Birgit Kersten

Thünen Institute | vTI · Institute of Forest Genetics

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 Pop...

Next-generation sequencing (NGS) approaches are attractive alternatives to the PCR-based characterisation of genetically modified plants for safety assessment and labelling since NGS is highly sensitive to the detection of T-DNA inserts as well as vector backbone sequences in transgenic plants. In this study, two independent transgenic male Populus...

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 duplicat...

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 se...

The diversity of inflorescences among flowering plants is captivating. Such charm is not only due to the variety of sizes, shapes, colors, and flowers displayed, but also to the range of reproductive systems. For instance, hermaphrodites occur abundantly throughout the plant kingdom with both stamens and carpels within the same flower. Nevertheless...

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 m...

Key message Cosexual Populus ×canescens plants are inconstant females with life course plasticity of sex phenotype and can reproduce by selfing. Abstract Populus species are dioecious, but deviations from dioecy are reported in some cases. The objectives of this study were to investigate the phenotypic expression and the inheritance of subdioecy i...

Table 4 in the original publication reports incomplete genotype names in the column "Cross" and wrong codes in the column "Generation".

Genetische Vielfalt ist eine wesentliche Grundlage von Waldbaumpopulationen, um sich an Veränderungen der Umweltbedingungen aus eigener Kraft anzupassen. Deshalb sind für die Baumart Buche deutschlandweit insgesamt 14 Monitoringflächen eingerichtet worden, auf denen sowohl der Zustand als auch die räumlichen und zeitlichen Veränderungen genetischer...

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translate...

Background: Herbivorous insects can have a profound impact on plant growth performance. In some years, canopy damage in poplar plantations exceeds 50% of the total leaf surface, thereby possibly compromising carbon fixation and biomass yield. To assess the transcriptional response of elite poplar clones to insect feeding and to test whether this re...

The Swiss pine (Pinus cembra) is a montane tree in Central Europe and, therefore, known for its hardiness against severe winter colds. The seeds are harvested and eaten as pine nuts. We assembled and characterized the complete chloroplast genome of P. cembra to serve as a valuable resource in future genetic studies. The complete plastome sequence i...

Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to env...

Key message Even though “supermale” (YY) poplar individuals are rarely found in natural populations or breeding collections, they can arise and can be as viable as regular male and female plants. Abstract Nearly all species of the genus Populus are dioecious, i.e., form male and female flowers on separate individuals. However, bisexual poplar can...

Main conclusion Poplar trees displayed an increased plant height due to the transgenic knockdown of PCBER1, a gene of lignan biosynthesis. The wood composition was slightly altered in both overexpression and knockdown lines. The gene PHENYLCOUMARAN BENZYLIC ETHER REDUCTASE1 (PCBER1) is well known as an important gene in the synthesis of lignans, a...

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 complete chloroplast genome of F. sylvatica to serve as a valuable resource in future genetic studies. The complete plastome sequence is 158,462 bp in le...

We developed a new set of 25 nuclear (nc), 12 chloroplast (cp) and 7 mitochondrial (mt) SNPs and used it to genotype 371 Mongolian oak ( Quercus mongolica Fisch. ex Ledeb.) trees from seven locations in a 200 km by 400 km area in the Russian Far East. One of the locations in an area of 15 km by 25 km east of the city Ussuriusk was analyzed more int...

The verification of the geographical origin of timber is of increasing importance with the entry into force of new regulations having become effective (EU Timber Regulation, US Lacey Act and Australia Illegal Logging Prohibition Act) that regulate the trade of timber. Larch timber represents a significant portion of timber traded on the European ma...

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 publishedAzadirachta indicaplastome. The five plastomes are circular and exhibit a quadripartite structure with high c...

Within the genus Populus, about 30 species are classified into six sections, of which some are cross-compatible. Besides naturally occurring hybrids, huge breeding programs have led to a high number of artificially produced hybrids, for which the determination of genetically involved species by morphological characteristics is often difficult. This...

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 screene...

Key words: next generation sequencing (NGS), genome skimming, SNPs, InDels, marker assisted selection The rapid development of NGS technologies and bioinformatic tools has paved the way for the assembly of complete genome sequences which may serve as references for the efficient development of molecular markers for different traits or the determin...

Key message: This review gives a comprehensive overview on the genomics of sex determination in dioecious woody plants and plants with a tree-like habitus, in particular considering species where sex-linked regions and/or markers have been identified. Abstract: Dioecious plant species are characterized by unisexual flowers located on separate male...

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 sel...

Populus trichocarpa and P. deltoides are the only Populus species known to date to have a publicly available nuclear genome sequence that has been assembled to chromosomes and annotated (https://phytozome.jgi.doe.gov/). Here we focus on the clone INRA 717-1B4, a female P. tremula x P. alba (P. x canescens) interspecific hybrid that is universally u...

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. mon...

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.

182 SNP markers were developed for Ayous (Triplochiton scleroxylon K. Schum) by incorporating information from two next generation sequencing approaches (RADseq Floragenex and AFLPseq IonTorrent PGM) into a single genotyping panel for MassARRAY® iPLEX™. This set of markers was successfully used to genotype 753 individuals from 43 populations in fiv...

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. mon...

Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organizatio...

Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organizatio...

Different species of the genus Eucalyptus, originally native to Australia, are being cultivated in different parts of the world due to their fast growth and beneficial wood properties. In Mexico, probably up to 25 different Eucalyptus species (many of them with unknown species declaration) were introduced early in the 20th century. Many Eucalyptus...

Key message We aim to develop, for the first time, poplar species-specific mitochondrial SNP markers which can be employed as diagnostic tool, e.g., to identify mitochondria belonging to different poplar species used in protoplast fusion experiments and for population genetics approaches. Abstract In most higher plant species, the inheritance of...

The genus Populus features a genetically controlled sex determination system, located on chromosome 19. However, different Populus species vary in the position of the sex-linked region on the respective chromosome and the apparent heterogametic sex, and the precise mechanism of sex determination in Populus is still unknown. Using next generation se...

Early view: http://onlinelibrary.wiley.com/doi/10.1111/plb.12048/pdf In the dioecious genus Populus, sex determination has been located to chromosome 19. However, despite a high degree of genome collinearity, various Populus species seem to differ with regard to the location of the sex-determining region on the respective chromosome and the appare...

The interaction between insect pests and their host plants is a never-ending race of evolutionary adaption. Plants have developed an armament against insect herbivore attacks, and attackers continuously learn how to address it. Using a combined transcriptomic and metabolomic approach, we investigated the molecular and biochemical differences betwee...

Auf den ersten Blick erschien die Mitteilung, die am 22. Mai 2013 veröffentlicht wurde, nichts Aufregendes zu beinhalten: der Wissenschaftswelt wurde die Veröffentlichung des kompletten Erbguts (Genom) einer weiteren Pflanzenart bekanntgegeben [1]. Nach der Entschlüsselung des Genoms der Ackerschmalwand (Arabidopsis thaliana) im Jahr 20002 als erst...

GabiPD is an integrative plant "omics" database that has been established as part of the German initiative for Genome Analysis of the Plant Biological System (GABI). Data from different "omics" disciplines are integrated and interactively visualized. Proteomics is represented by data and tools aiding studies on the identification of post-translatio...

Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). Understanding the molecular basis of resistance and susceptibility to late blight is therefore highly relevant for developing resistant cultivars, either by marker-assissted selection or by transgenic approaches. Specific P. infe...

Summary The mechanism of sex determination in Populus is still an open question. In the sequenced female P. trichocarpa, sex determination was located to the telomeric region of chromosome XIX. We mapped sex-linked SSR and SNP markers to a central position on the respective linkage group in a male P. tremuloides clone and localised a recombination...

Eichen waren im Laufe ihrer Evolutionsgeschichte vielfach drastischen und schnellen Umweltveränderungen ausgesetzt. Ihre Demographie während des Pleistozäns war geprägt durch wiederkehrende Zyklen von Fragmentierung und Verlagerung des Verbreitungsgebiets, Populationsreduktion und anschließender Expansion. Dennoch sind diese besonders langlebigen O...

Every multicellular organism consists of numerous organs, tissues and specific cell types. To gain detailed knowledge about the morphogenesis of these complex structures, it is inevitable to advance biochemical analyses to ultimate spatial and temporal resolution since individual cell types contribute differently to the overall performance of livin...

Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be...

The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 famil...

The PhosPhAt database of Arabidopsis phosphorylation sites was initially launched in August 2007. Since then, along with 10-fold increase in database entries, functionality of PhosPhAt (phosphat.mpimp-golm.mpg.de) has been considerably upgraded and re-designed. PhosPhAt is now more of a web application with the inclusion of advanced search function...

Rice Oryza sativa accelerated cell death and resistance 1 (OsACDR1) encodes a putative Raf-like mitogen-activated protein kinase kinase kinase (MAPKKK). We had previously reported upregulation of the OsACDR1 transcript by a range of environmental stimuli involved in eliciting defense-related pathways. Here we apply biochemical, gain and loss-of-fun...

In: Walker JM, ed, The protein protocols handbook. 3rd edition, Springer, Berlin, Heidelberg, New York.

GabiPD ("http://www.gabipd.org/":http://www.gabipd.org/) at the Max Planck Institute of Molecular Plant Physiology constitutes a repository and analysis platform of genomic, transcriptomic, proteomic, and metabolomic plant data provided by the GABI community (Riaño-Pachón et al., 2009). Beside the data, current versions of useful tools are being ma...

Phosphoproteomics involves identification of phosphoproteins, precise mapping, and quantification of phosphorylation sites, and eventually, revealing their biological function. In plants, several systematic phosphoproteomic analyses have recently been performed to optimize in vitro and in vivo technologies to reveal components of the phosphoproteom...

The oomycete Phytophthora infestans causes late blight, the most relevant disease of potato (Solanum tuberosum) worldwide. Field resistance to late blight is a complex trait. When potatoes are cultivated under long day conditions in temperate climates, this resistance is correlated with late plant maturity, an undesirable characteristic. Identifica...

Posttranslational modification of proteins by phosphorylation is the most abundant type of cellular regulation which affects essentially every intracellular process of eukaryotes. Phosphorylation of a protein can cause changes in its structure, stability, enzymatic activity, the ability to interact with other molecules, or its subcellular localizat...

The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array...

GabiPD ("http://gabi.rzpd.de":http://gabi.rzpd.de) was established within GABI-I and further developed in GABI-II and constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high throughput experiments developed by members of the GABI/WPG community. Currently, data from different fronts (genomics, transcri...

The GABI Primary Database, GabiPD, was established eight years ago in the frame of the German initiative for Genome Analysis of the Plant Biological System (Genomanalyse im biologischen System Pflanze, GABI), funded by the German Federal Ministry of Education, Research and Technology (BMBF) as well as a number of private enterprise companies. The m...

Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (Solanum tuberosum). Potat...

33.1 INTRODUCTION AND BRIEF BIBLIOGRAPHIC REVIEW: Reverse protein phosphorylation is a highly conserved mechanism for post-translational regulation of protein function, which has been found in all prokaryotes and eukaryotes examined (see also Chapter 29). Phosphorylation is mediated by protein kinases, which transfer the γ-phosphate of ATP on amino...

3.1.1 Einführung Das Wort Proteom wurde im September 1994 von Mark Wilkins eingeführt (Wilkins et al. 1996) und bezeichnet das gesamte Proteinkomplement, das von einem Genom exprimiert und nach der Expression modifiziert werden kann. Unter Proteomik („proteomics“) versteht man die systematische Untersuchung der Proteine eines Organismus, eines Gew...

The application of proteomics methods, such as the protein microarray technology, in plant science has been strongly supported by the completion of genome sequencing projects of Arabidopsis thaliana and rice. In this chapter we describe a method to generate plant protein microarrays and to use them for characterizing monoclonal antibodies or polycl...

Identifying protein kinase substrates is one major focus of protein kinase research and supports the elucidation of signal transduction pathways and their complex regulation. In this chapter we describe a protein microarray-based in vitro method, which permits a systematic screening of immobilized proteins for their phosphorylation by specific prot...

Proteomic approaches, such as protein microarray technology, play an important role in the study of complex biological systems. Their application in plant science has been strongly supported by the completion of genome sequence projects in the model plants Arabidopsis thaliana and rice. This chapter focuses on the identification of substrate phosph...

Phosphoproteomics can be defined as the comprehensive study of protein phosphorylation by identification of the phosphoproteins, exact mapping of the phosphorylation sites, quantification of phosphorylation, and eventually, revealing their biological function. Its place in today's research is vitally important to address the most fundamental questi...

Proteins mediate their biological function through interactions with other proteins. Therefore, the systematic identification and characterization of protein-protein interactions have become a powerful proteomic strategy to understand protein function and comprehensive cellular regulatory networks. For the screening of valosin-containing protein, c...

Definition: Proteomics is the large-scale systematic study of the proteins of an organism, a specific type of tissue or a cell, using biochemical, cell biological and genetic methods (2, 62). The word proteomics has traditionally been used to describe the separation of proteins prepared from tissues and cell lines by ▶twodimensional (2D) polyacryl...

Mitogen-activated protein kinase (MAPK) cascades are universal and highly conserved signal transduction modules in eucaryotes, including plants. These protein phosphorylation cascades link extracellular stimuli to a wide range of cellular responses. However, the underlying mechanisms are so far unknown as information about phosphorylation substrate...

The success of genome sequencing projects has provided the basis for systematic analysis of protein function and has led to a shift from the description of single molecules to the characterization of complex samples. Such a task would not be possible without the provision of appropriate high-throughput technologies, such as protein microarray techn...

Microarray technology plays an increasing role in proteomic research. We give an overview about recent developments in this technology focusing on molecular interaction studies using protein and antibody microarrays. We report about technical aspects in the development of protein microarrays and describe different surfaces and detection modes. Furt...

To gain insights into complex biological processes, such as transcription and replication, the analysis of protein-DNA interactions and the determination of their sequence requirements are of central importance. In this study, we probed protein microarray technology and ultraviolet crosslinking combined with mass spectrometry (MS) for their practic...

We have successfully established a novel protein microarray-based kinase assay, which we applied to identify target proteins of the barley protein kinase CK2alpha. As a source of recombinant barley proteins we cloned cDNAs specific for filial tissues of developing barley seeds into an E. coli expression vector. By using robot technology, 21,500 lib...

Proteomic approaches play an important role in the study of complex biological systems. The application of proteomic technologies in plant science has been strongly supported by the completion of genome sequence projects of the model plants Arabidopsis thaliana and rice. This review focuses on the state of proteomic technologies with special emphas...

Protein array technology has emerged as a new tool to enable ordered screening of proteins for expression and molecular interactions in high throughput. Besides classical solid-phase substrates, such as micro-titre plates and membrane filters, protein arrays have recently been devised with chip-sized supports. Several applications on protein chips...

Large-scale approaches increasingly gain a decisive role in the study of biological systems, which are per se highly complex. Therefore, they have to be investigated by extensive methods to receive information about the large genomic and proteomic networks. In plant biology, this purpose has a strong support through the accessibility of the complet...