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Local adaptation is key for ecotypic differentiation and species evolution1. Understanding the underlying genomic patterns allows the prediction of future maladaptation and ecosystem stability2. Here we report the whole-genome resequencing of 865 individuals from 100 range-wide populations of European beech (Fagus sylvatica), which is one of the most important forest tree species in Europe. We show that genetic variation closely mirrors geography. Adaptive variation identified by genotype-environment associations exhibits highly polygenic architectures, involving thousands of associated sequence variants across the genome. By modelling the ‘genomic offset’ of these sequence variants under projected future climate conditions, we identify broad- and fine-scale variation highlighting geographic regions as well as populations at potential elevated risk of mortality or local extinction. Our results emphasize the importance of considering natural genetic variation for forest conservation under climate change conditions.

The early-branching clades of Fabaceae subfamily Papilionoideae are characterized by their remarkable lability in floral architecture. In contrast, more derived papilionoid lineages are marked by evolutionary conservatism towards strongly bilateral, papilionate flowers. Here, we show an unexpected example of conservatism of a unique floral architecture during the early diversification history of the papilionoids. We built the most comprehensively sampled molecular phylogenetic tree with a focus on the early-diverging papilionoid Dipterygeae clade to evaluate conservatism of the winged papilionate architecture and associated traits related to flower specialization (e.g. zygomorphy, petal differentiation, stable stamen number and stamen sheath). Dipterygeae comprise c. 22 species of mostly giant trees from across tropical forests in Central America and the Amazon, but they are also ecologically dominant in the savannas of the Brazilian Central Plateau. Phylogenetic analyses of nuclear ribosomal ITS/5.8S and plastid matK and trnL intron sequences strongly supported inter-relationships and the monophyly of each genus (Dipteryx, Monopteryx, Pterodon and Taralea). Bayesian relaxed-clock dating and a Bayesian model of ancestral character estimation revealed c. 30 Myr of conservatism of all winged papilionate-related flower traits in a clade comprising the most recent common ancestor of Dipteryx, Pterodon and Taralea, but lability in fruit morphology during the diversification of the entire Dipterygeae clade. Despite Monopteryx and remaining Dipterygeae being florally discrepant, they are collectively defined by a floral synapomorphy that is unique among all papilionoid Fabaceae: the highly differentiated calyx, where the two upper lobes are enlarged and wing-like, whereas the other three lower lobes are reduced. We suggest that the different dispersal strategies and the ancient winged papilionate floral conservatism in Dipterygeae, which has maintained effective ecological interactions with specialized pollinators and ensured the protection of young flower buds and developing fruits, may explain successful evolutionary and ecological persistence of the clade across the main Neotropical biomes.

Pedunculate oak is seen as an alternative to other tree species for reforestation and mitigation programs in the face of climate change. Thus, the identification of suitable, well-adapted seed sources is of high priority. We perform a genetic inventory on 970 trees from 97 locations in Russia, Belarus, Ukraine and Latvia representing the eastern part of the natural species range. All samples were screened with a set of 348 gene markers covering the nuclear (n = 327) and the organelle genomes (chloroplast: n = 14, mitochondria: n = 7) using a genotyping-by-sequencing method. We identified 10 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 600 km. After excluding 47 potentially selected markers, significant spatial genetic structure up to 800 km was also observed at the selectively neutral nuclear loci. Bayesian clustering analysis indicated a sub-division into two gene pools present at all locations but with a shift of proportion from West to East. The genetic diversity was negatively correlated with longitude, showing higher values in the West and Centre and lower values at the northern, eastern and southeastern edges of the natural distribution range. We sub-divided the sampled area into six geographic regions and used the genetic composition of all samples in each region as a genetic reference for assignment tests. Self-assignment of groups of 10 individuals to their region of origin showed an average assignment success of 93 per cent. Samples of three artificial plantations of pedunculate oak in Siberia could be clearly assigned to the East–North and Centre–South regions. We discuss the implications of our results for the forest practice and in particular the proofing of seed sources.

PDF file - 163K, Homozygous CHD1 deletion in areas of prostatic intraepithelial neoplasia (PIN) and invasive cancer cells. Overwiew of a hematoxylin- and eosin stained tissue section containing areas of PIN (a, b) and invasive cancer (c). Corresponding FISH images show complete loss of CHD1 FISH signals (red) in PIN and cancer cells but not in stroma cells indicated by an asterix. The control FISH signals (green) correspond to centromere 6.

PDF file - 101K, GISTIC analysis of genomic rearrangements (cytoband) significantly associated with 5q21 deletion. The cytobands, significance (q value) and peak boundaries are indicated.

PDF file - 155K, Baseline CHD1 mRNA (a) and protein (b) expression levels in prostate cancer cell lines cells. Efficacy of ectopic overexpression of CHD1 in PC-3 cells on mRNA (c) and protein level (d) by Taqman PCR and immunoblot analysis, respectively.

PDF file - 44K, Overexpression of RB1 and PTEN in PC-3 cells transfected with PSG5L-RB1 and PSG5L-PTEN as compared to the control vector PLNGY. Lysates were analysed for RB1 (a) and PTEN (b) by immunoblot analysis. Tubulin immunoblot served as loading control.

PDF file - 92K, Impact of sh-RNA mediated knockdown of CHD1 (a), RB1 (b), PTEN (c) and mTOR (d) knockdown on mRNA and protein levels in BPH-1 cells by Taqman.

PDF file - 57K, COX regression multivariate analysis for the predictive factor biochemical recurrence (BCR).

PDF file - 68K, Localization of the CHD1 FISH probe made from two BAC clones relative to the CHD1 gene.

PDF file - 636K, Impact of CHD1 on colony formation, soft agar growth and cell invasiveness. a) Effect of CHD1 overexpression on cell growth. DU-145 cells were transfected with expression vectors encoding CHD1, PLNGY (control) and the known tumor suppressor genes RB1 and PTEN. Effect of CHD1 depletion on cell growth. DU-145 cells were transfected with shCHD1 vector. The control group consisted of shGFP, shRB1 and shPTEN vectors. Cells were selected with puromycin and cultured for two weeks, and colonies were fixed with methanol and stained with Giemsa. b) Soft agar assay showing the impaired anchorage-independent growth of shCHD1 PC-3 cells and control shNeg cells. Representative images of the stained colonies are shown. The bars represent the average number of colonies. c) CHD1 knockdown impairs invasion of PC-3 (shCHD1) cells through matrigel as compared to shNeg control cells. Photographs show representative fields of crystal-violet stained invading cells.

The large-scale spatial genetic structure of European beech, Fagus sylvatica, has been until now poorly studied. We conducted double digest RAD sequencing (ddRADseq) on 54 beech individuals stemming from 36 provenances to discover spatially informative nuclear SNP loci. In addition, two pools derived from 14 early and 14 late flushing individuals each were sequenced with Illumina HiSeq. From an initial amount of 5,464 loci detected by ddRADseq, we selected 559 informative loci. Further 27 additional loci showing significant allelic differences among early and late flushing individuals could be identified after a genotyping on 95 test individuals. The final selection of 578 loci was submitted to probe design for targeted genotyping by sequencing, which yielded 543 loci. The new set of SNP loci should be, after validation on a larger sample size, useful for large-scale genetic studies in this economically-important species.

Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive1. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR-Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes.

We used Double Digest Restriction site associated DNA sequencing (ddRAD) and Miseq to develop new geographically informative nuclear and plastid SNP and indel loci in Quercus robur and Q. petraea. Genotypes derived from sequence data of 95 individuals and two pools of 20 individuals each of Q. robur and Q. mongolica covering the distribution range of the species, were analysed to select geographically informative and polymorphic loci within Germany and Russia. We successfully screened a selected set of 431 nuclear single nucleotide polymorphism (nSNP), six nuclear Indel, six mitochondrial single nucleotide polymorphism (mtSNP) and ten chloroplast single nucleotide polymorphism (cpSNP) loci with a SeqSNP genotyping platform on 100 individuals Quercus petraea from 10 locations in Germany, 100 individuals Quercus robur from ten locations in Germany and 100 individuals Quercus robur from ten locations in Russia. The newly developed loci are useful for species identification and genetic studies on the genetic diversity and genetic differentiation of Quercus robur and Quercus petraea in Europe.

As for most other temperate broadleaved tree species, large-scale genetic inventories of pedunculate oak (Quercus robur L.) have focused on the plastidial genome, which showed the impact of post-glacial recolonization and manmade seed transfer. However, how have pollen mediated gene flow and introgression impacted the large-scale genetic structure? To answer these questions, we did a genetic inventory on 1970 pedunculate oak trees from 197 locations in 13 European countries. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs, and 5 mitochondrial SNPs). In a former analysis with additional 1763 putative Quercus petraea trees screened for the same gene markers we obtained estimates on the species admixture of all pedunculate oak trees. We identified 13 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 1250 km. Significant spatial genetic structure up to 1250 km was also observed at the nuclear loci. However, the differentiation at the nuclear gene markers was much lower compared to the organelle gene markers. The matrix of genetic distances among locations was partially correlated between nuclear and organelle genomes. Bayesian clustering analysis revealed the best fit to the data for a sub-division into two gene pools. One gene pool is dominating the west and the other is the most abundant in the east. The western gene pool was significantly influenced by introgression from Quercus petraea in the past. In Germany, we identified a contact zone of pedunculate oaks with different introgression intensity, likely resulting from different historical levels of introgression in glacial refugia or during postglacial recolonization. The main directions of postglacial recolonization were south to north and south to northwest in West and Central Europe, and for the eastern haplotypes also east to west in Central Europe. By contrast, the pollen mediated gene flow and introgression from Q. petraea modified the large-scale structure at the nuclear gene markers with significant west–east direction.

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

Made available in DSpace on 2019-10-06T15:52:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01 Illegal logging and trade of timber are major worldwide concerns, resulting in biodiversity and economic losses. Tropical tree species in the genus Cedrela, which have historically been heavily exploited, are still often illegally traded and there is an urgent need to develop tools to verify the origin of Cedrela products. A set of 351 SNP loci for Cedrela species from Bolivia, Brazil, Costa Rica, Cuba, Ecuador, French Guiana, Mexico, and Peru was developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing, and adapted for MassARRAY genotyping. After screening of 94 individuals covering most of the distribution of Cedrela, a final set of 136 SNP loci which included 92 nuclear SNPs, 22 chloroplast markers (20 SNPs and 2 INDELs), and 22 mitochondrial markers (19 SNPs and 3 INDELs) was selected and tested for potential to verify Cedrela timber origin. Carrera de Ingeniería Forestal Laboratorio de Dendrocronología Facultad de Ciencias Agrícolas Universidad Autónoma Gabriel René Moreno, Km 9 carretera al Norte, El Vallecito Thünen Institute of Forest Genetics, Sieker Landstrasse 2 Instituto de Investigaciones de la Amazonía Peruana (IIAP), Av. José A. Quiñones km 2.5 Instituto Florestal de São Paulo, CP 1322 Faculdade de Engenharia Universidade Estadual Paulista (Unesp) INRA UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane, Campus Agronomique, Avenue de France Centre for Ecology & Hydrology Edinburgh, Bush Estate Faculdade de Engenharia Universidade Estadual Paulista (Unesp)

RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four Populus species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species. In total, 355 RNA editing sites were identified with high confidence, their editing extents ranging from 10 to 100%. The most heavily edited transcripts were ccmB with the highest density of RNA editing sites (53.7 sites / kb) and ccmFn with the highest number of sites (39 sites). Most of the editing events are at position 1 or 2 of the codons, usually altering the encoded amino acid, and are highly conserved among the species, also with regard to their editing extent. However, one SNP was found in the newly sequenced and annotated mitochondrial genome of P. alba resulting in the loss of an RNA editing site compared to P. tremula and P. davidiana. This SNP causes a C-to-T transition and an amino acid exchange from Ser to Phe, highlighting the widely discussed role of RNA editing in compensating mutations.

The timber of the species Lophira alata (azobe) is very popular for outdoor constructions, which favours its overexploitation and illegal logging. We sampled individuals from Liberia, Ivory Coast, Ghana, Nigeria, Cameroon, Gabon, Congo Brazzaville and Republic Democratic of Congo to discover new nuclear and plastidial SNP and INDEL loci through restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. From an initial set of 397 loci, a final set of 126 loci was selected for timber tracking purposes., SCOPUS: ar.j, info:eu-repo/semantics/published

European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for Fagus, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus Fagus in DNA samples from tree tissues or wood products, including wood composite products.

Made available in DSpace on 2021-06-25T12:22:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-06-01 German Federal Ministry of Food and Agriculture (BMEL) by the LargeScale-project (Forderkennzeichen) Programa Nacional de Innovacion para la Competitividad y Productividad (Innovate Peru) Conseil Regional d'Aquitaine European Union, FEDER Investissements d'avenir Dipteryx timber has been heavily exploited in South America since 2000s due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to 6 different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial single nucleotide polymorphisms (SNPs), and 2 chloroplast and 5 mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78-96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in Dipteryx odorata and Dipteryx ferrea, obtaining self-assignment success rates of 91-100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbor approach (69-92%) compared to the Bayesian approach (33-80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber. Inst Invest Amazonia Peruana IIAP, Av Jose A Quinones Km 2-5, Iquitos, Peru Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745,EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRAE, BIOGECO, F-33610 Cestas, France Escola Nacl Bot Trop, Rua Pacheco Leao 2040, BR-22460030 Rio De Janeiro, RJ, Brazil Inst Pesquisas Jardim Bot Rio de Janeiro, Rua Pacheco Leao 915, BR-22460030 Rio De Janeiro, RJ, Brazil Univ Fed Bahia, Inst Biol, Rua Barao de Jeremoabo S-N, BR-40170115 Salvador, BA, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil German Federal Ministry of Food and Agriculture (BMEL) by the LargeScale-project (Forderkennzeichen): 281-001-01 Programa Nacional de Innovacion para la Competitividad y Productividad (Innovate Peru): 381-PNICP-PIAP-2014 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

There is a high international demand for timber from the genus Dipteryx, or “shihuahuaco” as it is known in Peru. Developing tools that allow the identification and discrimination of Dipteryx species is therefore important for supporting management of natural populations and to underpin legal trade of its timber. The objective of this study was the molecular characterization of Dipteryx species in the Peruvian Amazonia. Two plastid regions (cpDNA: trnH–psbA and matK) were sequenced and 11 microsatellite markers (nDNA) were genotyped for 32 individuals identified as Dipteryx charapilla, D. micrantha morphotype 1 and D. micrantha morphotype 2. Using the concatenated sequences of the plastid genes, we identified ten haplotypes that were not shared between the species or between the D. micrantha morphotypes. Haplotypic diversity was greater in D. micrantha morphotype 2 and D. charapilla than in D. micrantha morphotype 1, which presented only one haplotype with a wide distribution in Peru. The microsatellites allowed the discrimination of the same three clades and identified diagnostic alleles for each clade. These results allowed us to demonstrate that the two morphotypes of D. micrantha are different at both the plastid and nuclear markers, which supports the existence of three genetically distinct species in Peru. This study provides information for the genetic discrimination of Dipteryx species and emphasises the importance of conserving the genetic variability of this genus in the Peruvian Amazonia. Programa Nacional de Innovación para la Competitividad y Productividad Innóvate-Perú (contrato 381-PNICP-PIAP-2014); German Federal Ministry of Food and Agriculture (BMEL, Large Scale Project, Grant 28I-001-01) Revisión por pares.

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.

Made available in DSpace on 2019-10-04T12:40:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture (BMEL) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest European Union, FEDER We developed nuclear and chloroplastic single nucleotide polymorphism (SNP) and INDEL (insertion/deletion) markers using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing to set up a genetic tracking method of the geographical origin of Hymenaea sp. From two initial sets of 358 and 32 loci used to genotype at least 94 individuals, a final set of 75 nSNPs, 50 cpSNPs and 6 INDELs identifying significant population structure was developed. Univ Sao Paulo, Luiz de Queiroz Coll Agr, Dept Forest Sci, Ave Padua Dias,11,POB 9, BR-13418900 Sao Paulo, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia IIAP, LBGM, Ave Jose A Quinones Km 2-5, Iquitos, Peru Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRA, BIOGECO, 69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Dept Fitotecnia, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Univ Estadual Paulista, Dept Fitotecnia, Fac Engn Ilha Solteira, Ilha Solteira, SP, Brazil Investissements d'Avenir, Convention attributive d'aide EquipEx Xyloforest: ANR-10-EQPX-16-01 European Union, FEDER: ANR-10-EQPX-16-01 European Union, FEDER: 2003227 European Union, FEDER: ANR-10-LABX-25-01

Made available in DSpace on 2019-10-04T12:40:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture Conseil Regional d'Aquitaine European Union FEDER Investissements d'avenir Nuclear and plastidial single nucleotide polymorphism (SNP) and INDEL markers were developed using restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing for population genetics and timber tracking purposes in the Neotropical timber species Jacaranda copaia. We used 407 nuclear SNPs, 29 chloroplast, and 31 mitochondrial loci to genotype 92 individuals from Brazil, Bolivia, French Guiana, and Peru. Based on high amplification rates and genetic differentiation among populations, 113 nuclear SNPs, 11 chloroplast, and 4 mitochondrial loci were selected, and their use validated for genetic tracking of timber origin. Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia IIAP, Ave Jose A Quinones Km 2-5, Iquitos, Peru Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France Univ Bordeaux, INRA, BIOGECO, F-33610 Cestas, France Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA FEDER: 2003227 Investissements d'avenir: ANR-10-EQPX-16-01 Investissements d'avenir: CEBA: ANR-10-LABX-25-01 : 001-2016-SERFOR-DGGSPFFS-DGSPF

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

Made available in DSpace on 2019-10-04T12:40:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-01 German Federal Ministry of Food and Agriculture (BMEL) Programa Nacional de Innovacion para la Competitividad y Productividad Conseil Regional d'Aquitaine European Union, FEDER We developed nuclear and plastid single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) markers for Dipteryx species using a combination of restriction associated DNA sequencing (RADSeq) and low coverage MiSeq genome sequencing. Of the total 315 loci genotyped using a MassARRAY platform, 292 loci were variable and polymorphic among the 73 sampled individuals from French Guiana, Brasil, Peru, and Bolivia. A final set of 56 nuclear SNPs, 26 chloroplast SNPs, 2 chloroplast INDELs, and 32 mitochondrial SNPs identifying significant population structure was developed. This set of loci will be useful for studies on population genetics of Dipteryx species in Amazonia. IIAP, Ave Jose A Quinones Km 2-5, Iquitos, Peru Thunen Inst Forest Genet, Sieker Landstr 2, D-22927 Grosshansdorf, Germany Inst Florestal Sao Paulo, CP 1322, BR-01059970 Sao Paulo, SP, Brazil Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Univ Autonoma Gabriel Rene Moreno, Fac Ciencias Agr, Lab Dendrocronol, Carrera Ingn Forestal, Km 9 Carretera Norte, El Vallecito, Santa Cruz, Bolivia Univ Guyane, Univ Antilles, CNRS, INRA,UMR0745 EcoFoG,AgroParisTech,Cirad, Campus Agron,Ave France,BP97387, Kourou, France INRA, Plateforme Genome Transcriptome Bordeaux, Site Pierroton Batiment Artiga,69 Route Arcachon, F-33610 Cestas, France Univ Estadual Paulista, Fac Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, SP, Brazil Programa Nacional de Innovacion para la Competitividad y Productividad: 381-PNICP-PIAP-2014 Conseil Regional d'Aquitaine: 20030304002FA Conseil Regional d'Aquitaine: 20040305003FA European Union, FEDER: 2003227 European Union, FEDER: ANR-10-EQPX-16-01 European Union, FEDER: ANR-10-LABX-25-01

100 SNP and one Indel markers were developed for Khaya using a combination of restriction associated DNA sequencing and low coverage MiSeq genome sequencing. The marker set was successfully used to genotype a set of 1919 individuals, representing 5 Khaya species from 18 African countries, using MassARRAY®iPLEX™ genotyping.

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; Deforestation-reinforced by illegal logging-is a serious problem in many tropical regions and causes pervasive environmental and economic damage. Existing laws that intend to reduce illegal logging need efficient, fraud resistant control methods. We developed a genetic reference database for Jatoba (Hymenaea courbaril), an important, high value timber species from the Neotropics. The data set can be used for controls on declarations of wood origin. Samples from 308 Hymenaea trees from 12 locations in Brazil, Bolivia, Peru, and French Guiana have been collected and genotyped on 10 nuclear microsatellites (nSSRs), 13 chloroplast SNPs (cpSNP), and 1 chloroplast indel marker. The chloroplast gene markers have been developed using Illumina DNA sequencing. Bayesian cluster analysis divided the individuals based on the nSSRs into 8 genetic groups. Using self-assignment tests, the power of the genetic reference database to judge on declarations on the location has been tested for 3 different assignment methods. We observed a strong genetic differentiation among locations leading to high and reliable self-assignment rates for the locations between 50% to 100% (average of 88%). Although all 3 assignment methods came up with similar mean self-assignment rates, there were differences for some locations linked to the level of genetic diversity, differentiation, and heterozygosity. Our results show that the nuclear and chloroplast gene markers are effective to be used for a genetic certification system and can provide national and international authorities with a robust tool to confirm legality of timber.

The European beech (Fagus sylvatica) is one of the most important and widespread tree species in Central Europe and is widely managed for its valuable hard wood. We assembled and characterized the ...

// Martina Kluth 1, * , Simon Jung 1, * , Omar Habib 1 , Mina Eshagzaiy 1 , Anna Heinl 1 , Nina Amschler 1 , Sawinee Masser 1 , Malte Mader 1 , Frederic Runte 1 , Philipp Barow 1 , Sohall Frogh 1 , Jazan Omari 1 , Christina Moller-Koop 1 , Claudia Hube-Magg 1 , Joachim Weischenfeldt 2 , Jan Korbel 2 , Stefan Steurer 1 , Till Krech 1 , Hartwig Huland 3 , Markus Graefen 3 , Sarah Minner 1 , Guido Sauter 1 , Thorsten Schlomm 3, 4 and Ronald Simon 1 1 Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 2 Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany 3 Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany 4 Department of Urology, Section for Translational Prostate Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany * These authors have contributed equally to this work Correspondence to: Ronald Simon, email: r.simon@uke.de Keywords: prostate cancer; deletion lengthening; 6q; 16q; tissue microarray Received: September 11, 2017 Accepted: September 16, 2017 Published: November 11, 2017 ABSTRACT Prostate cancer is characterized by recurrent deletions that can considerably vary in size. We hypothesized that large deletions develop from small deletions and that this “deletion lengthening” might have a “per se” carcinogenic role through a combinatorial effect of multiple down regulated genes. In vitro knockdown of 37 genes located inside the 6q12-q22 deletion region identified 4 genes with additive tumor suppressive effects, further supporting a role of the deletion size for cancer aggressiveness. Employing fluorescence in-situ hybridization analysis on prostate cancer tissue microarrays, we determined the deletion size at 6q and 16q in more than 3,000 tumors. 16q and 6q deletion length was strongly linked to poor clinical outcome and this effect was even stronger if the length of both deletions was combined. To study deletion lengthening in cancer progression we eventually analyzed the entire cancers from 317 patients for 6q and 16q deletion length heterogeneity and found that the deletion expanded within 50-60% of 6q and 16q deleted cancers. Taken together, these data suggest continuous “deletion lengthening” as a key mechanism for prostate cancer progression leading to parallel down regulation of genes with tumor suppressive properties, some of which act cooperatively.

Deletion of 3p13 has been reported from about 20% of prostate cancers. The clinical significance of this alteration and the tumour suppressor gene(s) driving the deletion remain to be identified. We have mapped the 3p13 deletion locus using SNP array analysis and performed fluorescence in situ hybridization (FISH) analysis to search for associations between 3p13 deletion, prostate cancer phenotype and patient prognosis in a tissue microarray containing more than 3200 prostate cancers. SNP array analysis of 72 prostate cancers revealed a small deletion at 3p13 in 14 (19%) of the tumours, including the putative tumour suppressors FOXP1, RYBP and SHQ1. FISH analysis using FOXP1-specific probes revealed deletions in 16.5% and translocations in 1.2% of 1828 interpretable cancers. 3p13 deletions were linked to adverse features of prostate cancer, including advanced stage (p < 0.0001), high Gleason grade (p = 0.0125), and early PSA recurrence (p = 0.0015). In addition, 3p13 deletions were linked to ERG+ cancers and to PTEN deletions (p < 0.0001 each). A subset analysis of ERG+ tumours revealed that 3p13 deletions occurred independently from PTEN deletions (p = 0.3126), identifying tumours with 3p13 deletion as a distinct molecular subset of ERG+ cancers. mRNA expression analysis confirmed that all 3p13 genes were down regulated by the deletion. Ectopic over-expression of FOXP1, RYBP and SHQ1 resulted in decreased colony-formation capabilities, corroborating a tumour suppressor function for all three genes. In summary, our data show that deletion of 3p13 defines a distinct and aggressive molecular subset of ERG+ prostate cancers, which is possibly driven by inactivation of multiple tumour suppressors. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

SummaryEarly-onset prostate cancer (EO-PCA) represents the earliest clinical manifestation of prostate cancer. To compare the genomic alteration landscapes of EO-PCA with “classical” (elderly-onset) PCA, we performed deep sequencing-based genomics analyses in 11 tumors diagnosed at young age, and pursued comparative assessments with seven elderly-onset PCA genomes. Remarkable age-related differences in structural rearrangement (SR) formation became evident, suggesting distinct disease pathomechanisms. Whereas EO-PCAs harbored a prevalence of balanced SRs, with a specific abundance of androgen-regulated ETS gene fusions including TMPRSS2:ERG, elderly-onset PCAs displayed primarily non-androgen-associated SRs. Data from a validation cohort of > 10,000 patients showed age-dependent androgen receptor levels and a prevalence of SRs affecting androgen-regulated genes, further substantiating the activity of a characteristic “androgen-type” pathomechanism in EO-PCA.

To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for insertion/deletion (indel) polymorphisms to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indel and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.

The phosphatase and tensin homolog deleted on chromosome 10 (PTEN) gene is often altered in prostate cancer. To determine the prevalence and clinical significance of the different mechanisms of PTEN inactivation, we analyzed PTEN deletions in TMAs containing 4699 hormone-naïve and 57 hormone-refractory prostate cancers using fluorescence in situ hybridization analysis. PTEN mutations and methylation were analyzed in subsets of 149 and 34 tumors, respectively. PTEN deletions were present in 20.2% (458/2266) of prostate cancers, including 8.1% heterozygous and 12.1% homozygous deletions, and were linked to advanced tumor stage (P0.0001), high Gleason grade (P0.0001), presence of lymph node metastasis (P = 0.0002), hormone-refractory disease (P0.0001), presence of ERG gene fusion (P0.0001), and nuclear p53 accumulation (P0.0001). PTEN deletions were also associated with early prostate-specific antigen recurrence in univariate (P0.0001) and multivariate (P = 0.0158) analyses. The prognostic impact of PTEN deletion was seen in both ERG fusion-positive and ERG fusion-negative tumors. PTEN mutations were found in 4 (12.9%) of 31 cancers with heterozygous PTEN deletions but in only 1 (2%) of 59 cancers without PTEN deletion (P = 0.027). Aberrant PTEN promoter methylation was not detected in 34 tumors. The results of this study demonstrate that biallelic PTEN inactivation, by either homozygous deletion or deletion of one allele and mutation of the other, occurs in most PTEN-defective cancers and characterizes a particularly aggressive subset of metastatic and hormone-refractory prostate cancers.

The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously published Azadirachta indica plastome. The five plastomes are circular and exhibit a quadripartite structure with high conservation of gene content and order. They include 130 genes encoding 85 proteins, 37 tRNAs and 8 rRNAs. Inverted repeat expansion resulted in a duplication of rps19 in the five Meliaceae species, which is consistent with that in many other Sapindales, but different from many other rosids. Compared to Azadirachta indica, the four newly sequenced Meliaceae individuals share several large deletions, which mainly contribute to the decreased genome sizes. A whole-plastome phylogeny supports previous findings that the four species form a monophyletic sister clade to Azadirachta indica within the Meliaceae. SNPs and indels identified in all complete Meliaceae plastomes might be suitable targets for the future development of genetic markers at different taxonomic levels. The extended analysis of SNPs in the matK gene led to the identification of four potential Meliaceae-specific SNPs as a basis for future validation and marker development.

A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events. We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. A powerful search interface and a fast visualization engine provide a highly interactive visualization for such data. High quality image export enables the life scientist to easily communicate their results. A comprehensive data administration allows to keep track of the available data sets. We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before. The interactive nature of FISH Oracle 2 and the possibility to store, select and visualize large amounts of downstream processed data support life scientists in generating hypotheses. The export of high quality images supports explanatory data visualization, simplifying the communication of new biological findings. A FISH Oracle 2 demo server and the software is available at http://www.zbh.uni-hamburg.de/fishoracle .

Deletions involving the chromosomal band 5q21 are among the most frequent alterations in prostate cancer. Using single-nucleotide polymorphism (SNP) arrays, we mapped a 1.3 megabase minimally deleted region including only the repulsive guidance molecule B (RGMB) and chromodomain helicase DNA-binding protein 1 (CHD1) genes. Functional analyses showed that CHD1 is an essential tumor suppressor. FISH analysis of 2,093 prostate cancers revealed a strong association between CHD1 deletion, prostate-specific antigen (PSA) biochemical failure (P = 0.0038), and absence of ERG fusion (P < 0.0001). We found that inactivation of CHD1 in vitro prevents formation of ERG rearrangements due to impairment of androgen receptor (AR)-dependent transcription, a prerequisite for ERG translocation. CHD1 is required for efficient recruitment of AR to responsive promoters and regulates expression of known AR-responsive tumor suppressor genes, including NKX3-1, FOXO1, and PPARγ. Our study establishes CHD1 as the 5q21 tumor suppressor gene in prostate cancer and shows a key role of this chromatin remodeling factor in prostate cancer biology. Cancer Res; 73(9); 2795–805. ©2013 AACR.

Deletion of 3p13 has been reported from about 20% of prostate cancers. The clinical significance of this alteration and the tumour suppressor gene(s) driving the deletion remain to be identified. We have mapped the 3p13 deletion locus using SNP array analysis and performed fluorescence in situ hybridization (FISH) analysis to search for associations between 3p13 deletion, prostate cancer phenotype and patient prognosis in a tissue microarray containing more than 3200 prostate cancers. SNP array analysis of 72 prostate cancers revealed a small deletion at 3p13 in 14 (19%) of the tumours, including the putative tumour suppressors FOXP1, RYBP and SHQ1. FISH analysis using FOXP1-specific probes revealed deletions in 16.5% and translocations in 1.2% of 1828 interpretable cancers. 3p13 deletions were linked to adverse features of prostate cancer, including advanced stage (p0.0001), high Gleason grade (p = 0.0125), and early PSA recurrence (p = 0.0015). In addition, 3p13 deletions were linked to ERG(+) cancers and to PTEN deletions (p0.0001 each). A subset analysis of ERG(+) tumours revealed that 3p13 deletions occurred independently from PTEN deletions (p = 0.3126), identifying tumours with 3p13 deletion as a distinct molecular subset of ERG(+) cancers. mRNA expression analysis confirmed that all 3p13 genes were down regulated by the deletion. Ectopic over-expression of FOXP1, RYBP and SHQ1 resulted in decreased colony-formation capabilities, corroborating a tumour suppressor function for all three genes. In summary, our data show that deletion of 3p13 defines a distinct and aggressive molecular subset of ERG(+) prostate cancers, which is possibly driven by inactivation of multiple tumour suppressors.