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

Wöhner, Thomas; Emeriewen, Ofere Francis; Wittenberg, Alexander H. J.; Schneiders, Harrie; Vrijenhoek, Ilse; Halász, Júlia; Hrotkó, K.; Hoff, Katharina J.; Gabriel, Lars; Keilwagen, Jens; Berner, Thomas; Schuster, Mirko; Peil, Andreas; Wuensche, J.; Kropop, Stephan; Flachowsky, Henryk

doi:10.1101/2021.06.01.446499

Cited by 6 publications

(10 citation statements)

References 65 publications

(100 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this paper, after removing the K-mer mistake, the corrected genome size of T. rupestris was 976.97 Mb. These estimates were greater than the populations of Fragaria vesca (240 Mb) [22], Pyrus bretschneideri (527 Mb) [23] , Ficus erecta (341 Mb) [24] and Cydonia oblonga (686 Mb) [18], smaller than Arachis duranensis (1.25 Gb) [25] , Lupinus angustifolius (1.15 Gb) [26] and Prunus fruticose (1.2 Gb) [27], but are close to Begonia fuchsioides (935 Mb) [28] and Quercus suber (953 Mb) [29]. According to the heterozygosity and repetition, the genome was divided into lowheterozygosity (≥50%), micro-heterozygosity (0.5% 0.8%) , high-heterozygosity (≥0.8%) and high-repetition (repeated ratio≥50 %), which directly re ects the di culty of assembling the subsequent sequencing data [12,30].…”

Section: Discussionmentioning

confidence: 99%

A First Genome Survey and Microsatellite Motif Identification of Taihangia rupestris

Song

Chen

Zhou

et al. 2023

Preprint

View full text Add to dashboard Cite

Background:Taihangia rupestris is a perennial herb on the China species red list that is growing on the cliffs of Taihang Mountain in China. However research on the genome of T. rupestris has not been carried out, which severely restricts further research on it. The aim of this study was to conduct a first genome survey of T. rupestris and to develop SSR molecular markers of it. Methods: The genome size and characteristics of T. rupestris were estimated by Illumina Hi-SeqXTen and K-mer analysis. We designed SSR primers in batches with Misa and Primer3, and T. rupestris from different populations were used to verify the selected primers. Finally, datas were analysised by Cervus 3.0 and GenAlex 6.5 for genetic diversity. Results: The genome size of T. rupestris was estimated to be 976.97 Mb with a heterozygosity rate of 0.726% and a sequence repetition rate of 56.93%. The clean reads were assembled into 100973 contigs with the max length of 26073 bp and an N50 value of 2607 bp. Based on the genome data of T. rupestris, a total of 805600 SSR markers were identified and 72769 pairs of primers were designed. In the present study, 100 primers were used to verify that 82 primers were successfully amplified. Conclusion: In general, the genome of T. rupestris is difficult to assemble genome with micro-heterozygosity and high repetition. In this study, 15 pairs of primers with good polymorphism can effectively distinguish different populations of T. rupestris. These analyses laid a foundation for the subsequent whole genome sequencing of T. rupestris.

show abstract

Section: Discussionmentioning

confidence: 99%

A First Genome Survey and Microsatellite Motif Identification of Taihangia rupestris

Song

Chen

Zhou

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…This sequence was used to study structural changes present in the allotetraploid sour cherry genome after its emergence. Therefore, the sour cherry genome sequence was compared to the published genome sequences of Prunus avium 'Tieton' (PaT, Wang et al 2019) and Prunus fruticosa ecotype Hármashatárhegy (PfeH, Wöhner et al 2021a) representing genotypes of the two ancestral species. The size of the subgenome PceS originating from P. avium was 269 Mbp.…”

Section: Discussionmentioning

confidence: 99%

“…Data supporting the findings of this study are deposited into the Open Agrar repository (https://doi.org/10.5073/20230324-105730-0, Wöhner et al (2023)) and on personal request to the corresponding author. An assembly hub for genome and annotation visualization is permanently hosted at http://bioinf.uni-greifswald.de/privatehubs/pcer/hub.txt .…”

Section: Data Availabilitymentioning

confidence: 99%

“…Snap frozen Prunus cerasus L. 'Schattenmorelle' (accession KIZC99-2, Figure 1, supplements 1.1) young leaf material was sent to KeyGene N.V. (Wageningen, The Netherlands). High molecular weight extracted DNA (Wöhner et al 2021a) was used to generate 1D ligation (SQK-LSK109) libraries which were subsequently sequenced on two Oxford Nanopore Technologies (ONT) R9.4.1 PromethION flow cells. The same material was used to generate an Illumina PCR free paired-end library (insert size of ~550 bp) which was sequenced on a HiSeq 4000 TM platform using 150bp and 125bp paired-end sequencing.…”

Section: Plant Material Dna and Rna Extraction Sequencing And Iso-seq...mentioning

confidence: 99%

“…assembly Index (LAI) Ou et al (2018) was calculated with LTR_retriever 2.9.0 (https://github.com/oushujun/LTR_retriever) to evaluate the assembly continuity between the final genome sequence of P. cerasus 'Schattenmorelle' and Prunus fruticosa ecotype Hármashatárhegy (Wöhner et al 2021a, Pf_1.0), P. avium 'Tieton' (Wang et al 2020) and P. persica 'Lovell' (Verde et al 2017) respectively. LTR_harvest (genometools 1.6.1 implementation) was used to obtain LTR-RT candidates.…”

Section: Correctness Completeness and Contiguity Of The Prunus Cerasu...mentioning

confidence: 99%

See 2 more Smart Citations

The structure of the tetraploid sour cherry ‘Schattenmorelle’ (Prunus cerasusL.) genome reveals insights into its segmental allopolyploid nature

Wöhner

Emeriewen

Wittenberg

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Genome of tetraploid sour cherry (Prunus cerasus L.) ‘Montmorency’ identifies three distinct ancestral Prunus genomes

Goeckeritz

Rhoades

Childs

et al. 2023

Horticulture Research

View full text Add to dashboard Cite

Sour cherry (Prunus cerasus L.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant P. fruticosa (ground cherry) and P. avium (sweet cherry). Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant cultivar grown in the U.S. We also generated a draft assembly of P. fruticosa to use alongside a published P. avium sequence for syntelog-based subgenome assignments for ‘Montmorency’ and provide compelling evidence P. fruticosa is also an allotetraploid. Using hierarchal k-mer clustering and phylogenomics, we show ‘Montmorency’ is trigenomic, containing two distinct subgenomes inherited from a P. fruticosa-like ancestor (A and A’) and two copies of the same subgenome inherited from a P. avium-like ancestor (BB). The genome composition of ‘Montmorency’ is AA’BB and little-to-no recombination has occurred between progenitor subgenomes (A/A’ and B). In Prunus, two known classes of genes are important to breeding strategies: the self-incompatibility loci (S-alleles), which determine compatible crosses, successful fertilization, and fruit set, and the Dormancy Associated MADS-box genes (DAMs), which strongly affect dormancy transitions and flowering time. The S-alleles and DAMs in ‘Montmorency’ and P. fruticosa were manually-annotated and support subgenome assignments. Lastly, the hybridization event ‘Montmorency’ is descended from was estimated to have occurred less than 1.61 million years ago, making sour cherry a relatively recent allotetraploid. The ‘Montmorency’ genome highlights the evolutionary complexity of the genus Prunus and will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.

show abstract

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

Cited by 6 publications

References 65 publications

A First Genome Survey and Microsatellite Motif Identification of Taihangia rupestris

A First Genome Survey and Microsatellite Motif Identification of Taihangia rupestris

The structure of the tetraploid sour cherry ‘Schattenmorelle’ (Prunus cerasusL.) genome reveals insights into its segmental allopolyploid nature

Genome of tetraploid sour cherry (Prunus cerasus L.) ‘Montmorency’ identifies three distinct ancestral Prunus genomes

Contact Info

Product

Resources

About