary to develop robust functional validation methods to evaluate the role of specific aphid genes. this work represents the first study in which five different techniques, all based on rna interference and on oral acquisition of double-stranded rna (dsrna), were developed to silence two genes, aly and eph, potentially involved in polerovirus transmission by aphids. efficient silencing of only eph transcripts, which are less abund ...	2016	27869783
aphis glycines virus 2, a novel insect virus with a unique genome structure.	the invasive soybean aphid, aphis glycines, is a major pest in soybeans, resulting in substantial economic loss. we analyzed the a. glycines transcriptome to identify sequences derived from viruses of a. glycines. we identified sequences derived from a novel virus named aphis glycines virus 2 (apglv2). the assembled virus genome sequence was confirmed by reverse transcription polymerase chain reaction (rt-pcr) and sanger sequencing, conserved domains were characterized, and distribution, and tra ...	2016	27869772
when obligate partners melt down.	insect hosts derive benefits from their obligate symbionts, including nutrient supplementation and the ability to colonize otherwise inhospitable niches. but long-term symbionts sometimes also limit the ecological range of their hosts; in particular, they are often more temperature sensitive than the hosts themselves. even small increases in average temperature, comparable to those occurring under current conditions of climate change, can kill symbionts and, with them, their hosts. in some cases ...	2016	27935842
small genome of the fungus escovopsis weberi, a specialized disease agent of ant agriculture.	many microorganisms with specialized lifestyles have reduced genomes. this is best understood in beneficial bacterial symbioses, where partner fidelity facilitates loss of genes necessary for living independently. specialized microbial pathogens may also exhibit gene loss relative to generalists. here, we demonstrate that escovopsis weberi, a fungal parasite of the crops of fungus-growing ants, has a reduced genome in terms of both size and gene content relative to closely related but less speci ...	2016	26976598
de novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms.	grapevine phylloxera, an insect related to true aphids, is a major historic pest of viticulture only controlled through the selection of resistant rootstocks or through quarantine regulations where grapevine is cultivated own-rooted. transcriptomic data could help understand the bases of its original life-traits, including a striking case of polyphenism, with forms feeding on roots and forms feeding in leaf-galls. comparisons with true aphids (for which complete genomes have been sequenced) shou ...	2016	26968158
transcriptional errors and the drift barrier.		2016	26966235
conserved rates and patterns of transcription errors across bacterial growth states and lifestyles.	errors that occur during transcription have received much less attention than the mutations that occur in dna because transcription errors are not heritable and usually result in a very limited number of altered proteins. however, transcription error rates are typically several orders of magnitude higher than the mutation rate. also, individual transcripts can be translated multiple times, so a single error can have substantial effects on the pool of proteins. transcription errors can also contr ...	2016	26884158
heat stress affects facultative symbiont-mediated protection from a parasitoid wasp.	many insects carry facultative bacterial symbionts, which provide benefits including resistance to natural enemies and abiotic stresses. little is known about how these beneficial phenotypes are affected when biotic or abiotic threats occur simultaneously. the pea aphid (acyrthosiphon pisum) can host several well-characterized symbiont species. the symbiont known as x-type can protect against both parasitoid wasps and heat stress. here, we used three pea aphid genotypes that were naturally infec ...	2016	27875577
amino acid transporters implicated in endocytosis of buchnera during symbiont transmission in the pea aphid.	many insects host their obligate, maternally transmitted symbiotic bacteria in specialized cells called bacteriocytes. one of the best-studied insect nutritional endosymbioses is that of the aphid and its endosymbiont, buchnera aphidicola. aphids and buchnera are metabolically and developmentally integrated, but the molecular mechanisms underlying buchnera transmission and coordination with aphid development remain largely unknown. previous work using electron microscopy to study aphid asexual e ...	2016	27895889
loss of conserved noncoding rnas in genomes of bacterial endosymbionts.	the genomes of intracellular symbiotic or pathogenic bacteria, such as of buchnera, mycoplasma, and rickettsia, are typically smaller compared with their free-living counterparts. here we showed that noncoding rna (ncrna) families, which are conserved in free-living bacteria, frequently could not be detected by computational methods in the small genomes. statistical tests demonstrated that their absence is not an artifact of low gc content or small deletions in these small genomes, and thus it w ...	2016	26782934
stress-induced changes in abundance differ among obligate and facultative endosymbionts of the soybean aphid.	bacterial endosymbionts can drive evolutionary novelty by conferring adaptive benefits under adverse environmental conditions. among aphid species there is growing evidence that symbionts influence tolerance to various forms of stress. however, the extent to which stress inflicted on the aphid host has cascading effects on symbiont community dynamics remains poorly understood. here we simultaneously quantified the effect of host-plant induced and xenobiotic stress on soybean aphid (aphis glycine ...	2016	26865969
transcription factors exhibit differential conservation in bacteria with reduced genomes.	the description of transcriptional regulatory networks has been pivotal in the understanding of operating principles under which organisms respond and adapt to varying conditions. while the study of the topology and dynamics of these networks has been the subject of considerable work, the investigation of the evolution of their topology, as a result of the adaptation of organisms to different environmental conditions, has received little attention. in this work, we study the evolution of transcr ...	2016	26766575
ontogenetic differences in localization of glutamine transporter apglnt1 in the pea aphid demonstrate that mechanisms of host/symbiont integration are not similar in the maternal versus embryonic bacteriome.	obligate intracellular symbionts of insects are metabolically and developmentally integrated with their hosts. typically, reproduction fails in many insect nutritional endosymbioses when host insects are cured of their bacterial symbionts, and yet remarkably little is known about the processes that developmentally integrate host and symbiont. here in the best studied insect obligate intracellular symbiosis, that of the pea aphid, acyrthosiphon pisum, with the gammaproteobacterium buchnera aphidi ...	2016	26759710
intraspecific genetic variation in hosts affects regulation of obligate heritable symbionts.	symbiotic relationships promote biological diversification by unlocking new ecological niches. over evolutionary time, hosts and symbionts often enter intimate and permanent relationships, which must be maintained and regulated for both lineages to persist. many insect species harbor obligate, heritable symbiotic bacteria that provision essential nutrients and enable hosts to exploit niches that would otherwise be unavailable. hosts must regulate symbiont population sizes, but optimal regulation ...	2016	27799532
probing behavior of aposymbiotic green peach aphid (myzus persicae) on susceptible solanum tuberosum and resistant solanum stoloniferum plants.	the green peach aphid, myzus persicae sulzer (hemiptera: aphididae) is one of the potato important pests; it is the most efficient vector of potato viruses. myzus persicae harbors the endosymbiotic bacteria buchnera aphidicola which supplements their diet. there is increasing evidence that b. aphidicola is involved in plant-aphid interactions and we previously demonstrated that b. aphidicola disruption (aposymbiosis) affected the probing behavior of m. persicae on radish plants, delaying host pl ...	2016	27334419
the genetic diversity of smls (sitobion miscanthi l type symbiont) and its effect on the fitness, mitochondrial dna diversity and buchnera aphidicola dynamic of wheat aphid, sitobion miscanthi (hemiptera: aphididae).	smls (sitobion miscanthi l type symbiont) is a recently discovered aphid secondary symbiont. using evidence extracted from 16s rrna sequences, previous studies indicate that smls is the most widely distributed and most recently transferred secondary symbiont in chinese sitobion miscanthi populations. here, we further investigated genetic diversity among smls geographic strains with multiloci data. furthermore, the influence of smls on s. miscanthi was uncovered with ecological and evolutionary e ...	2016	27122251
assessment of a 16s rrna amplicon illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus.	the bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. the filtering out of contaminants from the results and the accurate taxonomic assignment of sequences are therefore crucial in arthropod microbiom ...	2016	26458227
prefiltering model for homology detection algorithms on gpu.	homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. however, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. thus, their acceleration is essential. the aim of this article was to prefilter a sequence database. to make this work, we have im ...	2016	28008220
modulation of legume defense signaling pathways by native and non-native pea aphid clones.	the pea aphid (acyrthosiphon pisum) is a complex of at least 15 genetically different host races that are native to specific legume plants, but can all develop on the universal host plant vicia faba. despite much research, it is still unclear why pea aphid host races (biotypes) are able to colonize their native hosts while other host races are not. all aphids penetrate the plant and salivate into plant cells when they test plant suitability. thus plants might react differently to the various pea ...	2016	28018405
functional evaluation of proteins in watery and gel saliva of aphids.	gel and watery saliva are regarded as key players in aphid-piant interactions. the salivary composition seems to be influenced by the variable environment encountered by the stylet tip. milieu sensing has been postulated to provide information needed for proper stylet navigation and for the required switches between gel and watery saliva secretion during stylet progress. both the chemical and physical factors involved in sensing of the stylet's environment are discussed. to investigate the saliv ...	2016	28018380
association between gut microbiota and diapause preparation in the cabbage beetle: a new perspective for studying insect diapause.	gut microbiota mediate the nutritional metabolism and play important roles in human obesity. diapausing insects accumulate large fat reserves and develop obese phenotypes in order to survive unfavorable conditions. however, the possibility of an association between gut microbiota and insect diapause has not been investigated. we used the illumina miseq platform to compare gut bacterial community composition in nondiapause- (i.e. reproductive) and diapause-destined female cabbage beetles, colaphe ...	2016	27934967
initiator trna genes template the 3' cca end at high frequencies in bacteria.	while the cca sequence at the mature 3' end of trnas is conserved and critical for translational function, a genetic template for this sequence is not always contained in trna genes. in eukaryotes and archaea, the cca ends of trnas are synthesized post-transcriptionally by cca-adding enzymes. in bacteria, trna genes template cca sporadically.	2016	27927177
annotation of the asian citrus psyllid genome reveals a reduced innate immune system.	citrus production worldwide is currently facing significant losses due to citrus greening disease, also known as huanglongbing. the citrus greening bacteria, candidatus liberibacter asiaticus (clas), is a persistent propagative pathogen transmitted by the asian citrus psyllid, diaphorina citri kuwayama (hemiptera: liviidae). hemipterans characterized to date lack a number of insect immune genes, including those associated with the imd pathway targeting gram-negative bacteria. the d. citri draft ...	2016	27965582
protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.	a functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. we investigated the use of protein domain architectures ...	2016	27703668
dcia is an ancestral replicative helicase operator essential for bacterial replication initiation.	delivery of the replicative helicase onto dna is an essential step in the initiation of replication. in bacteria, dnac (in escherichia coli) and dnai (in bacillus subtilis) are representative of the two known mechanisms that assist the replicative helicase at this stage. here, we establish that these two strategies cannot be regarded as prototypical of the bacterial domain since dnac and dnai (dna[ci]) are present in only a few bacterial phyla. we show that dna[ci] was domesticated at least seve ...	2016	27830752
circular helix-like curve: an effective tool of biological sequence analysis and comparison.	this paper constructed a novel injection from a dna sequence to a 3d graph, named circular helix-like curve (chc). the presented graphical representation is available for visualizing characterizations of a single dna sequence and identifying similarities and differences among several dnas. a 12-dimensional vector extracted from chc, as a numerical characterization of chc, was applied to analyze phylogenetic relationships of 11 species, 74 ribosomal rnas, 48 hepatitis e viruses, and 18 eutherian ...	2016	27403205
challenges with using names to link digital biodiversity information.		2016	27346955
origin and evolution of rickettsial plasmids.	rickettsia species are strictly intracellular bacteria that have undergone a reductive genomic evolution. despite their allopatric lifestyle, almost half of the 26 currently validated rickettsia species have plasmids. in order to study the origin, evolutionary history and putative roles of rickettsial plasmids, we investigated the evolutionary processes that have shaped 20 plasmids belonging to 11 species, using comparative genomics and phylogenetic analysis between rickettsial, microbial and no ...	2016	26866478
bacterial antisense rnas are mainly the product of transcriptional noise.	cis-encoded antisense rnas (asrnas) are widespread along bacterial transcriptomes. however, the role of most of these rnas remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. we show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asrnas is exponentially dependent on the genomic at content and that expression of asrna at low levels exerts little impact in terms of energy c ...	2016	26973873
winding paths to simplicity: genome evolution in facultative insect symbionts.	symbiosis between organisms is an important driving force in evolution. among the diverse relationships described, extensive progress has been made in insect-bacteria symbiosis, which improved our understanding of the genome evolution in host-associated bacteria. particularly, investigations on several obligate mutualists have pushed the limits of what we know about the minimal genomes for sustaining cellular life. to bridge the gap between those obligate symbionts with extremely reduced genomes ...	2016	27519426
the bacterial pangenome as a new tool for analysing pathogenic bacteria.	the bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. in this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. we have also shown that the pangenome may be used as a new tool ...	2015	26442149
recent functional insights into the role of (p)ppgpp in bacterial physiology.	the alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppgpp) are involved in regulating growth and several different stress responses in bacteria. in recent years, substantial progress has been made in our understanding of the molecular mechanisms of (p)ppgpp metabolism and (p)ppgpp-mediated regulation. in this review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the rela/spot homologue (rsh) ...	2015	25853779
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
identification and analysis of the bacterial endosymbiont specialized for production of the chemotherapeutic natural product et-743.	ecteinascidin 743 (et-743, yondelis) is a clinically approved chemotherapeutic natural product isolated from the caribbean mangrove tunicate ecteinascidia turbinata. researchers have long suspected that a microorganism may be the true producer of the anticancer drug, but its genome has remained elusive due to our inability to culture the bacterium in the laboratory using standard techniques. here, we sequenced and assembled the complete genome of the et-743 producer, candidatus endoecteinascidia ...	2015	26013440
draft genomes, phylogenetic reconstruction, and comparative genomics of two novel cohabiting bacterial symbionts isolated from frankliniella occidentalis.	obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. here we take a comparative genomics approach to investigate two prominent bacterial symbionts (bfo1 and bfo2) isolated from geographically separated populations of western flower thrips, frankli ...	2015	26185096
transcriptional slippage and rna editing increase the diversity of transcripts in chloroplasts: insight from deep sequencing of vigna radiata genome and transcriptome.	we performed deep sequencing of the nuclear and organellar genomes of three mungbean genotypes: vigna radiata ssp. sublobata tc1966, v. radiata var. radiata nm92 and the recombinant inbred line ril59 derived from a cross between tc1966 and nm92. moreover, we performed deep sequencing of the ril59 transcriptome to investigate transcript variability. the mungbean chloroplast genome has a quadripartite structure including a pair of inverted repeats separated by two single copy regions. a total of 2 ...	2015	26076132
scrambled and not-so-tiny genomes of fungal endosymbionts.		2015	26056315
the genome of diuraphis noxia, a global aphid pest of small grains.	the russian wheat aphid, diuraphis noxia kurdjumov, is one of the most important pests of small grains throughout the temperate regions of the world. this phytotoxic aphid causes severe systemic damage symptoms in wheat, barley, and other small grains as a direct result of the salivary proteins it injects into the plant while feeding.	2015	26044338
infection of host plants by cucumber mosaic virus increases the susceptibility of myzus persicae aphids to the parasitoid aphidius colemani.	plant viruses can profoundly alter the phenotypes of their host plants, with potentially far-reaching implications for ecology. yet few studies have explored the indirect, host-mediated, effects of plant viruses on non-vector insects. we examined how infection of cucurbita pepo plants by cucumber mosaic virus (cmv) impacted the susceptibility of aphids (myzus persicae) to attack by the parasitoid wasp aphidius colemani. in semi-natural foraging assays, we observed higher rates of aphid parasitis ...	2015	26043237
signatures of host/symbiont genome coevolution in insect nutritional endosymbioses.	the role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. here, we identify three coevolutionary signatures that characterize holobiont genomes. the first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. metabolic collaboration has evolved nu ...	2015	26039986
whole genome sequence of the soybean aphid endosymbiont buchnera aphidicola and genetic differentiation among biotype-specific strains.	endosymbiosis with microorganisms is common in insects, with more than 10% of species requiring the metabolic capabilities of intracellular bacteria for their nutrient acquisition. aphids harbor an obligate mutualism with the vertically transferred endosymbiont, buchnera aphidicola, which produces key nutrients lacking in the aphid's phloem-based diet that are necessary for normal development and reproduction. it is thought that, in some groups of insects, bacterial symbionts may play key roles ...	2015	26516375
the importance of spatial heterogeneity and self-restraint on mutualism stability - a quantitative review.	understanding the factors that enable mutualisms to evolve and to subsequently remain stable over time, is essential to fully understand patterns of global biodiversity and for evidence based conservation policy. theoretically, spatial heterogeneity of mutualists, through increased likelihood of fidelity between cooperative partners in structured populations, and 'self-restraint' of symbionts, due to selection against high levels of virulence leading to short-term host overexploitation, will res ...	2015	26434680
avoidance and potential remedy solutions of chimeras in reconstructing the phylogeny of aphids using the 16s rrna gene of buchnera: a case in lachninae (hemiptera).	it is known that pcr amplification of highly homologous genes from complex dna mixtures can generate a significant proportion of chimeric sequences. the 16s rrna gene is not only widely used in estimating the species diversity of endosymbionts in aphids but also used to explore the co-diversification of aphids and their endosymbionts. thus, chimeric sequences may lead to the discovery of non-existent endosymbiont species and mislead buchnera-based phylogenetic analysis that lead to false conclus ...	2015	26307984
following the footsteps of chlamydial gene regulation.	regulation of gene expression ensures an organism responds to stimuli and undergoes proper development. although the regulatory networks in bacteria have been investigated in model microorganisms, nearly nothing is known about the evolution and plasticity of these networks in obligate, intracellular bacteria. the phylum chlamydiae contains a vast array of host-associated microbes, including several human pathogens. the chlamydiae are unique among obligate, intracellular bacteria as they undergo ...	2015	26424812
yoc, a new strategy for pairwise alignment of collinear genomes.	comparing and aligning genomes is a key step in analyzing closely related genomes. despite the development of many genome aligners in the last 15 years, the problem is not yet fully resolved, even when aligning closely related bacterial genomes of the same species. in addition, no procedures are available to assess the quality of genome alignments or to compare genome aligners.	2015	25885358
infection dynamic of symbiotic bacteria in the pea aphid acyrthosiphon pisum gut and host immune response at the early steps in the infection process.	in addition to its obligatory symbiont buchnera aphidicola, the pea aphid acyrthosiphon pisum can harbor several facultative bacterial symbionts which can be mutualistic in the context of various ecological interactions. belonging to a genus where many members have been described as pathogen in invertebrates, serratia symbiotica is one of the most common facultative partners found in aphids. the recent discovery of strains able to grow outside their host allowed us to simulate environmental acqu ...	2015	25811863
bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16s ribosomal dna.	associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. the pea aphid, acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont buchnera aphidicola and several facultative symbionts. while obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protecti ...	2015	25807173
a facultative endosymbiont in aphids can provide diverse ecological benefits.	ecologically important traits of insects are often affected by facultative bacterial endosymbionts. this is best studied in the pea aphid acyrthosiphon pisum, which is frequently infected by one or more of eight facultative symbiont species. many of these symbiont species have been shown to provide one ecological benefit, but we have little understanding of the range of effects that a single strain can have. here, we describe the phenotypes conferred by three strains of the recently discovered b ...	2015	26206380
bacterial small rnas in the genus rickettsia.	rickettsia species are obligate intracellular gram-negative pathogenic bacteria and the etiologic agents of diseases such as rocky mountain spotted fever (rmsf), mediterranean spotted fever, epidemic typhus, and murine typhus. genome sequencing revealed that r. prowazekii has ~25 % non-coding dna, the majority of which is thought to be either "junk dna" or pseudogenes resulting from genomic reduction. these characteristics also define other rickettsia genomes. bacterial small rnas, whose biogene ...	2015	26679185
a metagenomic approach from aphid's hemolymph sheds light on the potential roles of co-existing endosymbionts.	aphids are known to live in symbiosis with specific bacteria, called endosymbionts which can be classified as obligate or accessory. buchnera aphidicola is generally the only obligatory symbiont present in aphids, supplying essential nutrients that are missing in the plants phloem to its host. pentalonia nigronervosa is the main vector of the banana bunchy top virus, one of the most damageable viruses in banana. this aphid is carrying two symbionts: b. aphidicola (bpn) and wolbachia sp. (wpn). t ...	2015	26667400
supergroup c wolbachia, mutualist symbionts of filarial nematodes, have a distinct genome structure.	wolbachia pipientis is possibly the most widespread endosymbiont of arthropods and nematodes. while all wolbachia strains have historically been defined as a single species, 16 monophyletic clusters of diversity (called supergroups) have been described. different supergroups have distinct host ranges and symbiotic relationships, ranging from mutualism to reproductive manipulation. in filarial nematodes, which include parasites responsible for major diseases of humans (such as onchocerca volvulus ...	2015	26631376
microbial communities can be described by metabolic structure: a general framework and application to a seasonally variable, depth-stratified microbial community from the coastal west antarctic peninsula.	taxonomic marker gene studies, such as the 16s rrna gene, have been used to successfully explore microbial diversity in a variety of marine, terrestrial, and host environments. for some of these environments long term sampling programs are beginning to build a historical record of microbial community structure. although these 16s rrna gene datasets do not intrinsically provide information on microbial metabolism or ecosystem function, this information can be developed by identifying metabolisms ...	2015	26285202
mutualism breakdown by amplification of wolbachia genes.	most insect species are associated with vertically transmitted endosymbionts. because of the mode of transmission, the fitness of these symbionts is dependent on the fitness of the hosts. therefore, these endosymbionts need to control their proliferation in order to minimize their cost for the host. the genetic bases and mechanisms of this regulation remain largely undetermined. the maternally inherited bacteria of the genus wolbachia are the most common endosymbionts of insects, providing some ...	2015	25668031
interchangeable allies: exploiting development and selection to swap symbionts.		2015	25675514
effects of the diet on the microbiota of the red palm weevil (coleoptera: dryophthoridae).	rhynchophorus ferrugineus, also known as the red palm weevil, is regarded as the major pest of palm trees. although studies of the microbiota associated with this species have been performed in recent years, little attention has been dedicated to the influence of the diet in shaping the host bacterial community. here, we investigated the influence of food sources (i.e. palm tissues vs apple based substrate) on the microbial diversity associated with rpw, which was compared with the microbiota as ...	2015	25635833
inside the pan-genome - methods and software overview.	the number of genomes that have been deposited in databases has increased exponentially after the advent of next-generation sequencing (ngs), which produces high-throughput sequence data; this circumstance has demanded the development of new bioinformatics software and the creation of new areas, such as comparative genomics. in comparative genomics, the genetic content of an organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences, ...	2015	27006628
evidence for specificity in symbiont-conferred protection against parasitoids.	many insects harbour facultative symbiotic bacteria, some of which have been shown to provide resistance against natural enemies. one of the best-known protective symbionts is hamiltonella defensa, which in pea aphid (acyrthosiphon pisum) confers resistance against attack by parasitoid wasps in the genus aphidius (braconidae).we asked (i) whether this symbiont also confers protection against a phylogenetically distant group of parasitoids (aphelinidae) and (ii) whether there are consistent diffe ...	2015	26136451
conservation and role of electrostatics in thymidylate synthase.	conservation of function across families of orthologous enzymes is generally accompanied by conservation of their active site electrostatic potentials. to study the electrostatic conservation in the highly conserved essential enzyme, thymidylate synthase (ts), we conducted a systematic species-based comparison of the electrostatic potential in the vicinity of its active site. whereas the electrostatics of the active site of ts are generally well conserved, the tss from minimal organisms do not c ...	2015	26612036
social niche construction and evolutionary transitions in individuality.	social evolution theory conventionally takes an externalist explanatory stance, treating observed cooperation as explanandum and the positive assortment of cooperative behaviour as explanans. we ask how the circumstances bringing about this positive assortment arose in the first place. rather than merely push the explanatory problem back a step, we move from an externalist to an interactionist explanatory stance, in the spirit of lewontin and the niche construction theorists. we develop a theory ...	2015	26709324
social niche construction and evolutionary transitions in individuality.	social evolution theory conventionally takes an externalist explanatory stance, treating observed cooperation as explanandum and the positive assortment of cooperative behaviour as explanans. we ask how the circumstances bringing about this positive assortment arose in the first place. rather than merely push the explanatory problem back a step, we move from an externalist to an interactionist explanatory stance, in the spirit of lewontin and the niche construction theorists. we develop a theory ...	2015	26709324
phylogenetic relationships of the symbiotic bacteria in the aphid sitobion avenae (hemiptera: aphididae).	aphids have developed symbiotic associations with different bacterial species, and some morphological and molecular analyses have provided evidence of the host relationship between the primary symbiotic bacteria (buchnera aphidicola) and the aphid while the contrary with the secondary symbiotic bacteria. in this study, we investigated the phylogenetic relationships of the bacterial endosymbionts in the aphid sitobion avenae (f.). we characterized all bacterial endosymbionts in 10 genetically def ...	2015	26314016