Publications by authors named "Jean Peccoud"

79 Publications

Occurrence data for the two cryptic species of (Hemiptera: Psylloidea).

Biodivers Data J 2021 1;9:e68860. Epub 2021 Jul 1.

ANSES-Laboratoire de la Santé des Végétaux, Montpellier, France ANSES-Laboratoire de la Santé des Végétaux Montpellier France.

Background: is a psyllid that has been known since 1998 as the vector of the bacterium ' Phytoplasma prunorum', responsible for the European stone fruit yellows (ESFY), a disease that affects species of . This disease is one of the major limiting factors for the production of stone fruits, most notably apricot () and Japanese plum (), in all EU stone fruit-growing areas. The psyllid vector is widespread in the Western Palearctic and evidence for the presence of the phytoplasma that it transmits to species of has been found in 15 of the 27 EU countries.Recent studies showed that is actually composed of two cryptic species that can be differentiated by molecular markers. A literature review on the distribution of was published in 2012, but it only provided presence or absence information at the country level and without distinction between the two cryptic species.Since 2012, numerous new records of the vector in several European countries have been published. We ourselves have acquired a large amount of data from sampling in France and other European countries. We have also carried out a thorough systematic literature review to find additional records, including all the original sources mentioning (or its synonyms) since the first description by Scopoli in 1763. Our aim was to create an exhaustive georeferenced occurrence catalogue, in particular in countries that are occasionally mentioned in literature with little detail. Finally, for countries that seem suitable for the proliferation of (USA, Canada, Japan, China etc.), we dug deeper into literature and reliable sources (e.g. published checklists) to better substantiate its current absence from those regions.Information on the distribution ranges of these vector psyllids is of crucial interest in order to best predict the vulnerability of stone fruit producing countries to the ESFY threat in the foreseeable future.

New Information: We give free access to a unique file of 1975 records of all occurrence data in our possession concerning , that we have gathered through more than twenty years of sampling efforts in Europe or through intensive text mining.We have made every effort to retrieve the source information for the records extracted from literature (1201 records). Thus, we always give the title of the original reference, together with the page(s) citing and, if possible, the year of sampling. To make the results of this survey publicly available, we give a URL to access the literature sources. In most cases, this link allows free downloads of a PDF file.We also give access to information extracted from GBIF (162 exploitable data points on 245 occurrences found in the database), which we thoroughly checked and often supplemented to make the information more easily exploitable.We give access to our own unpublished georeferenced and genotyped records from 612 samples taken over the last 20 years in several European countries (Switzerland, Belgium, Netherlands, Spain etc.). These include two countries (Portugal and North Macedonia), for which the presence of had not been reported before. As our specimens have been genotyped (74 sites with species A solely, 202 with species B solely and 310 with species A+B), our new data enable a better overview of the geographical distribution of the two cryptic species at the Palaearctic scale.
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http://dx.doi.org/10.3897/BDJ.9.e68860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8266796PMC
July 2021

Monitoring Insect Transposable Elements in Large Double-Stranded DNA Viruses Reveals Host-to-Virus and Virus-to-Virus Transposition.

Mol Biol Evol 2021 Aug;38(9):3512-3530

CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France.

The mechanisms by which transposable elements (TEs) can be horizontally transferred between animals are unknown, but viruses are possible candidate vectors. Here, we surveyed the presence of host-derived TEs in viral genomes in 35 deep sequencing data sets produced from 11 host-virus systems, encompassing nine arthropod host species (five lepidopterans, two dipterans, and two crustaceans) and six different double-stranded (ds) DNA viruses (four baculoviruses and two iridoviruses). We found evidence of viral-borne TEs in 14 data sets, with frequencies of viral genomes carrying a TE ranging from 0.01% to 26.33% for baculoviruses and from 0.45% to 7.36% for iridoviruses. The analysis of viral populations separated by a single replication cycle revealed that viral-borne TEs originating from an initial host species can be retrieved after viral replication in another host species, sometimes at higher frequencies. Furthermore, we detected a strong increase in the number of integrations in a viral population for a TE absent from the hosts' genomes, indicating that this TE has undergone intense transposition within the viral population. Finally, we provide evidence that many TEs found integrated in viral genomes (15/41) have been horizontally transferred in insects. Altogether, our results indicate that multiple large dsDNA viruses have the capacity to shuttle TEs in insects and they underline the potential of viruses to act as vectors of horizontal transfer of TEs. Furthermore, the finding that TEs can transpose between viral genomes of a viral species sets viruses as possible new niches in which TEs can persist and evolve.
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http://dx.doi.org/10.1093/molbev/msab198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8383894PMC
August 2021

Characterization of a Sex-Determining Region and Its Genomic Context via Statistical Estimates of Haplotype Frequencies in Daughters and Sons Sequenced in Pools.

Genome Biol Evol 2021 Aug;13(8)

Laboratoire Écologie et Biologie des Interactions, Équipe Écologie Évolution Symbiose, UMR CNRS 7267, Université de Poitiers, France.

Sex chromosomes are generally derived from a pair of autosomes that have acquired a locus controlling sex. Sex chromosomes may evolve reduced recombination around this locus and undergo a long process of molecular divergence. At that point, the original loci controlling sex may be difficult to pinpoint. This difficulty has affected many model species from mammals to birds to flies, which present highly diverged sex chromosomes. Identifying sex-controlling loci is easier in species with molecularly similar sex chromosomes. Here we aimed at pinpointing the sex-determining region (SDR) of Armadillidium vulgare, a terrestrial isopod with female heterogamety (ZW females and ZZ males) and whose sex chromosomes appear to show low genetic divergence. To locate the SDR, we assessed single-nucleotide polymorphism (SNP) allele frequencies in F1 daughters and sons sequenced in pools (pool-seq) in several families. We developed a Bayesian method that uses the SNP genotypes of individually sequenced parents and pool-seq data from F1 siblings to estimate the genetic distance between a given genomic region (contig) and the SDR. This allowed us to assign more than 43 Mb of contigs to sex chromosomes, and to demonstrate extensive recombination and very low divergence between these chromosomes. By taking advantage of multiple F1 families, we delineated a very short genomic region (∼65 kb) that presented no evidence of recombination with the SDR. In this short genomic region, the comparison of sequencing depths between sexes highlighted female-specific genes that have undergone recent duplication, and which may be involved in sex determination in A. vulgare.
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http://dx.doi.org/10.1093/gbe/evab121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8350356PMC
August 2021

Transposable Elements and the Evolution of Insects.

Annu Rev Entomol 2021 01 15;66:355-372. Epub 2020 Sep 15.

Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86073 Poitiers CEDEX 9, France.

Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between closely related species. The influence of insect traits on TE landscapes, however, remains unclear. Recent findings indicate that, in addition to being involved in insect adaptations and aging, TEs are seemingly at the cornerstone of insect antiviral immunity. Thus, TEs are emerging as essential insect symbionts that may have deleterious or beneficial consequences on their hosts, depending on context.
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http://dx.doi.org/10.1146/annurev-ento-070720-074650DOI Listing
January 2021

Securing the Exchange of Synthetic Genetic Constructs Using Digital Signatures.

ACS Synth Biol 2020 10 21;9(10):2656-2664. Epub 2020 Sep 21.

Colorado State University, Chemical and Biological Engineering, 1370 Campus Delivery, Fort Collins, Colorado 80523, United States.

The field of synthetic biology relies on an ever-growing supply chain of synthetic genetic material. Technologies to secure the exchange of this material are still in their infancy. Solutions proposed thus far have focused on watermarks, a dated security approach that can be used to claim authorship, but is subject to counterfeit, and does not provide any information about the integrity of the genetic material itself. In this manuscript, we describe how data encryption and digital signature algorithms can be used to ensure the integrity and authenticity of synthetic genetic constructs. Using a pilot software that generates digital signatures and other encrypted data for plasmids, we demonstrate that we can predictably extract information about the author, the identity, the integrity of plasmid sequences, and even annotations from sequencing data alone without a reference sequence, all without compromising the function of the plasmids. Encoding a digital signature into a DNA molecule provides an avenue for genetic designers to claim authorship of DNA molecules. This technology could help compliance with material transfer agreements and other licensing agreements.
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http://dx.doi.org/10.1021/acssynbio.0c00401DOI Listing
October 2020

Rapid, robust plasmid verification by de novo assembly of short sequencing reads.

Nucleic Acids Res 2020 10;48(18):e106

Department of Chemical & Biological Engineering, Colorado State University, USA.

Plasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and-depending on the application-security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.
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http://dx.doi.org/10.1093/nar/gkaa727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544192PMC
October 2020

A stochastic model for error correction of kinetochore-microtubule attachments in budding yeast.

PLoS One 2020 6;15(8):e0236293. Epub 2020 Aug 6.

Department of Biological Sciences, Virginia Polytechnic Institute & State University, Blacksburg, VA, United States of America.

To divide replicated chromosomes equally between daughter cells, kinetochores must attach to microtubules emanating from opposite poles of the mitotic spindle (biorientation). An error correction mechanism facilitates this process by destabilizing erroneous kinetochore-microtubule attachments. Here we present a stochastic model of kinetochore-microtubule attachments, via an essential protein Ndc80 in budding yeast, Saccharomyces cerevisiae. Using the model, we calculate the stochastic dynamics of a pair of sister kinetochores as they transition among different attachment states. First of all, we determine the kinase-to-phosphatase balance point that maximizes the probability of biorientation, while starting from an erroneous attachment state. We find that the balance point is sensitive to the rates of microtubule-Ndc80 dissociation and derive an approximate analytical formula that defines the balance point. Secondly, we determine the probability of transition from low-tension amphitelic to monotelic attachment and find that, despite this probability being approximately 33%, biorientation can be achieved with high probability. Thirdly, we calculate the contribution of the geometrical orientation of sister kinetochores to the probability of biorientation and show that, in the absence of geometrical orientation, the biorientation error rate is much larger than that observed in experiments. Finally, we study the coupling of the error correction mechanism to the spindle assembly checkpoint by calculating the average binding of checkpoint-related proteins to the kinetochore during the error correction process.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0236293PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7410253PMC
October 2020

Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants.

NPJ Syst Biol Appl 2020 05 6;6(1):11. Epub 2020 May 6.

Colorado State University, Chemical and Biological Engineering, Fort Collins, CO, USA.

Over the last 30 years, computational biologists have developed increasingly realistic mathematical models of the regulatory networks controlling the division of eukaryotic cells. These models capture data resulting from two complementary experimental approaches: low-throughput experiments aimed at extensively characterizing the functions of small numbers of genes, and large-scale genetic interaction screens that provide a systems-level perspective on the cell division process. The former is insufficient to capture the interconnectivity of the genetic control network, while the latter is fraught with irreproducibility issues. Here, we describe a hybrid approach in which the 630 genetic interactions between 36 cell-cycle genes are quantitatively estimated by high-throughput phenotyping with an unprecedented number of biological replicates. Using this approach, we identify a subset of high-confidence genetic interactions, which we use to refine a previously published mathematical model of the cell cycle. We also present a quantitative dataset of the growth rate of these mutants under six different media conditions in order to inform future cell cycle models.
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http://dx.doi.org/10.1038/s41540-020-0134-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203125PMC
May 2020

Challenges and opportunities for strain verification by whole-genome sequencing.

Sci Rep 2020 04 3;10(1):5873. Epub 2020 Apr 3.

Colorado State University, Colorado, USA.

Laboratory strains, cell lines, and other genetic materials change hands frequently in the life sciences. Despite evidence that such materials are subject to mix-ups, contamination, and accumulation of secondary mutations, verification of strains and samples is not an established part of many experimental workflows. With the plummeting cost of next generation technologies, it is conceivable that whole genome sequencing (WGS) could be applied to routine strain and sample verification in the future. To demonstrate the need for strain validation by WGS, we sequenced haploid yeast segregants derived from a popular commercial mutant collection and identified several unexpected mutations. We determined that available bioinformatics tools may be ill-suited for verification and highlight the importance of finishing reference genomes for commonly used laboratory strains.
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http://dx.doi.org/10.1038/s41598-020-62364-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125075PMC
April 2020

A hybrid stochastic model of the budding yeast cell cycle.

NPJ Syst Biol Appl 2020 03 27;6(1). Epub 2020 Mar 27.

Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.

The growth and division of eukaryotic cells are regulated by complex, multi-scale networks. In this process, the mechanism of controlling cell-cycle progression has to be robust against inherent noise in the system. In this paper, a hybrid stochastic model is developed to study the effects of noise on the control mechanism of the budding yeast cell cycle. The modeling approach leverages, in a single multi-scale model, the advantages of two regimes: (1) the computational efficiency of a deterministic approach, and (2) the accuracy of stochastic simulations. Our results show that this hybrid stochastic model achieves high computational efficiency while generating simulation results that match very well with published experimental measurements.
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http://dx.doi.org/10.1038/s41540-020-0126-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101447PMC
March 2020

Multi-scale spatial genetic structure of the vector-borne pathogen 'Candidatus Phytoplasma prunorum' in orchards and in wild habitats.

Sci Rep 2020 03 19;10(1):5002. Epub 2020 Mar 19.

BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France.

Inferring the dispersal processes of vector-borne plant pathogens is a great challenge because the plausible epidemiological scenarios often involve complex spread patterns at multiple scales. The spatial genetic structure of 'Candidatus Phytoplasma prunorum', responsible for European stone fruit yellows disease, was investigated by the application of a combination of statistical approaches to genotype data of the pathogen sampled from cultivated and wild compartments in three French Prunus-growing regions. This work revealed that the prevalence of the different genotypes is highly uneven both between regions and compartments. In addition, we identified a significant clustering of similar genotypes within a radius of 50 km or less, but not between nearby wild and cultivated Prunus. We also provide evidence that infected plants are transferred between production areas, and that both species of the Cacopsylla pruni complex can spread the pathogen. Altogether, this work supports a main epidemiological scenario where 'Ca. P. prunorum' is endemic in - and generally acquired from - wild Prunus by its immature psyllid vectors. The latter then migrate to shelter plants that epidemiologically connect sites less than 50 km apart by later providing infectious mature psyllids to their "migration basins". Such multi-scale studies could be useful for other pathosystems.
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http://dx.doi.org/10.1038/s41598-020-61908-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081303PMC
March 2020

Horizontal transfer and evolution of transposable elements in vertebrates.

Nat Commun 2020 03 13;11(1):1362. Epub 2020 Mar 13.

Laboratoire Evolution, Génomes, Comportement, Écologie, UMR 9191 CNRS, UMR 247 IRD, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.

Horizontal transfer of transposable elements (HTT) is an important process shaping eukaryote genomes, yet very few studies have quantified this phenomenon on a large scale or have evaluated the selective constraints acting on transposable elements (TEs) during vertical and horizontal transmission. Here we screen 307 vertebrate genomes and infer a minimum of 975 independent HTT events between lineages that diverged more than 120 million years ago. HTT distribution greatly differs from null expectations, with 93.7% of these transfers involving ray-finned fishes and less than 3% involving mammals and birds. HTT incurs purifying selection (conserved protein evolution) on all TEs, confirming that producing functional transposition proteins is required for a TE to invade new genomes. In the absence of HTT, DNA transposons appear to evolve neutrally within genomes, unlike most retrotransposons, which evolve under purifying selection. This selection regime indicates that proteins of most retrotransposon families tend to process their own encoding RNA (cis-preference), which helps retrotransposons to persist within host lineages over long time periods.
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http://dx.doi.org/10.1038/s41467-020-15149-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7070016PMC
March 2020

Sex chromosomes control vertical transmission of feminizing Wolbachia symbionts in an isopod.

PLoS Biol 2019 10 10;17(10):e3000438. Epub 2019 Oct 10.

Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, Poitiers, France.

Microbial endosymbiosis is widespread in animals, with major ecological and evolutionary implications. Successful symbiosis relies on efficient vertical transmission through host generations. However, when symbionts negatively affect host fitness, hosts are expected to evolve suppression of symbiont effects or transmission. Here, we show that sex chromosomes control vertical transmission of feminizing Wolbachia endosymbionts in the isopod Armadillidium nasatum. Theory predicts that the invasion of an XY/XX species by cytoplasmic sex ratio distorters is unlikely because it leads to fixation of the unusual (and often lethal or infertile) YY genotype. We demonstrate that A. nasatum X and Y sex chromosomes are genetically highly similar and that YY individuals are viable and fertile, thereby enabling Wolbachia spread in this XY-XX species. Nevertheless, we show that Wolbachia cannot drive fixation of YY individuals, because infected YY females do not transmit Wolbachia to their offspring, unlike XX and XY females. The genetic basis fits the model of a Y-linked recessive allele (associated with an X-linked dominant allele), in which the homozygous state suppresses Wolbachia transmission. Moreover, production of all-male progenies by infected YY females restores a balanced sex ratio at the host population level. This suggests that blocking of Wolbachia transmission by YY females may have evolved to suppress feminization, thereby offering a whole new perspective on the evolutionary interplay between microbial symbionts and host sex chromosomes.
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http://dx.doi.org/10.1371/journal.pbio.3000438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6805007PMC
October 2019

Hands-On Introduction to Synthetic Biology for Security Professionals.

Trends Biotechnol 2019 11 15;37(11):1143-1146. Epub 2019 Jul 15.

Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA; GenoFAB Inc., Fort Collins, CO, USA. Electronic address:

The rapid pace of life sciences innovations and a growing list of nontraditional actors engaging in biological research make it challenging to develop appropriate policies to protect sensitive infrastructures. To address this challenge, we developed a five-day awareness program for security professionals, including laboratory work, site visits, and lectures.
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http://dx.doi.org/10.1016/j.tibtech.2019.06.005DOI Listing
November 2019

Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot.

PLoS Genet 2019 02 1;15(2):e1007965. Epub 2019 Feb 1.

Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France.

More than any other genome components, Transposable Elements (TEs) have the capacity to move across species barriers through Horizontal Transfer (HT), with substantial evolutionary consequences. Previous large-scale surveys, based on full-genomes comparisons, have revealed the transposition mode as an important predictor of HT rates variation across TE superfamilies. However, host biology could represent another major explanatory factor, one that needs to be investigated through extensive taxonomic sampling. Here we test this hypothesis using a field collection of 460 arthropod species from Tahiti and surrounding islands. Through targeted massive parallel sequencing, we uncover patterns of HT in three widely-distributed TE superfamilies with contrasted modes of transposition. In line with earlier findings, the DNA transposons under study (TC1-Mariner) were found to transfer horizontally at the highest frequency, closely followed by the LTR superfamily (Copia), in contrast with the non-LTR superfamily (Jockey), that mostly diversifies through vertical inheritance and persists longer within genomes. Strikingly, across all superfamilies, we observe a marked excess of HTs in Lepidoptera, an insect order that also commonly hosts baculoviruses, known for their ability to transport host TEs. These results turn the spotlight on baculoviruses as major potential vectors of TEs in arthropods, and further emphasize the importance of non-vertical TE inheritance in genome evolution.
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http://dx.doi.org/10.1371/journal.pgen.1007965DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373975PMC
February 2019

The Genome of Armadillidium vulgare (Crustacea, Isopoda) Provides Insights into Sex Chromosome Evolution in the Context of Cytoplasmic Sex Determination.

Mol Biol Evol 2019 04;36(4):727-741

Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Poitiers, France.

The terrestrial isopod Armadillidium vulgare is an original model to study the evolution of sex determination and symbiosis in animals. Its sex can be determined by ZW sex chromosomes, or by feminizing Wolbachia bacterial endosymbionts. Here, we report the sequence and analysis of the ZW female genome of A. vulgare. A distinguishing feature of the 1.72 gigabase assembly is the abundance of repeats (68% of the genome). We show that the Z and W sex chromosomes are essentially undifferentiated at the molecular level and the W-specific region is extremely small (at most several hundreds of kilobases). Our results suggest that recombination suppression has not spread very far from the sex-determining locus, if at all. This is consistent with A. vulgare possessing evolutionarily young sex chromosomes. We characterized multiple Wolbachia nuclear inserts in the A. vulgare genome, none of which is associated with the W-specific region. We also identified several candidate genes that may be involved in the sex determination or sexual differentiation pathways. The A. vulgare genome serves as a resource for studying the biology and evolution of crustaceans, one of the most speciose and emblematic metazoan groups.
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http://dx.doi.org/10.1093/molbev/msz010DOI Listing
April 2019

Yeast genetic interaction screens in the age of CRISPR/Cas.

Curr Genet 2019 Apr 25;65(2):307-327. Epub 2018 Sep 25.

Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA.

The ease of performing both forward and reverse genetics in Saccharomyces cerevisiae, along with its stable haploid state and short generation times, has made this budding yeast the consummate model eukaryote for genetics. The major advantage of using budding yeast for reverse genetics is this organism's highly efficient homology-directed repair, allowing for precise genome editing simply by introducing DNA with homology to the chromosomal target. Although plasmid- and PCR-based genome editing tools are quite efficient, they depend on rare spontaneous DNA breaks near the target sequence. Consequently, they can generate only one genomic edit at a time, and the edit must be associated with a selectable marker. However, CRISPR/Cas technology is efficient enough to permit markerless and multiplexed edits in a single step. These features have made CRISPR/Cas popular for yeast strain engineering in synthetic biology and metabolic engineering applications, but it has not been widely employed for genetic screens. In this review, we critically examine different methods to generate multi-mutant strains in systematic genetic interaction screens and discuss the potential of CRISPR/Cas to supplement or improve on these methods.
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http://dx.doi.org/10.1007/s00294-018-0887-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420903PMC
April 2019

The Open Insulin Project: A Case Study for 'Biohacked' Medicines.

Trends Biotechnol 2018 12 13;36(12):1211-1218. Epub 2018 Sep 13.

Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA. Electronic address:

New innovation ecosystems are emerging that challenge the complex intellectual property and regulatory landscape surrounding drug development in the United States (US). A prime example is an initiative known as the Open Insulin Project. The goal of the project is to sidestep patents and enable generic manufacturers to produce cheaper insulin. However, the US regulatory environment, not patent exclusivity, is the main barrier to insulin affordability. If the Open Insulin Project succeeds in releasing an open protocol for insulin manufacturing, follow-on work could enable a number of new insulin production ecosystems, including 'home-brewed' insulin. Regulators will need to consider how to proceed in a future where commercial pharmaceuticals remain unaffordable, but patients are empowered to produce drugs for their personal use.
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http://dx.doi.org/10.1016/j.tibtech.2018.07.009DOI Listing
December 2018

A framework for estimating the effects of sequential reproductive barriers: Implementation using Bayesian models with field data from cryptic species.

Evolution 2018 11 27;72(11):2503-2512. Epub 2018 Sep 27.

BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France.

Determining how reproductive barriers modulate gene flow between populations represents a major step toward understanding the factors shaping the course of speciation. Although many indices quantifying reproductive isolation (RI) have been proposed, they do not permit the quantification of cross-direction-specific RI under varying species frequencies and over arbitrary sequences of barriers. Furthermore, techniques quantifying associated uncertainties are lacking, and statistical methods unrelated to biological process are still preferred for obtaining confidence intervals and P-values. To address these shortcomings, we provide new RI indices that model changes in gene flow for both directions of hybridization, and we implement them in a Bayesian model. We use this model to quantify RI between two species of the psyllid Cacopsylla pruni based on field genotypic data for mating individuals, inseminated spermatophores and progeny. The results showed that preinsemination isolation was strong, mildly asymmetric, and indistinguishably different between study sites despite large differences in species frequencies; that postinsemination isolation strongly affected the more common hybrid type; and that cumulative isolation was close to complete. In the light of these results, we discuss how these developments can strengthen comparative RI studies.
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http://dx.doi.org/10.1111/evo.13595DOI Listing
November 2018

Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races.

Mol Ecol 2018 Jul 16. Epub 2018 Jul 16.

INRA, UMR 1349 IGEPP, Le Rheu, France.

Identifying the genomic bases of adaptation to novel environments is a long-term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant-specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model-based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population-specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host-plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host-plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.
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http://dx.doi.org/10.1111/mec.14799DOI Listing
July 2018

Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants.

Genome Biol Evol 2018 06;10(6):1554-1572

INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France.

Effector proteins play crucial roles in plant-parasite interactions by suppressing plant defenses and hijacking plant physiological responses to facilitate parasite invasion and propagation. Although effector proteins have been characterized in many microbial plant pathogens, their nature and role in adaptation to host plants are largely unknown in insect herbivores. Aphids rely on salivary effector proteins injected into the host plants to promote phloem sap uptake. Therefore, gaining insight into the repertoire and evolution of aphid effectors is key to unveiling the mechanisms responsible for aphid virulence and host plant specialization. With this aim in mind, we assembled catalogues of putative effectors in the legume specialist aphid, Acyrthosiphon pisum, using transcriptomics and proteomics approaches. We identified 3,603 candidate effector genes predicted to be expressed in A. pisum salivary glands (SGs), and 740 of which displayed up-regulated expression in SGs in comparison to the alimentary tract. A search for orthologs in 17 arthropod genomes revealed that SG-up-regulated effector candidates of A. pisum are enriched in aphid-specific genes and tend to evolve faster compared with the whole gene set. We also found that a large fraction of proteins detected in the A. pisum saliva belonged to three gene families, of which certain members show evidence consistent with positive selection. Overall, this comprehensive analysis suggests that the large repertoire of effector candidates in A. pisum constitutes a source of novelties promoting plant adaptation to legumes.
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http://dx.doi.org/10.1093/gbe/evy097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6012102PMC
June 2018

Rapid evolution of aphid pests in agricultural environments.

Curr Opin Insect Sci 2018 04 8;26:17-24. Epub 2018 Jan 8.

Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions (EBI-Joint Research Unit 7267, CNRS), 86000 Poitiers, France.

Aphids constitute a major group of crop pests that inflict serious damages to plants, both directly by ingesting phloem and indirectly as vectors of numerous diseases. In response to intense and repeated human-induced pressures, such as insecticide treatments, the use of resistant plants and biological agents, aphids have developed a series of evolutionary responses relying on adaptation and phenotypic plasticity. In this review, we highlight some remarkable evolutionary responses to anthropogenic pressures in agroecosystems and discuss the mechanisms underlying the ecological and evolutionary success of aphids. We outline the peculiar mode of reproduction, the polyphenism for biologically important traits and the diverse and flexible associations with microbial symbionts as key determinants of adaptive potential and pest status of aphids.
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http://dx.doi.org/10.1016/j.cois.2017.12.009DOI Listing
April 2018

Cyberbiosecurity: An Emerging New Discipline to Help Safeguard the Bioeconomy.

Front Bioeng Biotechnol 2018 5;6:39. Epub 2018 Apr 5.

Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States.

Cyberbiosecurity is being proposed as a formal new enterprise which encompasses cybersecurity, cyber-physical security and biosecurity as applied to biological and biomedical-based systems. In recent years, an array of important meetings and public discussions, commentaries and publications have occurred that highlight numerous vulnerabilities. While necessary first steps, they do not provide a systematized structure for effectively promoting communication, education and training, elucidation and prioritization for analysis, research, development, test and evaluation and implementation of scientific, technological, standards of practice, policy, or even regulatory or legal considerations for protecting the bioeconomy. Further, experts in biosecurity and cybersecurity are generally not aware of each other's domains, expertise, perspectives, priorities, or where mutually supported opportunities exist for which positive outcomes could result. Creating, promoting and advancing a new discipline can assist with formal, beneficial and continuing engagements. Recent key activities and publications that inform the creation of Cyberbiosecurity are briefly reviewed, as is the expansion of Cyberbiosecurity to include biomanufacturing which is supported by a rigorous analysis of a biomanufacturing facility. Recommendations are provided to initialize Cyberbiosecurity and place it on a trajectory to establish a structured and sustainable discipline, forum and enterprise.
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http://dx.doi.org/10.3389/fbioe.2018.00039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895716PMC
April 2018

A Survey of Virus Recombination Uncovers Canonical Features of Artificial Chimeras Generated During Deep Sequencing Library Preparation.

G3 (Bethesda) 2018 03 28;8(4):1129-1138. Epub 2018 Mar 28.

Laboratoire Evolution, Génomes, Comportement, Écologie, UMR 9191 CNRS, UMR 247 IRD, Université Paris-Sud, 91198 Gif-sur-Yvette, France

Chimeric reads can be generated by recombination during the preparation of high-throughput sequencing libraries. Our attempt to detect biological recombination between the genomes of dengue virus (DENV; +ssRNA genome) and its mosquito host using the Illumina Nextera sequencing library preparation kit revealed that most, if not all, detected host-virus chimeras were artificial. Indeed, these chimeras were not more frequent than with control RNA from another species (a pillbug), which was never in contact with DENV RNA prior to the library preparation. The proportion of chimera types merely reflected those of the three species among sequencing reads. Chimeras were frequently characterized by the presence of 1-20 bp microhomology between recombining fragments. Within-species chimeras mostly involved fragments in opposite orientations and located less than 100 bp from each other in the parental genome. We found similar features in published datasets using two other viruses: Ebola virus (EBOV; -ssRNA genome) and a herpesvirus (dsDNA genome), both produced with the Illumina Nextera protocol. These canonical features suggest that artificial chimeras are generated by intra-molecular template switching of the DNA polymerase during the PCR step of the Nextera protocol. Finally, a published Illumina dataset using the Flock House virus (FHV; +ssRNA genome) generated with a protocol preventing artificial recombination revealed the presence of 1-10 bp microhomology motifs in FHV-FHV chimeras, but very few recombining fragments were in opposite orientations. Our analysis uncovered sequence features characterizing recombination breakpoints in short-read sequencing datasets, which can be helpful to evaluate the presence and extent of artificial recombination.
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http://dx.doi.org/10.1534/g3.117.300468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5873904PMC
March 2018

CrossPlan: systematic planning of genetic crosses to validate mathematical models.

Bioinformatics 2018 07;34(13):2237-2244

Department of Computer Science, Virginia Tech, Blacksburg, USA.

Motivation: Mathematical models of cellular processes can systematically predict the phenotypes of novel combinations of multi-gene mutations. Searching for informative predictions and prioritizing them for experimental validation is challenging since the number of possible combinations grows exponentially in the number of mutations. Moreover, keeping track of the crosses needed to make new mutants and planning sequences of experiments is unmanageable when the experimenter is deluged by hundreds of potentially informative predictions to test.

Results: We present CrossPlan, a novel methodology for systematically planning genetic crosses to make a set of target mutants from a set of source mutants. We base our approach on a generic experimental workflow used in performing genetic crosses in budding yeast. We prove that the CrossPlan problem is NP-complete. We develop an integer-linear-program (ILP) to maximize the number of target mutants that we can make under certain experimental constraints. We apply our method to a comprehensive mathematical model of the protein regulatory network controlling cell division in budding yeast. We also extend our solution to incorporate other experimental conditions such as a delay factor that decides the availability of a mutant and genetic markers to confirm gene deletions. The experimental flow that underlies our work is quite generic and our ILP-based algorithm is easy to modify. Hence, our framework should be relevant in plant and animal systems as well.

Availability And Implementation: CrossPlan code is freely available under GNU General Public Licence v3.0 at https://github.com/Murali-group/crossplan.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022539PMC
July 2018

Disentangling the Causes for Faster-X Evolution in Aphids.

Genome Biol Evol 2018 02;10(2):507-520

BIOEPAR, INRA, ONIRIS, La Chantrerie, Nantes, France.

The faster evolution of X chromosomes has been documented in several species, and results from the increased efficiency of selection on recessive alleles in hemizygous males and/or from increased drift due to the smaller effective population size of X chromosomes. Aphids are excellent models for evaluating the importance of selection in faster-X evolution because their peculiar life cycle and unusual inheritance of sex chromosomes should generally lead to equivalent effective population sizes for X and autosomes. Because we lack a high-density genetic map for the pea aphid, whose complete genome has been sequenced, we first assigned its entire genome to the X or autosomes based on ratios of sequencing depth in males (X0) to females (XX). Then, we computed nonsynonymous to synonymous substitutions ratios (dN/dS) for the pea aphid gene set and found faster evolution of X-linked genes. Our analyses of substitution rates, together with polymorphism and expression data, showed that relaxed selection is likely to be the greatest contributor to faster-X because a large fraction of X-linked genes are expressed at low rates and thus escape selection. Yet, a minor role for positive selection is also suggested by the difference between substitution rates for X and autosomes for male-biased genes (but not for asexual female-biased genes) and by lower Tajima's D for X-linked compared with autosomal genes with highly male-biased expression patterns. This study highlights the relevance of organisms displaying alternative chromosomal inheritance to the understanding of forces shaping genome evolution.
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http://dx.doi.org/10.1093/gbe/evy015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798017PMC
February 2018

Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects.

Bioessays 2018 02 28;40(2). Epub 2017 Dec 28.

UMR CNRS 9191, UMR 247 IRD Laboratoire Evolution, Génomes, Comportement, Écologie, Université Paris-Sud,, 91198 Gif-sur-Yvette, France.

Whoever compares the genomes of distantly related species might find aberrantly high sequence similarity at certain loci. Such anomaly can only be explained by genetic material being transferred through other means than reproduction, that is, a horizontal transfer (HT). Between multicellular organisms, the transferred material will likely turn out to be a transposable element (TE). Because TEs can move between loci and invade chromosomes by replicating themselves, HT of TEs (HTT) profoundly impacts genome evolution. Yet, very few studies have quantified HTT at large taxonomic scales. Indeed, this task currently faces difficulties that range from the variable quality of available genome sequences to limitations of analytical procedures, some of which have been overlooked. Here we review the many challenges that an extensive analysis of HTT must overcome, we expose biases and limits of current methods, suggest solutions or workarounds, and reflect upon approaches that could be developed to better quantify this phenomenon.
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http://dx.doi.org/10.1002/bies.201700177DOI Listing
February 2018

Cyberbiosecurity: From Naive Trust to Risk Awareness.

Trends Biotechnol 2018 01 7;36(1):4-7. Epub 2017 Dec 7.

Department of Electrical and Computer Engineering and Office of the Vice President, National Capital Region, Virginia Tech, Blacksburg, VA 24061, USA; Group website: www.peccoud.org; https://ncr.vt.edu/discovery/research_development_team.html.

The cyber-physical nature of biotechnology raises unprecedented security concerns. Computers can be compromised by encoding malware in DNA sequences, and biological threats can be synthesized using publicly available data. Trust within the biotechnology community creates vulnerabilities at the interface between cyberspace and biology. Awareness is a prerequisite to managing these risks.
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http://dx.doi.org/10.1016/j.tibtech.2017.10.012DOI Listing
January 2018

GraphSpace: stimulating interdisciplinary collaborations in network biology.

Bioinformatics 2017 Oct;33(19):3134-3136

Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA.

Summary: Networks have become ubiquitous in systems biology. Visualization is a crucial component in their analysis. However, collaborations within research teams in network biology are hampered by software systems that are either specific to a computational algorithm, create visualizations that are not biologically meaningful, or have limited features for sharing networks and visualizations. We present GraphSpace, a web-based platform that fosters team science by allowing collaborating research groups to easily store, interact with, layout and share networks.

Availability And Implementation: Anyone can upload and share networks at http://graphspace.org. In addition, the GraphSpace code is available at http://github.com/Murali-group/graphspace if a user wants to run his or her own server.

Contact: [email protected]

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btx382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860550PMC
October 2017
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