Prunus dulcis Lauranne Genome v1.0

Publication

Sánchez-Pérez R, Pavan S, Mazzeo R, Moldovan C, Aiese Cigliano R, Del Cueto J, Ricciardi F, Lotti C, Ricciardi L, Dicenta F, López-Marqués RL, Møller BL. Mutation of a bHLH transcription factor allowed almond domestication. Science. 2019 Jun 14;364(6445):1095-1098. doi: 10.1126/science.aav8197.

Abstract

Wild almond species accumulate the bitter and toxic cyanogenic diglucoside amygdalin. Almond domestication was enabled by the selection of genotypes harboring sweet kernels. We report the completion of the almond reference genome. Map-based cloning using an F1 population segregating for kernel taste led to the identification of a 46-kilobase gene cluster encoding five basic helix-loop-helix transcription factors, bHLH1 to bHLH5. Functional characterization demonstrated that bHLH2 controls transcription of the P450 monooxygenase-encoding genes PdCYP79D16 and PdCYP71AN24, which are involved in the amygdalin biosynthetic pathway. A nonsynonymous point mutation (Leu to Phe) in the dimerization domain of bHLH2 prevents transcription of the two cytochrome P450 genes, resulting in the sweet kernel trait.

Genome facts and statistics

The genome (2n =2x = 16, haploid genome size=246Mb) of the sweet homozygous almond cultivar Lauranne was sequenced with a combination of Illumina (paired-end and 5-kb mate pairs) and Pac Biotechnologies.The long PacBio reads were used to perform the genome assembly, whereas the Illumina reads were used to perform gap filling and scaffolding. The scaffolds obtained were organized in pseudomolecules using the P. persica reference genome, as the genomes across the Prunus genus are essentially collinear (23–25). The final assembly constitutes 4078 scaffolds, of which 2572 are organized in eight pseudomolecules, with a final N50 of 21.8Mb (where N50 ist heminimum contig length needed to cover 50% of the genome) and a L90 of 306 (where L90 is the smallest number of contigs whose length sum makes up 90% of genome size).