Jiri Stiller

Century-old chromatin architecture revealed in formalin-fixed vertebrates

Erin E. Hahn, Jiri Stiller, Marina R. Alexander, Alicia Grealy et autres

Abstract Gene expression is regulated by changes in chromatin architecture intrinsic to cellular differentiation and as an active response to environmental stimuli. Chromatin dynamics are a major driver of phenotypic diversity, regulation of development, and manifestation of disease. Remarkably, we know little …

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Transcriptomic insights into shared responses to Fusarium crown rot infection and drought stresses in bread wheat (Triticum aestivum L.)

Zhouyang Su, Shang Gao, Zhi Zheng, Jiri Stiller et autres

KEY MESSAGE: Shared changes in transcriptomes caused by Fusarium crown rot infection and drought stress were investigated based on a single pair of near-isogenic lines developed for a major locus conferring tolerance to both stresses. Fusarium crown rot (FCR) is a devastating …

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Hot alkaline lysis gDNA extraction from formalin-fixed archival tissues

Erin E. Hahn, Marina R. Alexander, Jiri Stiller, Peter M. Grewe et autres

Formalin fixation of natural history specimens and histopathological material has historically been viewed as an impediment to successful genomic analysis. However, the development of extraction methods specifically tailored to contend with heavily crosslinked archival tissues, re-contextualises millions of previously overlooked specimens as …

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Evolution of the germline mutation rate across vertebrates

Bergeron LA, Søren Besenbacher, Jiao Zheng, Peng Li et autres

In Brief: The authors conducted genome sequencing on 151 mother–father–offspring trios from 68 vertebrate animal species in order to estimate and compare germline mutation rates (GMRs). They found a 40-fold variation in GMR per generation between the species. Higher GMRs were observed …

Century-old chromatin architecture preserved with formaldehyde

Erin E. Hahn, Jiri Stiller, Marina R. Alexander, Alicia Grealy et autres

Abstract Co-ordinated regulation or dysregulation of chromatin architecture underpins fundamental biological processes, such as embryonic development, disease, cellular programming and response to environmental stress. The dynamic and plastic nature of chromatin accessibility is a major driver of phenotypic diversity, but we know …

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Transcriptome Analysis of Heat Shock Factor C2a Over-Expressing Wheat Roots Reveals Ferroptosis-like Cell Death in Heat Stress Recovery

Sundaravelpandian Kalaipandian, Jonathan Powell, Aneesh Karunakaran, Jiri Stiller et autres

Wheat (Triticum aestivum L.) growing areas in many regions of the world are subject to heat waves which are predicted to increase in frequency because of climate change. The engineering of crop plants can be a useful strategy to mitigate heat stress-caused …

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Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification

Cushla J. Metcalfe, Jingchuan Li, Bangyou Zheng, Jiri Stiller et autres

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Unlocking inaccessible historical genomes preserved in formalin

Erin E. Hahn, Marina R. Alexander, Alicia Grealy, Jiri Stiller et autres

Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable …

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Isolation and Sequencing of a Single Copy of an Introgressed Chromosome From a Complex Genome for Gene and SNP Identification

Cushla J. Metcalfe, Jingchuan Li, Bangyou Zheng, Jiri Stiller et autres

Abstract The large complex genomes of many crops constrain the use of new technologies for genome-assisted selection and genetic improvement. One method to simplify a genome is to break it into individual chromosomes by flow cytometry, however, in many crop species most …

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Translational control of fungal gene expression during the wheat- Fusarium graminearum interaction

Udaykumar Kage, Donald M. Gardiner, Jiri Stiller, Kemal Kazan

Summary To date, translational regulation of key genes controlling infection-related processes in fungal pathogens during their interactions with plants has not been studied. Here, we employed ribosome profiling (ribo-seq) to study translational responses and how such responses are coordinated with transcriptional changes …

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Unlocking inaccessible historical genomes preserved in formalin

Erin E. Hahn, Marina R. Alexander, Alicia Grealy, Jiri Stiller et autres

Abstract Background Museum specimens represent an unparalleled record of historical genomic data. However, the wide-spread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage …

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Differences between diploid donors are the main contributing factor for subgenome asymmetry measured in either gene ratio or relative diversity in allopolyploids

Xueling Ye, Haiyan Hu, Hong Zhou, Yunfeng Jiang et autres

Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, …

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