Abstract
Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.
Highlights
Petunia hybrida is a popular bedding plant that has a long history as a genetic model system
For P. axillaris N, we performed a hybrid de novo assembly using a combination of short read (Illumina; coverage 137X) and long read technologies (PacBio; coverage 21X), whereas for P. inflata S6 we produced exclusively short reads (Illumina; coverage 135X) and performed a short read de novo assembly
The resulting high-quality assemblies have a size of 1.26 Gb for P. axillaris and 1.29 Gb for P. inflata (Table 1)
Summary
Genome annotation identified 32,928 protein-coding genes for P. axillaris and 36,697 protein-coding genes for P. inflata with an average of 5.2 and 5.1 exons per protein coding gene and an average predicted protein size of 393 and 386 amino acids, respectively. Petunia genomes are rich in repetitive DNA (as are most other plant genomes), but its presence at 60–65% of the assembled genome is relatively low considering its genome size (Fig. 2a; Supplementary Note 2), indicating a larger gene, regulatory and low copy sequence space. Long terminal repeats (LTR)-retroelement-related sequences are abundant near centromeres (Fig. 2b), and within the assemblies, equal numbers of fragments and full-length Ty3/Gypsy-like and Ty1/Copia-like elements were detected. Non-LTR retroelements (SINES, LINES) Others (satellites, unkown, low complexity) b
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