ORCID Profile
0000-0001-8298-8937
Current Organisations
University of Queensland
,
Neubrandenburg University of Applied Sciences
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Publisher: MDPI AG
Date: 09-02-2023
DOI: 10.3390/PATHOGENS12020289
Abstract: Vascular wilt caused by the ascomycete fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) is a major constraint of banana production around the world. The virulent race, namely Tropical Race 4, can infect all Cavendish-type banana plants and is now widespread across the globe, causing devastating losses to global banana production. In this study, we characterized Foc Subtropical Race 4 (STR4) resistance in a wild banana relative which, through estimated genome size and ancestry analysis, was confirmed to be Musa acuminata ssp. malaccensis. Using a self-derived F2 population segregating for STR4 resistance, quantitative trait loci sequencing (QTL-seq) was performed on bulks consisting of resistant and susceptible in iduals. Changes in SNP index between the bulks revealed a major QTL located on the distal end of the long arm of chromosome 3. Multiple resistance genes are present in this region. Identification of chromosome regions conferring resistance to Foc can facilitate marker assisted selection in breeding programs and paves the way towards identifying genes underpinning resistance.
Publisher: Copernicus GmbH
Date: 30-10-2018
DOI: 10.5194/CP-2018-142
Abstract: Abstract. Ice wedges in the Yana Highlands of interior Yakutia – the most continental region of the Northern Hemisphere – were investigated to elucidate the winter climate and continentality during the Middle to Late Pleistocene. The Batagay megaslump exposes ice wedges and composite wedges that were s led from three cryostratigraphic units: the lower sand unit of Marine Isotope Stage (MIS) 6 age, the upper Ice Complex (Yedoma) and the upper sand unit (both MIS3 to MIS2). A terrace of the nearby Adycha River provides a Late Holocene (MIS1) ice wedge that serves as a modern endmember for analysis. Stable-isotope values of ice wedges in the MIS3 upper Yedoma Ice Complex at Batagay are more depleted (mean δ18O about −35 ‰) than those from 17 other ice-wedge sites across coastal and central Yakutia. This observation points to lower winter temperatures and, therefore, higher continentality in the Yana Highlands during MIS3. Likewise, more depleted isotope values compared to other sites in Yakutia are found in Holocene wedge ice (mean δ18O about −29 ‰). Ice-wedge isotopic signatures of the MIS6 lower sand unit (mean δ18O about −33 ‰) and of the MIS3-2 upper sand unit (mean δ18O from about −33 to −30 ‰) are less distinctive regionally and preserve traces of fast formation in rapidly accumulating sand sheets and of post-depositional fractionation.
Publisher: Cold Spring Harbor Laboratory
Date: 18-03-2020
DOI: 10.1101/2020.03.16.992933
Abstract: Sequencing technologies have advanced to the point where it is possible to generate high accuracy, haplotype resolved, chromosome scale assemblies. Several long read sequencing technologies are available on the market and a growing number of algorithms have been developed over the last years to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology as well as the most appropriate software for assembly and polishing. For this reason, it is important to benchmark different approaches applied to the same s le. Here, we report a comparison of three long read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii . We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION) and BGI (single-tube Long Fragment Read) technologies for the same s le. Several assemblers were benchmarked in the assembly of PacBio and Nanopore reads. Results obtained from combining long read technologies or short read and long read technologies are also presented. The assemblies were compared for contiguity, accuracy and completeness as well as sequencing costs and DNA material requirements. Overall, the three long read technologies produced highly contiguous and complete genome assemblies of Macadamia jansenii . At the time of sequencing, the cost associated with each method was significantly different but continuous improvements in technologies have resulted in greater accuracy, increased throughput and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
Publisher: American Geophysical Union (AGU)
Date: 14-10-2021
DOI: 10.1029/2021GL093881
Abstract: The response of permafrost to marine submergence can vary between ice‐rich late Pleistocene deposits and the thermokarst basins that thawed out during the Holocene. We hypothesize that inundated Alases offshore thaw faster than submerged Yedoma. To test this hypothesis, we estimated depths to the top of ice‐bearing permafrost offshore of the Bykovsky Peninsula in northeastern Siberia using electrical resistivity surveys. The surveys traversed submerged lagoon deposits, drained and refrozen Alas deposits, and undisturbed Yedoma from the coastline to 373 m offshore. While the permafrost degradation rates of the submerged Yedoma were in the range of similar sites, the submerged Alas permafrost degradation rates were up to 170 faster. Remote sensing analyses suggest that 54 of lagoons wider than 500 m along northeast Siberian and northwest American coasts originated in thermokarst basins. Given the abundance of thermokarst basins and lakes along parts of the Arctic coastline, their effect on subsea permafrost degradation must be similarly prevalent.
Publisher: Copernicus GmbH
Date: 02-08-2019
Abstract: Abstract. Ice wedges in the Yana Highlands of interior Yakutia – the most continental region of the Northern Hemisphere – were investigated to elucidate changes in winter climate and continentality that have taken place since the Middle Pleistocene. The Batagay megaslump exposes ice wedges and composite wedges that were s led from three cryostratigraphic units: the lower ice complex of likely pre-Marine Isotope Stage (MIS) 6 age, the upper ice complex (Yedoma) and the upper sand unit (both MIS 3 to 2). A terrace of the nearby Adycha River provides a Late Holocene (MIS 1) ice wedge that serves as a modern reference for interpretation. The stable-isotope composition of ice wedges in the MIS 3 upper ice complex at Batagay is more depleted (mean δ18O about −35 ‰) than those from 17 other ice-wedge study sites across coastal and central Yakutia. This observation points to lower winter temperatures and therefore higher continentality in the Yana Highlands during MIS 3. Likewise, more depleted isotope values are found in Holocene wedge ice (mean δ18O about −29 ‰) compared to other sites in Yakutia. Ice-wedge isotopic signatures of the lower ice complex (mean δ18O about −33 ‰) and of the MIS 3–2 upper sand unit (mean δ18O from about −33 ‰ to −30 ‰) are less distinctive regionally. The latter unit preserves traces of fast formation in rapidly accumulating sand sheets and of post-depositional isotopic fractionation.
Publisher: Cold Spring Harbor Laboratory
Date: 23-09-2022
DOI: 10.1101/2022.09.22.509021
Abstract: DNA replication stress is a hallmark of cancer that is exploited by chemotherapies. Current assays for replication stress have low throughput and poor resolution whilst being unable to map the movement of replication forks genome-wide. We present a new method that uses nanopore sequencing and artificial intelligence to map forks and measure their rates of movement and stalling in melanoma and colon cancer cells treated with chemotherapies. Our method can differentiate between fork slowing and fork stalling in cells treated with hydroxyurea, as well as inhibitors of ATR, WEE1, and PARP1. These different therapies yield different characteristic signatures of replication stress. We assess the role of the intra-S-phase checkpoint on fork slowing and stalling and show that replication stress dynamically changes over S-phase. This method requires sequencing on only a single nanopore flow cell, and the cost-effectiveness and high throughput enables functional screens to determine how human cancers respond to replication-targeted therapies.
Publisher: Copernicus GmbH
Date: 30-10-2018
Publisher: Oxford University Press (OUP)
Date: 12-2020
DOI: 10.1093/GIGASCIENCE/GIAA146
Abstract: Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same s le. Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same s le. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements. The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
Location: Germany
Location: No location found
No related grants have been discovered for Frank Günther.