The genome of the pear (Pyrus bretschneideri Rehd.)

Jun Wu, Zhiwen Wang, Zebin Shi, Shu Zhang, Ray Ming, Shilin Zhu, M. Awais Khan, Shutian Tao, Schuyler S. Korban, Hao Wang, Nancy J. Chen, Takeshi Nishio, Xun Xu, Lin Cong, Kaijie Qi, Xiaosan Huang, Yingtao Wang, Xiang Zhao, Juyou Wu, Cao DengCaiyun Gou, Weili Zhou, Hao Yin, Gaihua Qin, Yuhui Sha, Ye Tao, Hui Chen, Yanan Yang, Yue Song, Dongliang Zhan, Juan Wang, Leiting Li, Meisong Dai, Chao Gu, Yuezhi Wang, Daihu Shi, Xiaowei Wang, Huping Zhang, Liang Zeng, Danman Zheng, Chunlei Wang, Maoshan Chen, Guangbiao Wang, Lin Xie, Valpuri Sovero, Shoufeng Sha, Wenjiang Huang, Shujun Zhang, Mingyue Zhang, Jiangmei Sun, Linlin Xu, Yuan Li, Xing Liu, Qingsong Li, Jiahui Shen, Junyi Wang, Robert E. Paull, Jeffrey L. Bennetzen, Shaoling Zhang

Research output: Contribution to journalArticle

449 Citations (Scopus)

Abstract

The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 1943coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ~28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ~5.4-21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30-45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C39H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

Original languageEnglish
Pages (from-to)396-408
Number of pages13
JournalGenome Research
Volume23
Issue number2
DOIs
Publication statusPublished - 2013 Feb 1

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Wu, J., Wang, Z., Shi, Z., Zhang, S., Ming, R., Zhu, S., Khan, M. A., Tao, S., Korban, S. S., Wang, H., Chen, N. J., Nishio, T., Xu, X., Cong, L., Qi, K., Huang, X., Wang, Y., Zhao, X., Wu, J., ... Zhang, S. (2013). The genome of the pear (Pyrus bretschneideri Rehd.). Genome Research, 23(2), 396-408. https://doi.org/10.1101/gr.144311.112