Publications

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
correction for traverse and ochman, conserved rates and patterns of transcription errors across bacterial growth states and lifestyles.		2016	27402746
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
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
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
entometabolomics: applications of modern analytical techniques to insect studies.	metabolomic analyses can reveal associations between an organism's metabolome and further aspects of its phenotypic state, an attractive prospect for many life-sciences researchers. the metabolomic approach has been employed in some, but not many, insect study systems, starting in 1990 with the evaluation of the metabolic effects of parasitism on moth larvae. metabolomics has now been applied to a variety of aspects of insect biology, including behaviour, infection, temperature stress responses, ...	2015	27478203
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
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
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
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
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
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
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
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
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
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
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
symbiosis studies in microbial ecology.		2016	27682576
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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