Parental origins of the cultivated tetraploid sour cherry (<scp><i>Prunus cerasus</i></scp> L.)

Bird, Kevin A.; Jacobs, MacKenzie; Sebolt, Audrey; Rhoades, Kathleen E; Alger, Elizabeth I.; Colle, Marivi; Bies, Paulina K.; Cario, Adare J.; Chigurupati, Ramya S.; Collazo, Delaney R.; Garland, Brooke; Hein, Kaitlyn M.; Hillenberg, Annie R.; Kado, Lawrence I.; Kilian, Vanessa R.; Longueuil, Philip F.; Mahesha, Vibha; Munsell, Kat; Peters, Nicole M. L.; Steffes, Megan O.; Suryadevara, Sathvik; Urban, Grace; Walia, Aditya K.; Wirsing, Taylor B.; McKain, Michael R.; Iezzoni, Amy; Edger, Patrick P.

doi:10.1002/ppp3.10267

Cited by 8 publications

(13 citation statements)

References 38 publications

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“…In a second approach, translocations between the two subgenomes were localized by a short-read mapping analyses. Short-reads (RNAseq) from P. cerasus, P. avium and P. fruticosa obtained from Bird et al (2022) were mapped on Pce S . A total of 148 regions were intraspecific difference of %-covered bases from obtained RNAseq reads ( Pa and Pce S _a, Pf and Pce S _f) > than interspecific difference of %-covered bases from obtained RNAseq reads ( Pf and Pce S _a, Pa and Pce S _f) indicated homoeologous exchanges between the two subgenomes.…”

Section: Resultsmentioning

confidence: 99%

“…RNAseq raw data published by Bird et al (2022) was obtained from NCBI sequence read archive (SRA) for the following species: P. cerasus (SRX14816146, SRX14816142, SRX14816138), P. fruticosa (SRX14816141), P. avium (SRX14816143), P. canescens (SRX14816137), P. serrulata (SRX14816136), P. mahaleb (SRX14816140), P. pensylvanica (SRX14816144), P. maackii (SRX14816139), P. subhirtella (SRX14816145). Reads were adapter- and quality trimmed using the software Trim Galore (version 0.6.3, parameters --quality 30 –length 50).…”

Section: Methodsmentioning

confidence: 99%

“…Studies based on chloroplast DNA markers strongly suggest that hybridisation between P. avium and P. fruticosa led to the emergence of P. cerasus at least twice (Dirlewanger et al 2007). Furthermore, the hypothesis could also be confirmed by genomic in situ hybridisation (Schuster and Schreiber 2000) and transcriptome sequencing (Bird et al 2022).…”

Section: Introductionmentioning

confidence: 90%

“…RNAseq raw data published by Bird et al (2022) ). The same was done using the reads of P. fruticosa (SRX14816141).…”

Section: Read Mapping and Coverage Analysismentioning

confidence: 99%

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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

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 90%

“…RNAseq raw data published by Bird et al (2022) ). The same was done using the reads of P. fruticosa (SRX14816141).…”

Section: Read Mapping and Coverage Analysismentioning

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

View full text Add to dashboard Cite

show abstract

“…Sour cherry (Prunus cerasus) is an agriculturally important species with a tetraploid (4x) genome of unknown origin. Bird et al (2022) use phylogenetic analyses of wild species and historically important cultivars to pinpoint the tetraploid ground cherry ( Prunus fruticosa ) as the closest extant relative of the maternal donor for at least some sour cherry varieties, providing valuable insight for future breeding efforts. Taken together, these three studies on fruits of all sizes illustrate how both evolutionary history and current environmental conditions impact fruit characteristics and distribution.…”

Section: Fruits Of All Sizesmentioning

confidence: 99%

Fruit in focus: A sampler platter of research

Migicovsky

Forrestel

Warschefsky

2023

Plants People Planet

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Few plants have captured the imagination and palettes of the world like those which bear edible fruits, providing novel insights into the relationships between plants and people. This special collection of reviews and research highlights the unique challenges and opportunities we face when studying, breeding, and working to conserve these species. The 18 articles included here examine fruiting plants across diverse scales and topics, from the genome to global sustainability, and from fruit morphology to species' geographic distributions, yet they showcase only a fraction of the immense evolutionary, phenotypic, and genomic diversity present in fruit‐bearing plants. Across the special collection, our hope is to not only offer highlights of fruit diversity and importance but also provide a taste of future research in this area. We hope you enjoy the fruits of our labor.

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

Goeckeritz

Rhoades

Childs

et al. 2023

Horticulture Research

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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.

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Parental origins of the cultivated tetraploid sour cherry (Prunus cerasus L.)

Cited by 8 publications

References 38 publications

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

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

Fruit in focus: A sampler platter of research

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

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