Biology subjects

Woehner, T. W.

Publications and source records attributed to Woehner, T. W..

3 recordsLinked to original sources

bioRxiv2023

Occurrence of strawberry viruses in Fragaria germplasm and evaluation of cryotherapy as an eradication method for strawberry viruses

Strawberry plants are highly susceptible to viral infections, which pose significant threats to global strawberry production. This study aims to explore the efficacy of in vitro initiation and cryopreservation of shoot tips as a potential strategy for eradicating strawberry viruses. We tested plants for four important strawberry viruses namely: SMoV, SCV, SMEY and SVBV. The plants, which tested positive were either cultivated as in vitro cultures then returned to a green house or field collection cultivation, or treated by cryopreservation. After cryopreservation, the plants were cultivated again in vitro and then in the green house or field. The viruses were detected within each propagation step. Significant eradication effects were found for SMoV and SCV when plants were treated by in vitro initiation or with cryotherapy, but not for SMEY or SVBV. The results of this study show that cryotherapy or in vitro initiation can lead to the elimination of strawberry viruses, but the kind of therapy appears to depend on the type of virus.

plant biology↗

bioRxiv2023

The structure of the tetraploid sour cherry 'Schattenmorelle' (Prunus cerasus L.) genome reveals insights into its segmental allopolyploid nature

Sour cherry (Prunus cerasus L.) is an economically important allotetraploid cherry species believed to have evolved in the Caspian Sea and Black Sea regions. How, when and where exactly the evolution of this species took place is unclear. It resulted from a hybridization of the tetraploid ground cherry (Prunus fruticosa Pall.) and an unreduced (2n) pollen of the diploid ancestor sweet cherry (P. avium L.). Some indications implement that the genome of sour cherry is segmental allopolyploid, but how it is structured and to what extent is unknown. To get an insight, the genome of the sour cherry cultivar Schattenmorelle was sequenced at ~400x using Illumina NovaSeqTM short-read and Oxford Nanopore long-read technologies (ONT R9.4.1 PromethION). Additionally, the transcriptome of Schattenmorelle was sequenced using PacBio Sequel II SMRT cell sequencing at ~300x. The final assembly resulted in a ~629 Mbp long pseudomolecule reference genome, which could be separated into two subgenomes each split into eight chromosomes. Subgenome PceS_a which originates from P. avium has a length of 269 Mbp, whereas subgenome PceS_f which originates from P. fruticosa has a length of 299.5 Mbp. The length of unassembled contigs was 60 Mbp. The genome of the sour cherry shows a size-reduction compared to the genomes of its ancestral species. It also shows traces of homoeologous sequence exchanges throughout the genome. Comparative positional sequence and protein analyses provided evidence that the genome of sour cherry is segmental allotetraploid and that it has evolved in a very recent event in the past.

genomics↗

bioRxiv2021

The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

BackgroundCherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall. is one ancestor of cultivated sour cherry, an important tetraploid cherry species. Here, we present a long read chromosome-level draft genome assembly and related plastid sequences using the Oxford Nanopore Technology PromethION platform and R10.3 pore type. FindingThe final assemblies obtained from 117.3 Gb cleaned reads representing 97x coverage of expected 1.2 Gb tetraploid (2n=4x=32) and 0.3 Gb haploid (1n=8) genome sequence of P. fruticosa were calculated. The N50 contig length ranged between 0.3 and 0.5 Mb with the longest contig being [~]6 Mb. BUSCO estimated a completeness between 98.7 % for the 4n and 96.1 % for the 1n datasets. Using a homology and reference based scaffolding method, we generated a final consensus genome sequence of 366 Mb comprising eight chromosomes. The N50 scaffold was [~]44 Mb with the longest chromosome being 66.5 Mb. The repeat content was estimated to [~]190 Mb (52 %) and 58,880 protein-coding genes were annotated. The chloroplast and mitochondrial genomes were 158,217 bp and 383,281 bp long, which is in accordance with previously published plastid sequences. ConclusionThis is the first report of the genome of ground cherry (P. fruticosa) sequenced by long read technology only. The datasets obtained from this study provide a foundation for future breeding, molecular and evolutionary analysis in Prunus studies.

genomics↗