Articles
Fast construction of a reference genome: challenges and opportunities using ‘Royal Gala’ apple as a case study
Article number
1203_5
Pages
35 – 40
Language
English
Abstract
Quality reference genomes assembled to chromosomes are highly desirable and fundamental for advanced genome analyses, such as comparative genomics and genome-wide association studies.
In the last two decades, the dramatic decrease in genome sequencing costs coupled with significant increases in computing power has made genomics an essential tool in biological research.
However, a lack of sound experimental design, data contamination, inadequate sequencing depth, and fragmented assembly to only the scaffold level are common problems in genome assembly.
To date, only one fully sequenced genome in the genus Malus, that of ‘Golden Delicious’ (GD), has been published (Velasco et al., 2010). Here, we report an efficient approach to building a chromosome-level whole-genome assembly for tetra-haploid ‘Royal Gala’ (RG) apple.
A hybrid de-novo genome assembly from 22 SMRT Cells PacBio RSII data, along with Illumina data from three paired-end and two mated-pair libraries, achieved 31,411 scaffolds with a total of 620 million nucleotides.
Proximity-guided assembly using Hi-C data anchored and ordered 590 MB (95.1%) of the RG draft assembly to 17 pseudo-chromosomes, leaving 4093 scaffolds of 21 MB unanchored.
Of the 248 most conserved eukaryotic genes (COGs) in CEGMA, 99.2% were either completely or partially assembled.
Although it is a progeny of GD, RG is remarkably different from GD in many phenotypic traits of commercial importance, such as fruit skin colour, fruit texture and storage life.
Our RG genome research provides a valuable resource for future research and opens opportunities for studying the comparative genomics of RG and GD, as well as the phylogenetics of significant gene families and the molecular genetics controlling elite fruit traits in RG.
In the last two decades, the dramatic decrease in genome sequencing costs coupled with significant increases in computing power has made genomics an essential tool in biological research.
However, a lack of sound experimental design, data contamination, inadequate sequencing depth, and fragmented assembly to only the scaffold level are common problems in genome assembly.
To date, only one fully sequenced genome in the genus Malus, that of ‘Golden Delicious’ (GD), has been published (Velasco et al., 2010). Here, we report an efficient approach to building a chromosome-level whole-genome assembly for tetra-haploid ‘Royal Gala’ (RG) apple.
A hybrid de-novo genome assembly from 22 SMRT Cells PacBio RSII data, along with Illumina data from three paired-end and two mated-pair libraries, achieved 31,411 scaffolds with a total of 620 million nucleotides.
Proximity-guided assembly using Hi-C data anchored and ordered 590 MB (95.1%) of the RG draft assembly to 17 pseudo-chromosomes, leaving 4093 scaffolds of 21 MB unanchored.
Of the 248 most conserved eukaryotic genes (COGs) in CEGMA, 99.2% were either completely or partially assembled.
Although it is a progeny of GD, RG is remarkably different from GD in many phenotypic traits of commercial importance, such as fruit skin colour, fruit texture and storage life.
Our RG genome research provides a valuable resource for future research and opens opportunities for studying the comparative genomics of RG and GD, as well as the phylogenetics of significant gene families and the molecular genetics controlling elite fruit traits in RG.
Authors
C.H. Deng, Y. Tian, C. Zhang, D. Chagné, A. Gleave, S.E. Gardiner, V. Bus, S. Sullivan, I. Liachko, P. Cong, J.-L. Yao
Keywords
genome sequencing, genome assembly, Hi-C, proximity-guided assembly (PGA), comparative genomics, Malus
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