In an article published in Nature Genetics this June, researchers have assembled the most comprehensive apple (Malus domestica Borkh.) genome to date using Bionano optical genome mapping and hybrid scaffolding.

The study centers around the Golden Delicious variety of the apple, though here at Bionano, we’re partial to Granny Smith apples. Regardless, the new assembly showed some golden improvements, including 50x greater contiguity over a recent assembly built using PacBio and Illumina technologies alone, and enables analysis of structure, transposable elements, epigenetic regulation of transcription, and fruit development like never before.

Bionano Hybrid Scaffolding for Improved Contiguity

To build the improved assembly, researchers utilized an innovative combination of the latest sequencing and optical mapping technologies, including PacBio, Illumina paired-end sequencing, and three mate pair libraries with various insert sizes. Bionano’s hybrid scaffolding technology was used to scaffold the sequence with optical genome mapping to improve assembly contiguity 9-fold.

Of note is the fact that the increased contiguity seen was achieved using only a single-enzyme Bionano genome map. Bionano now offers two-enzyme hybrid scaffolding capabilities, which would improve contiguity even further!

Importance of High-Quality Assemblies

High-quality assemblies are critical for performing genomic research. For example, without information around the order and orientation of genomic elements, researchers cannot study how the genome is regulated. In addition, complete and accurate reference genomes help facilitate determination of biological processes and support translation of research findings into improved sustainable agricultural technologies.

Until now, the study of epigenetically controlled characteristics in the apple genome was hindered by an incomplete draft, including inaccurate contig positions. Bionano’s long-range optical genome mapping data is well suited for assembly of highly repetitive regions found in perennial plants such as the apple.

Application of the Improved Assembly

With the improved apple assembly, researchers were able to investigate uncharacterized regions of the highly repetitive tree genome to discover interesting historical information. For example, researchers identified a new hyper-repetitive retrotransposon sequence that was overrepresented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. This TE burst coincided with the uplift of the Tian Shan mountains, the birthplace of the apple, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly its divergence from the pear.

To learn more about this study, read the full paper published in Nature Genetics: High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development.
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