Schneeberger K

References (6)

Title : Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes - Campoy_2020_Genome.Biol_21_306
Author(s) : Campoy JA , Sun H , Goel M , Jiao WB , Folz-Donahue K , Wang N , Rubio M , Liu C , Kukat C , Ruiz D , Huettel B , Schneeberger K
Ref : Genome Biol , 21 :306 , 2020
Abstract : Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes enabling separation of the whole-genome sequencing reads into haplotype-specific reads sets. After assembling the reads of each haplotype, the contigs are scaffolded to chromosome level using a genetic map derived from the gametes. We assemble the two genomes of a diploid apricot tree based on whole-genome sequencing of 445 individual pollen grains. The two haplotype assemblies (N50: 25.5 and 25.8 Mb) feature a haplotyping precision of greater than 99% and are accurately scaffolded to chromosome-level.
ESTHER : Campoy_2020_Genome.Biol_21_306
PubMedSearch : Campoy_2020_Genome.Biol_21_306
PubMedID: 33372615
Gene_locus related to this paper: pruar-a0a6j5xc26 , pruar-a0a6j5xjr9

Title : Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity - Stuttmann_2016_PLoS.Genet_12_e1005990
Author(s) : Stuttmann J , Peine N , Garcia AV , Wagner C , Choudhury SR , Wang Y , James GV , Griebel T , Alcazar R , Tsuda K , Schneeberger K , Parker JE
Ref : PLoS Genet , 12 :e1005990 , 2016
Abstract : Plants have a large panel of nucleotide-binding/leucine rich repeat (NLR) immune receptors which monitor host interference by diverse pathogen molecules (effectors) and trigger disease resistance pathways. NLR receptor systems are necessarily under tight control to mitigate the trade-off between induced defenses and growth. Hence, mis-regulated NLRs often cause autoimmunity associated with stunting and, in severe cases, necrosis. Nucleocytoplasmic ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) is indispensable for effector-triggered and autoimmune responses governed by a family of Toll-Interleukin1-Receptor-related NLR receptors (TNLs). EDS1 operates coincidently or immediately downstream of TNL activation to transcriptionally reprogram cells for defense. We show here that low levels of nuclear-enforced EDS1 are sufficient for pathogen resistance in Arabidopsis thaliana, without causing negative effects. Plants expressing higher nuclear EDS1 amounts have the genetic, phenotypic and transcriptional hallmarks of TNL autoimmunity. In a screen for genetic suppressors of nuclear EDS1 autoimmunity, we map multiple, independent mutations to one gene, DM2h, lying within the polymorphic DANGEROUS MIX2 cluster of TNL RPP1-like genes from A. thaliana accession Landsberg erecta (Ler). The DM2 locus is a known hotspot for deleterious epistatic interactions leading to immune-related incompatibilities between A. thaliana natural accessions. We find that DM2hLer underlies two further genetic incompatibilities involving the RPP1-likeLer locus and EDS1. We conclude that the DM2hLer TNL protein and nuclear EDS1 cooperate, directly or indirectly, to drive cells into an immune response at the expense of growth. A further conclusion is that regulating the available EDS1 nuclear pool is fundamental for maintaining homeostatic control of TNL immune pathways.
ESTHER : Stuttmann_2016_PLoS.Genet_12_e1005990
PubMedSearch : Stuttmann_2016_PLoS.Genet_12_e1005990
PubMedID: 27082651

Title : Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms - Zapata_2016_Proc.Natl.Acad.Sci.U.S.A_113_E4052
Author(s) : Zapata L , Ding J , Willing EM , Hartwig B , Bezdan D , Jiao WB , Patel V , Velikkakam James G , Koornneef M , Ossowski S , Schneeberger K
Ref : Proc Natl Acad Sci U S A , 113 :E4052 , 2016
Abstract : Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising approximately 3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.
ESTHER : Zapata_2016_Proc.Natl.Acad.Sci.U.S.A_113_E4052
PubMedSearch : Zapata_2016_Proc.Natl.Acad.Sci.U.S.A_113_E4052
PubMedID: 27354520
Gene_locus related to this paper: arath-At1g73750 , arath-At1g15070 , arath-a0a1p8awg3

Title : Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation - Willing_2015_Nat.Plants_1_14023
Author(s) : Willing EM , Rawat V , Mandakova T , Maumus F , James GV , Nordstrom KJ , Becker C , Warthmann N , Chica C , Szarzynska B , Zytnicki M , Albani MC , Kiefer C , Bergonzi S , Castaings L , Mateos JL , Berns MC , Bujdoso N , Piofczyk T , de Lorenzo L , Barrero-Sicilia C , Mateos I , Piednol M , Hagmann J , Chen-Min-Tao R , Iglesias-Fernandez R , Schuster SC , Alonso-Blanco C , Roudier F , Carbonero P , Paz-Ares J , Davis SJ , Pecinka A , Quesneville H , Colot V , Lysak MA , Weigel D , Coupland G , Schneeberger K
Ref : Nat Plants , 1 :14023 , 2015
Abstract : Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
ESTHER : Willing_2015_Nat.Plants_1_14023
PubMedSearch : Willing_2015_Nat.Plants_1_14023
PubMedID: 27246759
Gene_locus related to this paper: araal-a0a087gz21 , araal-a0a087h4k1

Title : Rice perception of symbiotic arbuscular mycorrhizal fungi requires the karrikin receptor complex - Gutjahr_2015_Science_350_1521
Author(s) : Gutjahr C , Gobbato E , Choi J , Riemann M , Johnston MG , Summers W , Carbonnel S , Mansfield C , Yang SY , Nadal M , Acosta I , Takano M , Jiao WB , Schneeberger K , Kelly KA , Paszkowski U
Ref : Science , 350 :1521 , 2015
Abstract : In terrestrial ecosystems, plants take up phosphate predominantly via association with arbuscular mycorrhizal fungi (AMF). We identified loss of responsiveness to AMF in the rice (Oryza sativa) mutant hebiba, reflected by the absence of physical contact and of characteristic transcriptional responses to fungal signals. Among the 26 genes deleted in hebiba, DWARF 14 LIKE is, the one responsible for loss of symbiosis . It encodes an alpha/beta-fold hydrolase, that is a component of an intracellular receptor complex involved in the detection of the smoke compound karrikin. Our finding reveals an unexpected plant recognition strategy for AMF and a previously unknown signaling link between symbiosis and plant development.
ESTHER : Gutjahr_2015_Science_350_1521
PubMedSearch : Gutjahr_2015_Science_350_1521
PubMedID: 26680197

Title : The Arabidopsis lyrata genome sequence and the basis of rapid genome size change - Hu_2011_Nat.Genet_43_476
Author(s) : Hu TT , Pattyn P , Bakker EG , Cao J , Cheng JF , Clark RM , Fahlgren N , Fawcett JA , Grimwood J , Gundlach H , Haberer G , Hollister JD , Ossowski S , Ottilar RP , Salamov AA , Schneeberger K , Spannagl M , Wang X , Yang L , Nasrallah ME , Bergelson J , Carrington JC , Gaut BS , Schmutz J , Mayer KF , Van de Peer Y , Grigoriev IV , Nordborg M , Weigel D , Guo YL
Ref : Nat Genet , 43 :476 , 2011
Abstract : We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3x dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged from A. lyrata 10 million years ago, likely constitutes the derived state for the family. We found evidence for DNA loss from large-scale rearrangements, but most of the difference in genome size can be attributed to hundreds of thousands of small deletions, mostly in noncoding DNA and transposons. Analysis of deletions and insertions still segregating in A. thaliana indicates that the process of DNA loss is ongoing, suggesting pervasive selection for a smaller genome. The high-quality reference genome sequence for A. lyrata will be an important resource for functional, evolutionary and ecological studies in the genus Arabidopsis.
ESTHER : Hu_2011_Nat.Genet_43_476
PubMedSearch : Hu_2011_Nat.Genet_43_476
PubMedID: 21478890
Gene_locus related to this paper: arall-d7kc59 , arall-d7kfz1 , arall-d7kjk9 , arall-d7kk58 , arall-d7kuj1 , arall-d7kwx5 , arall-d7kzq8 , arall-d7laf7 , arall-D7LAK6 , arall-d7ltj2 , arall-d7lu11 , arall-d7ly06 , arall-d7lyn6 , arall-d7m1k0 , arall-d7m1k1 , arall-d7m1k3 , arall-d7m1l4 , arall-d7m814 , arall-d7mbk0 , arall-d7mbn8 , arall-d7mgs1 , arall-d7mi04 , arall-d7mld7 , arall-d7mpg7 , arall-d7mul9 , arath-At2g45610 , arath-At1g05790 , arath-At1g09980 , arath-At1g18360 , arath-AT1G29120 , arath-AT1G73920 , arath-AT1G76140 , arath-AT2G05260 , arath-At2g15230 , arath-At2g24280 , arath-AT2G42690 , arath-At2g47630 , arath-AT3G12150 , arath-At3g61680 , arath-AT3g62590 , arath-AT4G00500 , arath-AT4G25770 , arath-AT4g30610 , arath-At5g11650 , arath-At5g13640 , arath-AT5G19050 , arath-AT5G20060 , arath-AT5G20520 , arath-AT5G27320 , arath-At5g42930 , arath-At5g47330 , arath-CGEP , arath-clh1 , arath-clh2 , arath-F1N13.220 , arath-F2G14.100 , arath-F12A4.4 , arath-F14O10.2 , arath-SCP27 , arath-HNL , arath-GID1B , arath-LIP2 , arath-At5g17670 , arath-pip , arath-PLA11 , arath-PLA12 , arath-PLA13 , arath-PLA15 , arath-PLA17 , arath-Q8LPF5 , arath-Q9FFZ1 , arath-Q9FJ29 , arath-Q9FKP9 , arath-Q9FNF6 , arath-q9lhe8 , arath-Q9SFF6 , arath-q84w08 , arath-SCP7 , arath-SCP8 , arath-SCP26 , arath-SCP28 , arath-SCP33 , arath-SCP40 , arath-SCPL34 , arath-At4g12230 , arath-MES14 , arath-T19F11.2 , arath-MES10 , arath-At5g11790 , arath-T26B15.8 , arath-ZW18 , arall-d7l971 , arall-d7lfd3 , arall-d7lg04 , arall-d7lg05 , arall-d7lg06 , arall-d7lg07 , arall-d7mb17 , arall-d7mb18 , arall-d7l7v2 , arall-d7l7v3 , arall-d7lst0 , arall-d7lfw9 , arall-d7mgs6 , arall-d7mur3 , arall-d7kjr5 , arall-d7l7v1 , arall-d7ls88 , arall-d7kzg6 , arall-d7kcm6 , arall-d7krm0 , arall-d7kwe4 , arall-d7lri7 , arall-d7kq26