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Research Project: Innovative Strategies and Methods for Improving the Management, Availability, and Utility of Plant Genetic Resource Collections

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Title: A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

Author
item ZHANG, LIYI - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item HU, JIANG - NEXTOMICS BIOSCIENCES CO., LTD
item HAN, XIAOLEI - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item LI, JINGJING - NEXTOMICS BIOSCIENCES CO., LTD
item GAO, YUAN - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item Richards, Christopher
item ZHANG, CAIXIA - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item TIAN, YI - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item LIU, GUIMING - BEIJING ACADEMY OF AGRICULTURAL SCIENCES
item GUL, HERA - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item YANG, CHUANXIN - NEXTOMICS BIOSCIENCES CO., LTD
item MENG, MINGHUI - NEXTOMICS BIOSCIENCES CO., LTD
item YUAN, GAOPENG - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item KANG, GUODONG - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item WU, YONGLONG - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item WANG, KUN - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item ZHANG, HENGTAO - CHINESE ACADEMY OF AGRICULTURAL SCIENCES
item WANG, DEPENG - NEXTOMICS BIOSCIENCES CO., LTD
item CONG, PEIHUA - CHINESE ACADEMY OF AGRICULTURAL SCIENCES

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/2/2019
Publication Date: 4/2/2019
Citation: Zhang, L., Hu, J., Han, X., Li, J., Gao, Y., Richards, C.M., Zhang, C., Tian, Y., Liu, G., Gul, H., Yang, C., Meng, M., Yuan, G., Kang, G., Wu, Y., Wang, K., Zhang, H., Wang, D., Cong, P. 2019. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nature Communications. https://doi.org/10.1038/s41467-019-09518-x.
DOI: https://doi.org/10.1038/s41467-019-09518-x

Interpretive Summary: This study develops the first comprehensive genome sequence of Malus sieversii using a combination of next generation sequencing methods including long read PacBio, Optical mapping techniques and High-C chromosome conformation sequencing that reveal the spatial organization of chromatin in the cell and the genome-wide interaction among loci. Using these complimentary methods allows researchers to understand how structural feature of genome variation like copy number variation and presence absence variation contribute to genome evolution and can provide insights into the biological basis and architecture of key agronomic traits. In this study the data showed how a transposable element upstream of a developmental promoter was associated with red coloration of apple skin.

Technical Abstract: A complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. Here, we assemble a high-quality genome (contig N50 of 6.99'Mb) of the apple anther-derived homozygous line HFTH1, including 22 telomere sequences, using a combination of PacBio single-molecule real-time (SMRT) sequencing, chromosome conformation capture (Hi-C) sequencing, and optical mapping. In comparison to the Golden Delicious reference genome, we identify 18,047 deletions, 12,101 insertions and 14 large inversions. We reveal that these extensive genomic variations are largely attributable to activity of transposable elements. Interestingly, we find that a long terminal repeat (LTR) retrotransposon insertion upstream of MdMYB1, a core transcriptional activator of anthocyanin biosynthesis, is associated with red-skinned phenotype. This finding provides insights into the molecular mechanisms underlying red fruit coloration, and highlights the utility of this high-quality genome assembly in deciphering agriculturally important trait in apple.