Search

Mycoplasma feriruminatorisis a fast-growingMycoplasmaspecies isolated from wildCaprinaeand first described in 2013.M. feriruminatorisisolates have been associated with arthritis, keratoconjunctivitis, pneumonia and septicemia, but were also recovered from apparently healthy animals. To better understand what defines this species, we performed a genomic survey on 14 strains collected from free-ranging or zoo-housed animals between 1987 and 2017. The average chromosome size of theM. feriruminatorisstrains was 1,040 ± 0,024 kbp, with 24% G+C and 852 ± 31 CDS. The core genome and pan-genome of theM. feriruminatorisspecies contained 628 and 1,312 protein families, respectively. TheM. feriruminatorisstrains displayed a relatively closed pan-genome, with many features and putative virulence factors shared with species from theM. mycoidescluster, including the MIB-MIP Ig cleavage system, a repertoire of DUF285 surface proteins and a complete biosynthetic pathway for galactan.M. feriruminatorisgenomes were found to be mostly syntenic, although repertoires of mobile genetic elements, including Mycoplasma Integrative and Conjugative Elements, insertion sequences, and a single plasmid varied. Phylogenetic- and gene content analyzes confirmed thatM. feriruminatoriswas closer to theM. mycoidescluster than to the ruminant speciesM. yeatsiiandM. putrefaciens. Ancestral genome reconstruction showed that the emergence of theM. feriruminatorisspecies was associated with the gain of 17 gene families, some of which encode defense enzymes and surface proteins, and the loss of 25 others, some of which are involved in sugar transport and metabolism. This comparative study suggests that theM. mycoidescluster could be extended to includeM. feriruminatoris. We also find evidence that the specific organization and structure of the DnaA boxes around theoriCofM. feriruminatorismay contribute to drive the remarkable fast growth of this minimal bacterium.

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene-environment association (GEA) analyses to detect signatures of divergent selection.Beech range-wide genetic structure was consistent with the species’ previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype-climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology-related genes. The range-wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress-related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best-case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within-population neutral diversity and selection maintaining between-population adaptive differentiation.

The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol, or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in the wheat phyllosphere would lead to new insights into STB management. This article provides fungal and bacterial metabarcoding datasets obtained by sampling wheat leaves with and without symptoms caused by Z. tritici. Tissues were sampled from three commercial wheat varieties on three sampling dates during a cropping season. Weeds around wheat fields were sampled as well. In total, more than 450 leaf samples were collected. The pathogen Z. tritici was quantified using quantitative PCR. We provide the raw metabarcoding datasets, the amplicon sequence variant tables obtained after bioinformatic processing, the metadata associated with each sample (sampling date, wheat variety and tissue health condition), a preliminary descriptive analysis of the data, and the code used for bioinformatic and descriptive statistical analysis. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in the wheat phyllosphere would lead to new insights into STB management. This resource announcement provides fungal and bacterial metabarcoding datasets obtained by sampling wheat leaves differing in the presence of symptoms caused by Z. tritici. Tissues were sampled from three wheat commercial varieties on three sampling dates during a cropping season. Weeds around wheat fields were sampled as well. In total, more than 450 leaf samples were collected. The pathogen Z. tritici was quantified using qPCR. We provide the raw metabarcoding datasets, the Amplicon Sequence Variant (ASV) tables obtained after bioinformatic processing, the metadata associated to each sample (sampling date, wheat variety and tissue health condition), a preliminary descriptive analysis of the data, and the code used for bioinformatic and descriptive statistical analysis.

Patients with obesity are known to exhibit gut microbiota dysbiosis and memory deficits. Bariatric surgery (BS) is currently the most efficient anti-obesity treatment and may improve both gut dysbiosis and cognition. However, no study has investigated association between changes of gut microbiota and cognitive function after BS. We prospectively evaluated 13 obese patients on anthropometric data, memory functions, and gut microbiota-mycobiota before and six months after BS. The Rey Auditory Verbal Learning Test (AVLT) and the symbol span (SS) of the Weschler Memory Scale were used to assess verbal and working memory, respectively. Fecal microbiota and mycobiota were longitudinally analyzed by 16S and ITS2 rRNA sequencing respectively. AVLT and SS scores were significantly improved after BS (AVLT scores: 9.7 ± 1.7 vs. 11.2 ± 1.9, p = 0.02, and SS scores: 9.7 ± 23.0 vs. 11.6 ± 2.9, p = 0.05). An increase in bacterial alpha-diversity, and Ruminococcaceae, Prevotella, Agaricus, Rhodotorula, Dipodascus, Malassezia, and Mucor were significantly associated with AVLT score improvement after BS, while an increase in Prevotella and a decrease in Clostridium, Akkermansia,&nbsp, Dipodascus and Candida were linked to SS scores improvement. We identified several changes in the microbial communities that differ according to the improvement of either the verbal or working memories, suggesting a complex gut-brain-axis that evolves after BS.

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in

INISEFOR Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™ genotyping. These markers can be used for population genetic studies and timber tracking purposes. Las especies de Swietenia son las maderas tropicales estadounidenses más valiosas y han sido muy sobreexplotadas durante décadas. los Tres especies están incluidas como vulnerables o en peligro de extinción por la UICN y están incluidas en el Apéndice II de la CITES, pero son ilegales. la explotación continúa. Aquí, utilizamos la secuenciación de ADN asociada a la restricción para desarrollar un nuevo conjunto de 120 marcadores SNP para Swietenia sp., Adecuada para el genotipado MassARRAY®iPLEX ™. Estos marcadores se pueden utilizar para estudios genéticos de poblaciones. y seguimiento de la madera. As espécies de Swietenia são as madeiras tropicais americanas mais valiosas e têm sido fortemente superexploradas por décadas. As três espécies estão listadas como vulneráveis ​​ou em perigo pela IUCN e estão incluídas no Apêndice II da CITES, mas a exploração ilegal continua. Aqui, usamos o sequenciamento de DNA associado à restrição para desenvolver um novo conjunto de 120 marcadores SNP para Swietenia sp., Adequado para genotipagem MassARRAY®iPLEX ™. Esses marcadores podem ser usados ​​para estudos de genética populacional e fins de rastreamento de madeira. Thünen Institute of Forest Genetics, Germany Instituto Nacional de Pesquisas da Amazônia, Brazil Universidad Nacional, Costa Rica Centre for Ecology & Hydrology, United Kingdom Instituto Florestal de São Paulo, Brazil University of Bordeaux, France Mahogany for the Future Inc., USA Bush Estate, United Kingdom Instituto de Investigación y Servicios Forestales

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome- wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.

International audience; To better study and manage chestnut trees and species, we identified nuclear single nucleotide polymorphism (SNP) markers using restriction-associated DNA sequencing. Out of 343 loci tested, 68 SNP markers were selected that withhold stringent quality criteria such as quasi-systematic amplification across species and Mendelian segregation in both purebred and hybrid individuals. They provide sufficient power for species, hybrids and backcross characterization as well as for clonal identification, as shown by a comparison with single sequenced repeat (SSR) loci.

International audience; Biomonitoring ecosystems is necessary in order to evaluate risks and to efficiently manage ecosystems and their associated services. Agrosystems are the target of multiple stressors that can affect many species through effects cascading along food webs. However, classic biomonitoring, focused on species diversity or indicator species, might be a poor predictor of the risk of such whole-ecosystem perturbations. Thanks to high-throughput sequencing methods, however, it might be possible to obtain sufficient information about entire ecological communities to infer the functioning of their associated interaction networks, and thus monitor more closely the risk of the collapse of entire food webs due to external stressors. In the course of the ‘next-generation biomonitoring’ project, we collectively sought to experiment with this idea of inferring ecological networks on the basis of metabarcoding information gathered on different systems. We here give an overview of issues and preliminary results associated with this endeavour and highlight the main difficulties that such next-generation biomonitoring is still facing. Going from sampling protocols up to methods for comparing inferred networks, through biomolecular, bioinformatic, and network inference, we review all steps of the process, with a view towards generality and transferability towards other systems. © 2022 Elsevier Ltd

International audience; Isolating genetic markers is often costly and time-consuming for non-model fungal species. However, these markers are of primary importance to identify the origin of invasive species and to infer their reproductive mode and dispersal ability. We slightly modified a recent molecular method to quickly isolate and validate single-nucleotide polymorphism (SNP) markers, from a first Erysiphe alphitoides draft genome, one of the main causal agent of oak powdery mildew in Europe. Although the draft assembly was strongly fragmented (555,289 contigs), we successfully isolated 1700 SNPs from 75 single-copy genes conserved in most fungal genomes. Ninety percent of them allowed to clearly distinguish the two main Erysiphe species reported on European oaks: E. alphitoides and E. quercicola. Thirty-six SNPs, located in distinct genes, were then validated using a strategy of MassArray genotyping on 95 E. alphitoides isolates sampled in Europe. This genotyping showed that only monospore isolates had the expected haploid signature, whereas direct genotyping from field leaves showed signature of mixed infection. Considering haploid isolates, these markers led to the first results of population genetic diversity, and suggested that E. quercicola may have a more asexual reproduction than its sister species, E. alphitoides.

[Key message]: In our study of colonisation of abandoned farmland byJuniperus thurifera L., environmental and geographic distances were stronger drivers of functional differentiation among trees than genetic distance and tree intrinsic features. However, these effects varied both along the colonisation gradient and across predictors’ values, highlighting the complexity of the conditions under which functional diversity of forests is maximised. Context: Forest expansion after land abandonment is changing Mediterranean landscapes, but the underlying ecological and evolutionary processes remain poorly understood., [Aims]: We evaluated whether forest expansion reduces within-stand tree functional distances and whether its environmental, geographical and genetic drivers vary along the expansion gradient., [Methods]: We sampled Juniperus thurifera in mature, transition and expanding stands along a colonisation gradient in Spain. We measured functional traits, genetic relatedness, surrounding vegetation cover and intrinsic features (size, phytosanitary status) on trees. We calculated within-stand pairwise functional distances and quantified the effects of genetic relatedness, geographic distance, vegetation cover and intrinsic tree features., [Results]: Functional and genetic distances showed no consistent patterns along the expansion gradient. Functional distance was unrelated with genetic distance and strongly driven by geographic distance, likely representing unmeasured environmental factors. Vegetation cover and intrinsic tree features affected functional traits in transition and expanding stands. The effects on functional distance changed across predictors’ values., [Conclusion]: The role of environmental and geographic factors on tree functional divergence varied along the farmland colonisation gradient, while we did not detect effects of genetic distance. Accounting for this context-dependence and for non-linear effects on functional traits can improve our understanding and management of forest expansions., This study was funded by the grants SPONFOREST (BiodivERsA3-2015-58, PCIN-2016-055, financed by the Spanish Research Agency, AEI and the Spanish Ministry of Economy, Industry and Competitiveness, MINECO), COMEDIAS (MINECO, CGL2017-83170-R) and REMEDINAL TE (Ref. TE-CM.S2018/EMT-4338, 2019-2023-Comunidad de Madrid).

Chestnut species have large ecological, cultural and economic importance. Developing genetic markers for these species is of interest for conservation, breeding or evolutionary studies. We designed 192 primer pairs targeting microsatellites detected in the Castanea mollissima reference genome and tested them on C. sativa and C. crenata. We PCR amplified 3 × 50 microsatellites in 106 chestnut trees. Microhaplotype calling accounting for all polymorphisms resulted in a total of 98 high confidence polymorphic markers. Mean number of haplotypes per marker was 9.05 with respectively 71%, 12% and 16% of the variation corresponding to microsatellite variation in repeats number, SNP within the repeat motif and SNP or INDEL in the flanking sequence. Overall, the simple protocol described here generated a powerful multilocus genetic dataset for chestnut genetic investigations.

We used double digest restriction site associated DNA sequencing (ddRAD) to develop new geographically informative nuclear SNP loci in Quercus robur and Quercus petraea. Genotypes derived from sequence data of 95 individuals covering the distribution range of the species were analysed to select geographically informative and polymorphic loci within Russia and Germany. We successfully screened a selected set of 119 loci on a MassARRAY® iPLEX™ platform on 190 individuals from 19 locations in Russia. The newly developed loci will be useful for genetic studies over the whole distribution range of both species.

In the last two decades, the massive genome sequencing of strains belonging to the Saccharomyces genus revealed the complex reticulated evolution of this group. Among the various evolutionary mechanisms described, the introgression of large chromosomal regions resulting from interspecific hybridization has recently shed light on the Saccharomyces uvarum species. In this work we provide the de novo assembled genomes of four S. uvarum strains presenting more than 712 kb of introgressed loci inherited from both S. eubayanus and S. kudriavzevii species. In order to study the prevalence of such introgressions in a large population, we designed multiplexed PCR- markers able to survey the inheritance of 8 chromosomal regions. Our data confirm that introgressions are widely disseminated in Holarctic S. uvarum population and are more frequently found in strains isolated from human-related fermentations. According to the origin of the strains (nature, cider or wine related process) some loci are overrepresented suggesting their positive selection by human activity. Except one locus located on chromosome 7, the introgressions present a low level of heterozygozity similar to that observed for nine neutral markers (microsatellites). Finally, most of these loci tested showed an expected Mendelian segregation after meiosis and can recombined with their chromosomal counterpart in S. uvarum.

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast,de novo ad hocprimer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20 to 40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence, quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

The eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become a classic model for studying the genetic nature of species in a syngameon. Genetic work over the past two decades has demonstrated the reality of oak species, but gene flow between sympatric oaks raises the question of whether there are conserved regions of the genome that define oak species. Does gene flow homogenize the entire genome? Do the regions of the genome that distinguish a species in one part of its range differ from the regions that distinguish it in other parts of its range, where it grows in sympatry with different species? Or are there regions of the genome that are relatively conserved across species ranges? In this study, we revisit seven species of the eastern North American white oak syngameon using a set of 80 SNPs selected in a previous study because they show differences among, and consistency within, the species. We test the hypothesis that there exist segments of the genome that do not become homogenized by repeated introgression, but retain distinct alleles characteristic of each species. We undertake a rangewide sampling to investigate whether SNPs that appeared to be fixed based on a relatively small sample in our previous work are fixed or nearly fixed across the range of the species. Each of the seven species remains genetically distinct across its range, given our diagnostic set of markers, with relatively few individuals exhibiting admixture of multiple species. SNPs map back to all 12Quercuslinkage groups (chromosomes) and are separated from each other by an average of 7.47 million base pairs (± 8.74 million bp, s.d.), but are significantly clustered relative to a random null distribution, suggesting that our SNP toolkit reflects genome-wide patterns of divergence while potentially being concentrated in regions of the genome that reflect a higher-than-average history of among-species divergence. This application of a DNA toolkit designed for the simple problem of identifying species in the field has an important implication: the eastern North American white oak syngameon is composed of entities that most taxonomists would consider “good species,” and species in the syngameon retain their genetic cohesion because characteristic portions of the genome do not become homogenized despite a history of introgression.

International audience; The genus Khaya includes some of the highest-value timber species in natural forests in Africa, which are under heavy exploitation pressure. Genetic identification of Khaya species is important to confirm the taxonomic classification for biodiversity conservation purposes and as a forensic tool aiding law enforcement in the fight against illegal logging. We collected samples from a total of 2222 trees belonging to five or six (depending on classification) different Khaya species (K. ivorensis, K. anthotheca/K. nyasica, K. grandifoliola, K. senegalensis, K. madagascariensis). Representative sampling was conducted over the natural ranges of all sampled Khaya species, in humid tropical forest and savanna zones. We genotyped individuals based on 101 molecular markers (67 nuclear, 11 chloroplast and 22 mitochondrial SNPs, 1 chloroplast indel). Bayesian clustering produced three main genetic groups assigning all K. ivorensis and all K. senegalensis trees, respectively, in two different clusters and all remaining individuals in a third cluster. Genetic self-assignment tests with all 101 SNPs had success rates of 97-100% for all species except for K. nyasica and K. madagascariensis, which could not be clearly distinguished from each other. A success rate for species identification nearly as high was observed using a subset of 15 highly differentiated SNPs. There was only very little evidence for hybridization among species and the vast majority (> 97%) of individuals were assigned to the same species group as identified based on morphological characters.

International audience; The role of evolution in biological invasion studies is often overlooked. In order to evaluate the evolutionary mechanisms behind invasiveness, it is crucial to identify the source populations of the introduction. Studies in population genetics were carried out on Robinia pseudoacacia L., a North American tree which is now one of the worst invasive tree species in Europe. We realized large‐scale sampling in both the invasive and native ranges: 63 populations were sampled and 818 individuals were genotyped using 113 SNPs. We identified clonal genotypes in each population and analyzed between and within range population structure, and then, we compared genetic diversity between ranges, enlarging the number of SNPs to mitigate the ascertainment bias. First, we demonstrated that European black locust was introduced from just a limited number of populations located in the Appalachian Mountains, which is in agreement with the historical documents briefly reviewed in this study. Within America, population structure reflected the effects of long‐term processes, whereas in Europe it was largely impacted by human activities. Second, we showed that there is a genetic bottleneck between the ranges with a decrease in allelic richness and total number of alleles in Europe. Lastly, we found more clonality within European populations. Black locust became invasive in Europe despite being introduced from a reduced part of its native distribution. Our results suggest that human activity, such as breeding programs in Europe and the seed trade throughout the introduced range, had a major role in promoting invasion; therefore, the introduction of the missing American genetic cluster to Europe should be avoided.

International audience; The eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become a classic model for studying the genetic nature of species in a syngameon. Genetic work over the past two decades has demonstrated the reality of oak species, but gene flow between sympatric oaks raises the question of whether there are conserved regions of the genome that define oak species. Does gene flow homogenize the entire genome? Do the regions of the genome that distinguish a species in one part of its range differ from the regions that distinguish it in other parts of its range, where it grows in sympatry with different species? Or are there regions of the genome that are relatively conserved across species ranges? In this study, we revisit seven species of the eastern North American white oak syngameon using a set of 80 single-nucleotide polymorphisms (SNPs) selected in a previous study because they show differences among, and consistency within, the species. We test the hypothesis that there exist segments of the genome that do not become homogenized by repeated introgression, but retain distinct alleles characteristic of each species. We undertake a range-wide sampling to investigate whether SNPs that appeared to be fixed based on a relatively small sample in our previous work are fixed or nearly fixed across the range of the species. Each of the seven species remains genetically distinct across its range, given our diagnostic set of markers, with relatively few individuals exhibiting admixture of multiple species. SNPs map back to all 12 Quercus linkage groups (chromosomes) and are separated from each other by an average of 7.47 million bp ((+) 8.74 million bp, SD), but are significantly clustered relative to a random null distribution, suggesting that our SNP toolkit reflects genome-wide patterns of divergence while potentially being concentrated in regions of the genome that reflect a higher-than-average history of among-species divergence. This application of a DNA toolkit designed for the simple problem of identifying species in the field has two important implications. First, the eastern North American white oak syngameon is composed of entities that most taxonomists would consider "good species." Second, and more fundamentally, species in the syngameon are genetically coherent because characteristic portions of the genome remain divergent despite a history of introgression. Understanding the conditions under which some loci diverge while others introgress is key to understanding the origins and maintenance of global tree diversity.

Made available in DSpace on 2019-10-06T15:45:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-15 Bundesministerium für Ernährung und Landwirtschaft Conseil Régional Aquitaine Agence Nationale de la Recherche Low coverage MiSeq genome sequencing and restriction associated DNA sequencing (RADseq) were used to identify nuclear and plastid SNP and INDEL genetic markers in Carapa guianensis. 261 genetic markers including 237 nuclear SNPs, 22 plastid SNPs, and 2 plastid INDELs are described based on 96 genotyped individuals from French Guiana, Brazil, Peru, and Bolivia. The best 117 SNPs for identifying population structure and performing individual assignment are assembled into four multiplexes for MassARRAY genotyping. INRA UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane, Campus Agronomique, Avenue de France Thünen Institute of Forest Genetics, Sieker Landstrasse 2 School of Natural Sciences and Engineering São Paulo State University (UNESP) Carrera de Ingeniería Forestal Laboratorio de Dendrocronología Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5 Instituto Florestal de São Paulo, CP 1322 BIOGECO INRA University Bordeaux School of Natural Sciences and Engineering São Paulo State University (UNESP) Conseil Régional Aquitaine: 20030304002FA Conseil Régional Aquitaine: 20040305003FA Agence Nationale de la Recherche: ANR-10-EQPX-16-01 Agence Nationale de la Recherche: ANR-10-LABX-25-01

International audience; Spring shoot phenology is an adaptive trait highly responsive to climatic conditions that influences plant growth and development, as well as plant–herbivore interactions. We investigated if the geographic origin of cork oak influenced spring shoot phenology (timing of budburst) and if the variation among provenances (advances and/or delays) had consequences for leaf pest damage. The study was conducted in two provenance trials (planted in 1998) located in central and southern Portugal; each trial was surveyed during a two-year period. The variation in budburst timing was compared for 35 cork oak (Quercus suber L.) provenances sampled from the entire natural distribution of the species. Budburst exhibited high broad-sense heritability (0.79–0.94). Two East/West groups effectively separated Q. suber genetic structure and the timing of budburst. Provenances from the western part of the natural range tended to burst later than provenances from the eastern part. Budburst provenance ranking was similar between sites and years. Climate strongly influenced budburst date: in the year with warmer winter months (2004), all provenances in both sites exhibited earlier budburst in comparison with 2003 and 2005. Leaf pest damage was assessed at the southern provenance trial. Differences in the timing of budburst had a significant effect on insect activity (herbivory), which was more concentrated in time and thus more important in the year with later budburst. However, North African provenances with earlier budburst were more exposed to insect herbivory within each year. This study demonstrated a significant provenance effect on budburst timing of Q. suber that is partly genetically determined and has consequences for exposure to herbivory. Knowledge of cork oak locally adapted provenances is important for sustainable forest management in Mediterranean climate conditions, particularly for (re)forestation actions, because it favors higher survival and growth.

In the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs −218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity (θπ) and differentiation (FST) across genic regions are also described for the first time in those species, with a mean n θπ close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and a mean FST ~0.13 across SNPs. The magnitude of diversity across genes is within the range estimated for long-term perennial outcrossers, and can be considered relatively high in the plant kingdom, with an estimate across the genome of 41 to 51 million SNPs expected in both species. Individuals with typical species morphology were more easily assigned to their corresponding genetic cluster for Q. robur than for Q. petraea, revealing higher or more recent introgression in Q. petraea and a stronger species integration in Q. robur in this particular discovery panel. We also observed robust patterns of a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. To explain these patterns, we discuss an alternative and non-exclusive hypothesis of stronger selective constraints in Q. robur, the most pioneering species in oak forest stand dynamics, additionally to the recognized and documented introgression history in both species despite their strong reproductive barriers. The quality of the data provided here and their representativity in terms of species genomic diversity make them useful for possible applications in medium-scale landscape and molecular ecology projects. Moreover, they can serve as reference resources for validation purposes in larger-scale resequencing projects. This type of project is preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and the low levels of linkage disequilibrium revealed.

Evolutionary history of tropical tree species complexes: species delimitation and adaptive genetic variation in the Brazil nut clade (Lecythidaceae). European Conference of Tropical Ecology (GTOE2018)

International audience; DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite-associated DNA sequencing (RAD-seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof-of-concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q.michauxii, Q.montana, Q muehlenbergii/Q.prinoides, and Q.stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q.alba and Q.macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q.michauxii mother tree, the acorns of which exhibited high admixture from either Q.alba or Q.stellata and Q.macrocarpa, and a hybrid between Q.stellata that appears to have backcrossed almost exclusively to Q.alba. Together, RAD-seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.

Made available in DSpace on 2019-10-04T12:34:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-12-01 German Federal Ministry of Food and Agriculture Conseil Regional d'Aquitaine European Union, FEDER Investissements d'avenir Chico Mendes Biodiversity Institute A combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing was used for the development of single nucleotide polymorphisms (SNP) and INDEL (insertion/deletions) genetic markers for Ipe (Handroanthus sp.). Of the 402 putative loci identified, 389 SNPs and INDELs (315 nuclear SPNs, six chloroplast INDELs, 15 chloroplast SNPs, 12 mitochondrial INDELs and 41 mitochondrial SNPs) were successfully genotyped at 93 individuals from Brazil, Bolivia and French Guiana using a - MassARRAY (R) iPLEX (TM) platform. This set of markers will be invaluable for population genetics, phylogeography and DNA fingerprinting studies. Univ Estadual Paulista, Dept Fitotecnia Tecnol Alimentos & Socioecon, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Carrera Ingn Forestal, Lab Dendrocronol, Km 6 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, INRA, UMR0745 EcoFoG,AgroParisTech,Cirad,CNRS, Campus Agron,Ave France,BP97387, Kourou, France Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil INRA Pierroton, Plateforme Genome Transcriptome Bordeaux, 69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Dept Fitotecnia Tecnol Alimentos & Socioecon, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01 Chico Mendes Biodiversity Institute: 47960 Chico Mendes Biodiversity Institute: 49369

International audience; Cacao (Theobroma cacao L.) is an important economic crop, yet studies of its domestication history and early uses are limited. Traditionally, cacao is thought to have been first domesticated in Mesoamerica. However, genomic research shows that T. cacao’s greatest diversity is in the upper Amazon region of northwest South America, pointing to this region as its centre of origin. Here, we report cacao use identified by three independent lines of archaeological evidence—cacao starch grains, absorbed theobromine residues and ancient DNA—dating from approximately 5,300 years ago recovered from the Santa Ana-La Florida (SALF) site in southeast Ecuador. To our knowledge, these findings constitute the earliest evidence of T. cacao use in the Americas and the first unequivocal archaeological example of its pre-Columbian use in South America. They also reveal the upper Amazon region as the oldest centre of cacao domestication yet identified.

International audience; We describe the development of new nuclear SNP markers for the genetic timber tracking of the geographical origin of Sapelli, Entandrophragma cylindricum (Meliaceae). Restriction associated DNA sequencing (RADseq) of two reference individuals yielded 1131 putative SNPs. Among those, 131 were selected to design four MassARRAY multiplexes and screened at 178 individuals. Seventy-two loci were selected for further use in genetic tracking.

International audience; Genomic resources are a valuable research tool for understanding and forecasting the response of forest trees to global change and for developing science-based management strategies. Yet, many ecologically relevant tree species still lack such resources. The conifer genus Juniperus contains >70 species that are widely distributed through the Northern Hemisphere, including several keystone species that form extensive forests in arid landscapes. To date, single-nucleotide polymorphism (SNP) markers have not been described for this ecologically important tree genus and the few described simple sequence repeat (SSR) markers result insufficient for performing reliable population demographic inference. Here, we report on the successful development of 19 new SSR and 147 SNP markers for Phoenician juniper (Juniperus phoenicea ssp. turbinata), a species widely distributed along the coasts of the Mediterranean Basin. We calculate a series of population genetic diversity estimates for each set of markers independently and for both sets combined. Our comparison shows that the higher per-locus information content of SSRs makes them the marker of choice for parentage and assignment studies, whereas SNPs provide more reliable demographic inferences (N-e and detection of a recent bottleneck). We also test and confirm the transferability of the new set of SNP markers to the closely related tetraploid species J. thurifera. Finally, we perform an orthology analysis with two gymnosperm model species to search for SNPs linked with functional genes.

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favoring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally-inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management., This research was supported by the European Research Council, through the Advanced Grant Project TREEPEACE (#FP7-339728) and the Consolidator PEGASUS (#H2020-681605). Sequencing was performed at the Danish National High-Throughput Sequencing Centre, Copenhagen, Denmark.

Multispecies population genetics is an emerging field that provides insight relevant to conservation biology and community ecology. However, to date, this approach is limited to species with available genetic resources. The use of thousands of single-nucleotide polymorphism (SNP) markers developed from recent genotyping-by-sequencing (GBS) technologies is a roadmap for the study of nonmodel species, but remains cost prohibitive when several, distantly related species are involved. We aimed to overcome this issue using a single HiSeq3000 run of restriction-site associated DNA sequencing (RAD-Seq) to retrieve SNP markers for 40 diverse species including plants, invertebrates, fish, and mammals. We developed a Python-based pipeline to isolate c. 100–500 high-quality SNP markers for each species that could be genotyped through classical PCR amplification methods. To assess the quality of these markers, we validated our approach on c. 160 of the characterized SNPs for each of 18 Neotropical fish species from the river Maroni (French Guiana, South America), using the MassARRAY iPLEX platform from Agena Bioscience (San Diego, CA, USA). A run of the pipeline applying stringent filtering parameters enabled the successful design of between 130 and 3,492 SNP markers for 30 of the 40 study species. Relaxing pipeline parameters allows for an increase in the number of detected SNPs. Across the 18 species from French Guiana, an average of 85% of markers were successfully amplified, polymorphic, and scored in ≥90% of individuals (c. 200 individuals per species). The great majority (>98%) of these markers were at Hardy–Weinberg equilibrium in each sampling site from the river Maroni. This SNP discovery was performed at the cost of c. $US110 for each of the 40 species. Genotyping was performed at the cost of c. $US6000 for each of the 18 fish species with an average of 200 individuals per species. This strategy was found cost-and-time efficient to develop hundreds of SNP markers for a large range of nonmodel species, which can be used to investigate ecological and evolutionary questions that do not require whole-genome coverage.

Subtropical East Asia harbours a large plant diversity that is often attributed to allopatric speciation in this topographically complex region characterized by a relative climate stability. Here, we use observations of Platycarya, a widespread subtropical Asian tree genus, to explore the consequences of past climate stability on species’ evolutionary history in subtropical China. This genus has a controversial taxonomy: while it is now prevailingly treated as monotypic, two species have been originally described, Platycarya strobilacea and P. longipes. Previous information from species distribution models, fossil pollen data and genetic data based on chloroplast DNA (cpDNA) were integrated with newly obtained genetic data from the two putative species. We used both cpDNA (psbA-trnH and trnL-F intergenic spacers, including a partial trnL gene sequence) and nuclear markers. The latter included sequences of the internal transcribed spacer region (ITS1–5.8S–ITS2) of the nuclear ribosomal DNA and random genomic single nucleotide polymorphisms. Using these nuclear genetic markers, we found interspecific genetic divergence fitting with the ‘two species’ scenario and geographically structured intraspecific variation. Using cpDNA markers, we also found geographically structured intraspecific variation. Despite deep inter- and intraspecific genetic divergence, we detected genetic admixture in southwest China. Overall, our findings of genetic divergence within Platycarya support the hypothesis of allopatric speciation. However, episodes of population interconnection were identified, at least in southwest China, suggesting that the genus has had a dynamic population history.

Hybridization and patterns of adaptive genetic variation in tropical trees of the Bertholletia clade (Lecythidaceae) in French Guiana. Meeting of the German Society for Tropical Ecology (GTOE2017)

Restriction associated DNA sequencing was conducted on two genetically independent individuals of Iroko, Milicia excelsa, for the discovery of nuclear SNPs. Ninety-four samples, well-distributed over the natural range and including timber DNA, were screened at 138 loci on a MassARRAY iPLEX system. Amplification success was high and 77 loci were selected to design a set of markers for genetic timber tracking purposes.

Understanding the mechanisms behind the typicity of regional wines inevitably brings attention to microorganisms associated with their production. Oenococcus oeni is the main bacterial species involved in wine and cider making. It develops after the yeast-driven alcoholic fermentation and performs the malolactic fermentation, which improves the taste and aromatic complexity of most wines. Here, we have evaluated the diversity and specificity of O. oeni strains in six regions. A total of 235 wines and ciders were collected during spontaneous malolactic fermentations and used to isolate 3,212 bacterial colonies. They were typed by multilocus variable analysis, which disclosed a total of 514 O. oeni strains. Their phylogenetic relationships were evaluated by a second typing method based on single nucleotide polymorphism (SNP) analysis. Taken together, the results indicate that each region holds a high diversity of strains that constitute a unique population. However, strains present in each region belong to diverse phylogenetic groups, and the same groups can be detected in different regions, indicating that strains are not genetically adapted to regions. In contrast, greater strain identity was seen for cider, white wine, or red wine of Burgundy, suggesting that genetic adaptation to these products occurred. IMPORTANCE This study reports the isolation, genotyping, and geographic distribution analysis of the largest collection of O. oeni strains performed to date. It reveals that there is very high diversity of strains in each region, the majority of them being detected in a single region. The study also reports the development of an SNP genotyping method that is useful for analyzing the distribution of O. oeni phylogroups. The results show that strains are not genetically adapted to regions but to specific types of wines. They reveal new phylogroups of strains, particularly two phylogroups associated with white wines and red wines of Burgundy. Taken together, the results shed light on the diversity and specificity of wild strains of O. oeni , which is crucial for understanding their real contribution to the unique properties of wines.

The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.

International audience; The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.

Aim Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species. Location Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocoand Central America. Methods Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH-psbA and trnC-ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times. Results Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu )a nd C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal. Main conclusions The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.

National audience