Papers by Alexander Wittenberg
Genome content and characteristics of 41 transposable element families in C. higginsianum. (PDF 5... more Genome content and characteristics of 41 transposable element families in C. higginsianum. (PDF 521 kb)
Size distribution of Simple Sequence Repeats (SSR) in the C. higginsianum genome. (PDF 245 kb)
List of the secondary metabolism key genes and their catalytic domains. (PDF 132 kb)
(A) Gene category predictions and transcriptomic analysis by RNA-Seq of four developmental stages... more (A) Gene category predictions and transcriptomic analysis by RNA-Seq of four developmental stages of C. higginsianum. VA: appressoria in vitro, PA: appressoria in planta, BP: biotrophic phase, NP: necrotrophic phase. (B) Annotation of secondary metabolism key genes and clusters. (XLSX 4943 kb)
Characteristics and contents of the 12 largest unitigs in the new genome assembly, corresponding ... more Characteristics and contents of the 12 largest unitigs in the new genome assembly, corresponding to the 12 chromosomes of C. higginsianum. (PDF 129 kb)
Summary of unitigs comprising the C. higginsianum assembly. (PDF 91 kb)
List of all PKS and PKS-NRPS protein sequences used in the phylogenetic analysis. (XLSX 19 kb)
Genbank accession numbers of Colletotrichum transposon sequences used in the REPET annotation pip... more Genbank accession numbers of Colletotrichum transposon sequences used in the REPET annotation pipeline. (PDF 81 kb)
Gene content of six segmental duplications identified in the C. higginsianum genome assembly and ... more Gene content of six segmental duplications identified in the C. higginsianum genome assembly and polymorphisms between the duplicated genes. (PDF 319 kb)
Characteristics of six segmental duplications identified in the C. higginsianum genome assembly. ... more Characteristics of six segmental duplications identified in the C. higginsianum genome assembly. (PDF 257 kb)
Genomic locations of TE copies from clusters 2 and 3 showing extreme expression profiles. (PDF 22... more Genomic locations of TE copies from clusters 2 and 3 showing extreme expression profiles. (PDF 222 kb)
Stage-specific expression of C. higginsianum transposable elements (TEs). (A) Heatmap showing the... more Stage-specific expression of C. higginsianum transposable elements (TEs). (A) Heatmap showing the expression profiles of TEs. (B) K-means clustering of 441 TE copies considered to be expressed in at least one fungal stage (VA = in vitro appressoria, PA = in planta appressoria, BP = biotrophic phase). For each of the five clusters, the average profile is shown in red. (C) Localization of in planta-expressed LTR transposon fragments in the 3' UTR regions of C. higginsianum effector genes. IGV screenshots showing the genomic locations of TE copies RXX_R113 and RLX_P25.13 (red) in relation to effector genes ChEC35 and ChEC117 (green), respectively. RNA-Seq reads are displayed for appressoria in vitro (VA) and the biotrophic phase (BP). The RLX_P25.13 copy comprises a 'solo'-LTR, likely produced by homologous recombination between two LTRs, leading to deletion of the internal retrotransposon sequence. (PDF 2850 kb)
Schematic representation of the 77 secondary metabolism gene clusters of C. higginsianum. (PDF 37... more Schematic representation of the 77 secondary metabolism gene clusters of C. higginsianum. (PDF 374 kb)
Genomics, 2021
Background Cherries are stone fruits and belong to the economically important plant family of Ros... more Background Cherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall. is one ancestor of cultivated sour cherry, an important tetraploid cherry species. Here, we present a long read chromosome-level draft genome assembly and related plastid sequences using the Oxford Nanopore Technology PromethION platform and R10.3 pore type. Finding The final assemblies obtained from 117.3 Gb cleaned reads representing 97x coverage of expected 1.2 Gb tetraploid (2n=4x=32) and 0.3 Gb haploid (1n=8) .
BMC genomics, Jan 29, 2017
The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops an... more The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposa...
Genome Announcements, 2016
Colletotrichum higginsianum is an ascomycete fungus causing anthracnose disease on numerous culti... more Colletotrichum higginsianum is an ascomycete fungus causing anthracnose disease on numerous cultivated plants in the family Brassicaceae , as well as the model plant Arabidopsis thaliana . We report an assembly of the nuclear genome and gene annotation of this pathogen, which was obtained using a combination of PacBio long-read sequencing and optical mapping.
Genome research, Aug 20, 2016
Genomic plasticity enables adaptation to changing environments, which is especially relevant for ... more Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in 'arms races' with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent genetic duplications are enhanced in LS regions, against an older episode of duplication events. Finally, LS regions are enriched in active transposons, which contribute to local genome plasticity. Thus, we provide evidence for genome shapi...
The Plant journal : for cell and molecular biology, May 15, 2016
In nature, plants have to cope with a wide range of stress conditions that often occur simultaneo... more In nature, plants have to cope with a wide range of stress conditions that often occur simultaneously or in sequence. To investigate how plants cope with multi-stress conditions, we analyzed the dynamics of whole-transcriptome profiles of Arabidopsis thaliana exposed to six sequential double stresses inflicted by combinations of (1) infection by the fungus Botrytis cinerea, (2) herbivory by Pieris rapae, and (3) drought stress. Each of these stresses induced specific expression profiles over time, in which one third of all differentially expressed genes was shared by at least two single stresses. Of these, 394 genes were differentially expressed during all three stress conditions, albeit often in opposite directions. When two stresses were applied in sequence, plants displayed transcriptome profiles that were very similar to the second stress, irrespective of the nature of the first stress. Nevertheless, significant first-stress-signatures could be identified in the sequential stres...
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Papers by Alexander Wittenberg