Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing

Abstract

Sweet cherry (Prunus avium) is an economically significant fruit species in the genus Prunus. However, in contrast to other important fruit trees in this genus, only one draft genome assembly is available for sweet cherry, which was assembled using only Illumina short-read sequences. The incompleteness and low quality of the current sweet cherry draft genome limit its use in genetic and genomic studies. A high-quality chromosome-scale sweet cherry reference genome assembly is therefore needed. A total of 65.05 Gb of Oxford Nanopore long reads and 46.24 Gb of Illumina short reads were generated, representing~190x and 136x coverage, respectively, of the sweet cherry genome. The final de novo assembly resulted in a phased haplotype assembly of 344.29 Mb with a contig N50 of 3.25 Mb. Hi-C scaffolding of the genome resulted in eight pseudochromosomes containing 99.59% of the bases in the assembled genome. Genome annotation revealed that more than half of the genome (59.40%) was composed of repetitive sequences, and 40,338 protein-coding genes were predicted, 75.40% of which were functionally annotated. With the chromosomescale assembly, we revealed that gene duplication events contributed to the expansion of gene families for salicylic acid/jasmonic acid carboxyl methyltransferase and ankyrin repeat-containing proteins in the genome of sweet cherry. Four auxin-responsive genes (two GH3s and two SAURs) were induced in the late stage of fruit development, indicating that auxin is crucial for the sweet cherry ripening process. In addition, 772 resistance genes were identified and functionally predicted in the sweet cherry genome. The high-quality genome assembly of sweet cherry obtained in this study will provide valuable genomic resources for sweet cherry improvement and molecular breeding.

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

“…Using RNA-Seq data from P. cerasus ‘Schattenmorelle’ [44] and the augmented gene predictions from BRAKER with eight homology-based gene predictions from GeMoMa we predicted 58.880 protein-coding transcripts representing 84.524 orthologs within Pf_1.0 with a mean length of 3.580 bp and a mean protein length of 355 aa (Table 4). The number of protein-coding transcripts was considerably larger in this study than 38.275 predicted for P. avium ‘Tieton’ [28] and 43.349 transcripts predicted in P. avium ‘Satonishiki’ [25]. A total of 86.7 % (75,113) proteins was functionally annotated by InterproScan resulting in 852.470 annotated protein domains and sites from 15 protein databases (Table 4).…”

“…The longest scaffold is 66,497,422 bp (Table 2). Compared to the genome sequences available so far in Prunus [24, 25, 28], the genome of P. fruticosa is the most complete obtained from long read sequencing only.…”

“…Our approach detected 189,7 Mb of repetitive sequences (51.75 % of the genome) and 42,1 Mb (11.5 %) unknown elements. Repetitive sequences observed in other Prunus species [25–27, 29, 33] ranged from 37.1% in P. persica [50] to 59.4 % in P. avium [28]. However, similar to P .…”

“…As indicated in Table S3, a higher percentage of transcripts (77.5 % to 87.3 %) were mapped between the homologues chromosomes from P. persica and Pf_1.0 compared to the transcripts from P. avium (72.1% to 56.3 %). In general, the assembled genome of P. fruticosa shows a good synteny with the genomes of P. persica [24] and P. avium [28]. Figure 6b shows the synteny analysis using masked sequences (i.e.…”

Chromosome-level draft genome of a diploid plum (Prunus salicina)

“…Genome resources are already available for a number of Rosaceae fruit crops [ 12 ], including apple [ 13–16 ], peach [ 17 ], pear [ 18–21 ], strawberry [ 22 , 23 ], almond [ 24 , 25 ], black raspberry [ 26 ], sweet cherry [ 27 , 28 ], apricot [ 29 , 30 ], loquat [ 31 ], and Prunus mume [ 32 ]. However, whole-genome sequencing and chromosome-level assembly for plums have not been reported until now.…”