A Chromosome-level Sequence Assembly Reveals the Structure of the<i>Arabidopsis thaliana</i>Nd-1 Genome and its Gene Set

Pucker, Boas; Holtgräwe, Daniela; Stadermann, Kai Bernd; Frey, Karl; Huettel, Bruno; Reinhardt, Richard; Weißhaar, Bernd

doi:10.1101/407627

Cited by 7 publications

(9 citation statements)

References 94 publications

(148 reference statements)

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“…As a result, all participants were generating new scientific knowledge contributing to the field of Arabidopsis genomics. To bridge the time for ordered oligonucleotides to arrive, some experiments derived from recent genome research projects [11], [29], [30], [31] were repeated on different biological material. Therefore, participants were carrying out actual research with unknown outcome.…”

Section: Resultsmentioning

confidence: 99%

Integrating Molecular Biology and Bioinformatics Education

Pucker

Schilbert

Schumacher

2019

Journal of Integrative Bioinformatics

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Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand of scientists with a combined background in both fields, the education of dry and wet lab subjects are often still separated. This work describes an example of integrated education with a focus on genomics and transcriptomics. Participants learned computational and molecular biology methods in the same practical course. Peer-review was applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. The positive evaluation results indicate that this approach was accepted by the participants and would likely be suitable for wider scale application.

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Section: Resultsmentioning

confidence: 99%

Integrating Molecular Biology and Bioinformatics Education

Pucker

Schilbert

Schumacher

2019

Journal of Integrative Bioinformatics

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“…New TE insertions are likely to generate DNA methylation diversity [21] but analysis of this will have to await long-read genome sequencing of many lines, which will let us capture rare insertions, and study de novo silencing. [12, 22, 23].…”

Section: Discussionmentioning

confidence: 99%

Common alleles ofCMT2andNRPE1are major determinants ofde novoDNA methylation variation inArabidopsis thaliana

Sasaki

Kawakatsu

Ecker

et al. 2019

Preprint

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DNA cytosine methylation is an epigenetic mark associated with silencing of transposable elements (TEs) and heterochromatin formation. In plants, it occurs in three sequence contexts: CG, CHG, and CHH (where H is A, T, or C). The latter does not allow direct inheritance of methylation during DNA replication due to lack of symmetry, and methylation must therefore be re-established every cell generation. Genome-wide association studies (GWAS) have previously shown that CMT2 and NRPE1 are major determinants of genome-wide patterns of TE CHH-methylation. Here we instead focus on CHH-methylation of individual TEs and TE-families, allowing us to identify the pathways involved in CHH-methylation simply from natural variation and confirm the associations by comparing them with mutant phenotypes. Methylation at TEs targeted by the RNA-directed DNA methylation (RdDM) pathway is unaffected by CMT2 variation, but is strongly affected by variation at NRPE1, which is largely responsible for the longitudinal cline in this phenotype. In contrast, CMT2-targeted TEs are affected by both loci, which jointly explain 7.3% of the phenotypic variation (13.2% of total genetic effects). There is no longitudinal pattern for this phenotype, however, because the geographic patterns appear to compensate for each other in a pattern suggestive of stabilizing selection. Author SummaryDNA methylation is a major component of transposon silencing, and essential for genomic integrity. Recent studies revealed large-scale geographic variation as well as the existence of major trans-acting polymorphisms that partly explained this variation. In this study, we re-analyze previously published data (The 1001 Epigenomes), focusing on de novo DNA methylation patterns of individual TEs and TE families rather than on genome-wide averages (as was done in previous studies). GWAS of the patterns reveals the underlying regulatory networks, and allowed us to comprehensively characterize 1/17 trans-regulation of de novo DNA methylation and its role in the striking geographic pattern for this phenotype. 1 DNA cytosine-methylation (DNA methylation) is an epigenetic mark associated with 2 diverse molecular functions, such as silencing of transposable elements (TEs) and 3 heterochromatin formation. The majority of plant methylation is found in TEs, and 4 there are three types of DNA methylation contexts: CG and CHG, both of which are 5 symmetric, and CHH, which is not (H is A, T, or C). CG-methylation (mCG) and 6 CHG-methylation (mCHG) can be maintained in a semi-conservative manner during 7 DNA replication by DNA METHYLTRANSFERASE 1 (MET1 ) and 8 CHROMOMETHYLASE 3 (CMT3 ), respectively, whereas CHH-methylation (mCHH) 9 must be re-established every cell generation, presumably by one of two de novo 10 pathways, one involving CHROMOMETHYLASE 2 (CMT2 ), the other RNA-directed 11 DNA methylation (RdDM) [1-3]. CMT2 preferentially methylates heterochromatic 12 non-CG cytosines that are marked by H3 Lys9 (H3K9) di-and tri-methylation [4, 5], 13 whiles RdDM involves small RNAs...

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“…BWA-MEM (v.0.7.13) [17] was applied to map all genomic pairedend Illumina reads to the corresponding reference genome sequence using default parameters as well as -m to discard secondary alignments. For A. thaliana, all available 1135 datasets [18] (Additional file 1) were subjected to a mapping against the AthNd-1_v2c genome sequence [19]. The resulting BAM files of these mappings were subjected to QUOD.…”

Section: Selection and Preprocessing Of Datasetsmentioning

confidence: 99%

“…As a control, the sequences were also searched against themselves. Peptide sequences of Nd-1 with a score ratio ≥ 0.8 were considered plastidlike sequences when comparing BLAST hits on the plastome sequences against self-hits [19]. Genes structurally annotated in AthNd-1_v2c were classified with BUSCO v3 [21] running in protein mode on the encoded peptide sequences using 'brassicales odb10' (order level) as reference [22].…”

Section: Identification Of Plastid Sequencesmentioning

confidence: 99%

“…A list of Nd-1 transposable element (TE) genes, which are Nd-1 gene structures overlapping with sequences annotated as TEs, was obtained from Pucker et al [19]. First, the score distribution of TE and non-TE genes was determined using a Mann-Whitney U test implemented in the Python package SciPy [25] (https ://githu b.com/ ksiel emann /QUOD/blob/maste r/analy se_TE_genes _and_score s.py).…”

Section: Identification Of Plastid Sequencesmentioning

confidence: 99%

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Reference-based QUantification Of gene Dispensability (QUOD)

2021

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Background Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as ‘core’ or ‘dispensable’ is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Even when extended to ‘conditionally dispensable’, this concept still requires the assignment of genes to distinct groups. Results Here, we present a new method which overcomes this distinct classification by quantifying gene dispensability and present a dedicated tool for reference-based QUantification Of gene Dispensability (QUOD). As a proof of concept, sequence data of 966 Arabidopsis thaliana accessions (Ath-966) were processed to calculate a gene-specific dispensability score for each gene based on normalised coverage in read mappings. We validated this score by comparison of highly conserved Benchmarking Universal Single Copy Orthologs (BUSCOs) to all other genes. The average scores of BUSCOs were significantly lower than the scores of non-BUSCOs. Analysis of variation demonstrated lower variation values between replicates of a single accession than between iteratively, randomly selected accessions from the whole dataset Ath-966. Functional investigations revealed defense and antimicrobial response genes among the genes with high-dispensability scores. Conclusions Instead of classifying a gene as core or dispensable, QUOD assigns a dispensability score to each gene. Hence, QUOD facilitates the identification of candidate dispensable genes, associated with high dispensability scores, which often underlie lineage-specific adaptation to varying environmental conditions.

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A Chromosome-level Sequence Assembly Reveals the Structure of theArabidopsis thalianaNd-1 Genome and its Gene Set

Cited by 7 publications

References 94 publications

Integrating Molecular Biology and Bioinformatics Education

Integrating Molecular Biology and Bioinformatics Education

Common alleles ofCMT2andNRPE1are major determinants ofde novoDNA methylation variation inArabidopsis thaliana

Reference-based QUantification Of gene Dispensability (QUOD)

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