July 7, 2019  |  

Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica).

Authors: Li, Xuewei and Kui, Ling and Zhang, Jing and Xie, Yinpeng and Wang, Liping and Yan, Yan and Wang, Na and Xu, Jidi and Li, Cuiying and Wang, Wen and van Nocker, Steve and Dong, Yang and Ma, Fengwang and Guan, Qingmei

Domesticated apple (Malus?×?domestica Borkh) is a popular temperate fruit with high nutrient levels and diverse flavors. In 2012, global apple production accounted for at least one tenth of all harvested fruits. A high-quality apple genome assembly is crucial for the selection and breeding of new cultivars. Currently, a single reference genome is available for apple, assembled from 16.9?×?genome coverage short reads via Sanger and 454 sequencing technologies. Although a useful resource, this assembly covers only ~89 % of the non-repetitive portion of the genome, and has a relatively short (16.7 kb) contig N50 length. These downsides make it difficult to apply this reference in transcriptive or whole-genome re-sequencing analyses.Here we present an improved hybrid de novo genomic assembly of apple (Golden Delicious), which was obtained from 76 Gb (~102?×?genome coverage) Illumina HiSeq data and 21.7 Gb (~29?×?genome coverage) PacBio data. The final draft genome is approximately 632.4 Mb, representing?~?90 % of the estimated genome. The contig N50 size is 111,619 bp, representing a 7 fold improvement. Further annotation analyses predicted 53,922 protein-coding genes and 2,765 non-coding RNA genes.The new apple genome assembly will serve as a valuable resource for investigating complex apple traits at the genomic level. It is not only suitable for genome editing and gene cloning, but also for RNA-seq and whole-genome re-sequencing studies.

Journal: GigaScience
DOI: 10.1186/s13742-016-0139-0
Year: 2016

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