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

Sour cherry (Prunus cerasus L.) is an agriculturally valuable tree that produces fruits used in a range of culinary dishes, beverages, and other products. The progenitor species number origins sour remain unresolved. Here, we performed phylogenetic analyses plastid genomes nuclear genes from nine wild three historically important cultivars. Our identified Prunus fruticosa avium as the closest extant relatives tetraploid cherry. Furthermore, our revealed P. likely maternal contributor. These findings transcriptomic datasets should serve new resources to guide future breeding efforts fruit crop with genome structure (2n = 4x 32) native Europe, its extending Turkey northern Russia (Hedrick et al., 1915). Oldén Nybom (1968) first proposed were diploid sweet ground (Prunos Pall.). Their theory was supported by intermediate morphological phenotypes artificial hybridizations between cherry, overlapping ranges, predominately disomic inheritance (Beaver & Iezzoni, 1993; Wang, 1998), genomic situ hybridization karyotype (Schuster Schreibner, 1999). However, strong support for well insight into parentage allopolyploid origins, has been difficult produce due technical challenges generating analyzing data polyploid (Bird 2021). Although some previous studies limited resolution chloroplast DNA suggested more frequent parent (Badenes Parfitt, 1995; Brettin 2000) study using ribosomal rRNA internal transcribed spacer (ITS) showed weak bootstrap species, rigorous genetic analysis needed. potential sustained introgression putative progenitors (Macková 2018) suggests complex evolutionary relationship requires rich untangle. Phylogenetic whole (plastome) have obtain estimates relationships and, because it maternally inherited, can be determine donor repeated interspecific hybrids allopolyploids (Edger, Hall, 2018). alone insufficient identify paternal or differentiate unknown autopolyploid. A complete picture obtained comparing results plastomes transcriptomes McKain, We had major goals this study: (1) strongly estimate cultivated cherries, (2) (3) evaluate if there multiple single (parental direction). Twelve accessions two subgenera (Table 1). maackii subgenus Padus while all cherries are Cerasus. Within set, four classified section Cerasus (P. cerasus, avium, fruticosa, canescens), Pseudocerasus serrulata, subhirtella, × yedoensis), Mahaleb mahaleb pensylvanica) (Rehder, 1927). cerasus) clones represent different traditional varieties France, Hungary, Germany, avium) clone also variety Germany. All vegetatively propagated humans who presumably selected them their superior quality. eight remaining seedlings grown ornamental floral display. plant materials collected either Michigan State University (MSU) germplasm collection at Clarksville Research Center, Clarksville, MSU Campus Woody Plant Collection, East Lansing, Michigan. Total RNA extracted fresh leaf material Invitrogen PureLink Mini Kit (Carlsbad, CA, USA). Illumina libraries constructed TruSeq stranded mRNA library prep kit (SanDiego, USA) sequenced paired-end 150-bp reads on HiSeq 4000 platform Sequencing core. list which generated provided Table 1. yedoensis downloaded NCBI SRA (PRJNA283061). Raw part deposited database under BioProject PRJNA788510. Plastid assembled Fast-Plast (https://github.com/mrmckain/Fast-Plast). Transcripts de novo transcriptome Trinity v.2.2.0 (Grabherr 2011) quality adapter trimming Trimmomatic (Bolger 2014) (packaged Trinity), sequence, seed mismatch one, palindrome clip threshold 30, simple 10. Reads then trimmed sliding window 10 base pairs minimum average PHRED score 20. less than 40 after these steps removed. Read coverage normalized 100 Trinity. Using utility scripts, aligned transcript bowtie v1.1.0 (Langmead 2009), abundance estimated RSEM v.1.2.29 (Li Dewey, through align_and_estimate_abundance.pl script packaged 1% fragments per isoform mapped based FPKM removed filter_fasta_by_rsem_values.pl utilities. Final transcripts translated RefTrans pipeline (https://github.com/mrmckain/RefTrans). Filtered blasted against Fragaria vesca v 2.01 e-value 1 10−10 TBLASTX (Camacho 2009). BLAST hits filtered best hit least 75% bidirectional overlap target gene model F. vesca. translations GeneWise (Wise2 v2.2.0) (Birney 2004) where longest kept each transcript. It noted that, Trinity, term “gene” will include splice allelic variants, so inflated compared true space This distinction bear mind; however, simplicity, refer models outputted simply “genes” throughout manuscript. length, removing sequences shorter 300 bp, any premature stop codon predictions. Orthofinder v1 (Emms Kelly, 2015), Diamond v0.8.36 (Buchfink 2015)), Arabidopsis thaliana, vesca, apple (Malus x domestica), peach persica) VanBuren, 2018; Velasco 2010; Verde 2013). Multi-species orthogroups, presence 12 downstream analyses. Coding amino acid separated orthogroup-specific FASTA files. Amino MAFFT v7.215 (Katoh Standley, 2013) “auto” parameter, PAL2NAL v14 (Suyama 2006) default parameters create alignment MAFFT-aligned acids. Codon alignments removal columns 90% gaps unaligned lengths 30% length (McKain 2016). Orthogroup trees reconstructed RAxML v8.0.6 (Stamatakis, 500 replicates GTR + gamma model. Each orthogroup analyzed PhyDS (Phylogenetic iDentification Subgenomes) (https://github.com/mrmckain/PhyDS) described Figure filtering cutoff (>80%). Putative paralogs estimate_paralogs_from_trees.pl PhyDS. No taxa designated “ignore_taxa” parameter. final available Dryad Digital Repository (https://doi.org/10.5061/dryad.r7sqv9sf7). Transcriptome young leaves listed GC content similar transcriptomes, ranging 41.1% 41.6%. Contig N50 values ranged 1184 bp Pandy 38) 1667 1419 contig ~723 ~946 same accessions, respectively. pensylvanica lowest predicted (94,271) total bases (~117 Mb), English Morello greatest (147,173) (~170 Mb). 2015) infer 14,237 orthogroups 282,737 canescens, mahaleb, pensylvanica, maackii) A. woodland strawberry (F. vesca), outgroups Lamesch 2012; 2). 87.3% assigned orthogroup, mean median size 17.3 genes, Of 139 (0.97%) specific, 1355 (9.5%) contained 15 used. having highest showing sister (Figures 2a). found larger (601 value [BSV] 80 more) (272 BSV 80). observe small supporting cerasus. incomplete matrices phylotranscriptomic methods, dynamic patterns among genus, lineage sorting within (Maddison Knowles, 2006; Wiens, 2006). sampled Steele 2012) 1), plus clade (Figure 2b). branch separating samples substantial divergence relative species. origin remained open question sampling low investigations. Advances genomics allowed investigations previously intractable 2021; McKain Vallejo-Marín set robust phylogeny whether formed origins. provide much needed clarity crop. Ground fruticosa) long suspected Previous produced mixed results, markers 1995) others implicating (Shi consistently could not resolve polytomy. whole-plastome provides most date. plastome unambiguously surveyed 100% Multiple involving populations parent, possibility, would benefit expanding collections further For example, polymorphisms Hungarian (Brettin 2000). rootstock disease resistance breeding. Morphological characteristics fertility F1 conflicting accounts canescens properly belonged (Iezzoni 1991; Rehder, 1927; Schuster, 2001), only prior comprehensive result ambiguous sample included hybrid, accession (Zhang canescens' inclusion along sweet, ground, ITS region clusters (Bortiri 2001). weak, sole reliance called (Edger 2014). With use approach, able generate thousands implement novel tree-counting method (PhyDS) individuals. approach again progenitor, providing strongest hypothesis 1968. demonstrate power approaches identifying even when homoeologous subgenome. As selections investigated varieties, maintained consumption, possible increased proportion resulted combination recombination 2018), admixture human selection genes. In geographic regions prevalent, pressure cold-hardiness, prominent feature relaxed. disparity asymmetric subgenome expression creates systematic biases missing Additionally, levels flow phenomena interesting directions take species; high-quality reference assignments required. work NSF-GRFP DGE-1424871 Distinguished Fellowship KAB, NSF Traineeship program DGE-1828149 MJ, Honors College funding, AgBioResearch, PGRP 2029959 PPE, USDA National Institute Food Agriculture-Specialty Crop Initiative Projects, “RosBREED: Enabling marker-assisted Rosaceae” (2009-51181-05858) AFI Combining horticultural rosaceous cultivars” (2014-51181-22378) PPE. authors declare research conducted absence commercial financial construed conflict interest. AFI, MRM, PPE planned designed research. EIA, MC, AS, KR, MLA, PKB, AJC, RSC, DRC, SF, BG, KMH, JH, ARH, LIK, VRK, PFL, VM, CM, KM, RMP, NMLP, MOS, SS, AT, GU, AKW, TBW, analysis, collection, and/or interpretation. wrote reviewed edited openly Sequence Archive (SRA) [https://www.ncbi.nlm.nih.gov/sra]