Biology subjects

Dolezel, J.

Publications and source records attributed to Dolezel, J..

24 records · Page 2Linked to original sources

bioRxiv2020

DNA replication and chromosome positioning throughout the interphase in three-dimensional space of plant nuclei

Despite the recent progress, our understanding of the principles of plant genome organization and its dynamics in three-dimensional space of interphase nuclei remains limited. In this study, DNA replication timing and interphase chromosome positioning was analyzed in seven Poaceae species differing in genome size. A multidisciplinary approach combining newly replicated DNA labelling by EdU, nuclei sorting by flow cytometry, three-dimensional immuno-FISH, and confocal microscopy revealed similar replication timing order for telomeres and centromeres as well as for euchromatin and heterochromatin in all seven species. The Rabl configuration of chromosomes that lay parallel to each other and their centromeres and telomeres are localized at opposite nuclear poles, was observed in wheat, oat, rye and barley with large genomes, as well as in Brachypodium with a small genome. On the other hand, chromosomes of rice with a small genome and maize with relatively large genome did not assume proper Rabl configuration. In all species, the interphase chromosome positioning inferred from the location of centromeres and telomeres was stable throughout the interphase. These observations extend earlier studies indicating a more complex relation between genome size and interphase chromosome positioning, which is controlled by factors currently not known. HighlightTelomere and centromere replication timing and interphase chromosome positioning in seven grass species differing in genome size indicates a more complex relation between genome size and the chromosome positioning.

plant biology↗

bioRxiv2019

LYS3 encodes a prolamin-box-binding transcription factor that controls embryo growth in barley and wheat

Mutations at the LYS3 locus in barley have multiple effects on grain development, including an increase in embryo size and a decrease in endosperm starch content. The gene underlying LYS3 was identified by genetic mapping and mutations in this gene were identified in all four barley lys3 alleles. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF). Its role in controlling embryo size was confirmed using wheat TILLING mutants. To understand how PBF controls embryo development, we studied its spatial and temporal patterns of expression in developing grains. The PBF gene is expressed in both the endosperm and the embryos, but the timing of expression in these organs differs. PBF expression in wild-type embryos precedes the onset of embryo enlargement in lys3 mutants, suggesting that PBF suppresses embryo growth. We predicted the down-stream target genes of PBF in wheat and found them to be involved in a wide range of biological processes, including organ development and starch metabolism. Our work suggests that PBF may influence embryo size and endosperm starch synthesis via separate gene control networks. HIGHLIGHTSO_LILYS3 encodes a transcription factor called Prolamin Binding Factor (PBF) that is expressed in grains only. C_LIO_LIWheat and barley LYS3/PBF mutants have enlarged embryos suggesting that this gene suppresses embryo growth. C_LIO_LIThe down-stream target genes of PBF in wheat are predicted to be involved in a wide range of biological processes including organ development and starch metabolism. C_LI

plant biology↗

bioRxiv2019

Identification of a dominant chlorosis phenotype through a forward screen of the Triticum turgidum cv. Kronos TILLING population

Durum wheat (Triticum turgidum) derives from a hybridization event approximately 400,000 years ago which led to the creation of an allotetraploid genome. Unlike with more ancient whole genome duplications, the evolutionary recent origin of durum wheat means that its genome has not yet been fully diploidised. As a result, many of the genes present in the durum genome act in a redundant fashion, meaning that, in many cases, loss-of-function mutations must be present in both gene copies to observe a phenotypic effect. This redundancy has hindered the use of forward genetic screens in durum wheat. Here we use a novel set of induced variation within the cv. Kronos TILLING population to identify a locus controlling a dominant, environmentally-dependent chlorosis phenotype. We carried out a forward screen of the sequenced cv. Kronos TILLING lines for senescence phenotypes and identified a single line with a dominant early senescence and chlorosis phenotype. Mutant plants contained overall less chlorophyll throughout their development and displayed premature flag leaf senescence. A segregating population was classified into discrete phenotypic groups and subjected to bulked-segregant analysis using exome capture followed by next-generation sequencing. This allowed the identification of a single region on chromosome 3A, Yellow Early Senescence 1 (YES-1), which was associated with the mutant phenotype. To obtain further SNPs for fine-mapping, we isolated chromosome 3A using flow sorting and sequenced the entire chromosome. By mapping these reads against both the cv. Chinese Spring reference sequence and the cv. Kronos assembly, we could identify high-quality, novel EMS-induced SNPs in non-coding regions within YES-1 that were previously missed in the exome capture data. This allowed us to fine-map YES-1 to 4.3 Mb, containing 59 genes. Our study shows that populations containing induced variation can be sources of novel dominant variation in polyploid crop species, highlighting their importance in future genetic screens. We also demonstrate the value of using cultivar-specific genome assemblies alongside the gold-standard reference genomes particularly when working with non-coding regions of the genome. Further fine-mapping of the YES-1 locus will be needed to identify the causal SNP underpinning this dominant, environmentally dependent phenotype.

plant biology↗

bioRxiv2019

The genome of cowpea (Vigna unguiculata Walp.)

Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. A high-quality assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single molecule real-time sequencing, optical and genetic mapping, and a novel assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared to other warm-season legumes that have been sequenced. A surprising outcome of this study is the identification of a chromosomal inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence also facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A new numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris).

genomics↗

bioRxiv2018

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.\n\nResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining a new independent assembly based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.\n\nConclusionsSufficient genome sequence information is shown to be now available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and yield attributes are affected by five f-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

genomics↗

bioRxiv2017

Large-scale structural variation detection in subterranean clover subtypes using optical mapping validated at nucleotide level

Whole genome sequencing has been widely used to detect structural variations (SVs). However, the limited single molecule size makes it difficult to characterize large-scale SVs in a genome because they cannot fully cover such vast and complex regions. Recently, optical mapping in nanochannels has provided novel resolution to detect large-scale SVs by comparing the physical location of the nickase recognition sequence in genomes. Other than in humans, SVs discovered in plants by optical mapping have not been validated. To assess the accuracy of SV calling in plants by optical mapping, we selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The SVs discovered by BioNano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases.

bioinformatics↗