The Assembly of the Domesticated Apple Genome

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Li et al. (2016) reported in GigaScience the assemblage of an improved hybrid de novo genome of domesticated apple (Malus X domesticus) – ‘hybrid’ because the method utilized involves the assemblage of shorter sequences from different sequencing technologies.  In this case, these technologies include Illumina Sequencing and PacBio Sequencing.  Illumina sequencing produces shorter sequences than PacBio but with a higher precision.

The first draft genome for apple (Malus X domesticus) was assembled in 2010 by Velasco et al. and reported in Nature Genetics.  This draft only covered 89% of the non-repetitive portions of the genome and was generated from Sanger and 454 Sequencing Technologies.  Li et al (2016) reported that while this initial draft genome may be viable as a reference genome in a number of studies, it is utterly pointless in transcriptive and whole genome re-sequencing analysis.

A major improvement of the newly assembled genome over the first is in the size of the contig N50.  This is the average length of the set of sequences assembled to form the genome.  It is a yardstick to measure the quality of the assembled genome.  The newly assembled genome of the domesticated apple by Li et al. has a contig N50 of 111.6 kbp, which is seven fold improvement over the first (16.9 bp).  Other information obtained from the genome sequence analysis include 53,922 protein coding genes which doubles that reported from the human genome project and 2,765 non-coding RNA genes.  The resultant genome which is 632.4 MB is nearly 90% of the estimated genome.

What are the benefits of assembling these genomes?

Drafting genomes enables genome-wide functional studies which help bridge the ‘gap’ between genotypes and phenotypes, and thus help establish clear gene-trait relationships.  Referring to a statement by Albert Szent-Gyorgyi;

“My own scientific life was a descent from higher to lower dimensions, led by the desire to understand life.  I went from animals to cells, from cells to bacteria, from bacteria to molecules, from molecules to electrons.  The story had its irony, for molecules and electrons have no life at all. On my way, life ran out between my fingers” (Hartl & Clark, 2007).

A solution to a scientific question raises more questions to be answered.  In Gyorgyi’s dilemma, an expedition to understand life led into the world of molecules, which raised questions of how to establish the link between life and the ‘molecules of life.’  Similarly, the same translation into molecules also created disconnect between phenotypes and genotypes, in which direct relationship between genes and traits became fuzzy.  Drafted genomes could help in reconnecting genotypes to phenotypes.

Moreover, a high quality genome is very valuable in selection and breeding experiments.  These experiments have proven useful in tackling famine and nutrient deficiencies in the world.   For Apple, being a major fruit crop that accounted for 10% of the world harvested fruits in 2012 (Li et al., 2016), the need to develop new and improved cultivars is crucial.

Hartl, D. L., & Clark., A. G. (2007). Principles of Population Genetics (4th ed.). Sinauer Associates, Inc. Publishers.

Li, X., Kui, L., Zhang, J., Xie, Y., Wang, L., Yan, Y., . . . Guan, Q. (2016). Improved hybrid de novo genome assembly of domesticated apple (Malus X domestica). GigaScience, 5(35). doi:10.1186/s13742-016-0139-0


Velasco, R., Zharkikh, A., Dhingra, A., Cestaro, A., Kalyanaraman, A., Fontana, P., . . . Viola, R. (2010). The genome of the domesticated apple (Malus X domestica Borkh.). Nature Genetics, 833-841. doi:10.1038/ng.654


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