2012•Genome ResearchOpen access
The genome of the pear ( Pyrus bretschneideri Rehd.)
Jun Wu, Zhiwen Wang, Zebin Shi, Shu Zhang, Ray Ming, Shilin Zhu, Muhammad 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 Deng, Caiyun Gou, Weili Zhou, Hao Yin, Gaihua Qin, Yuhui Sha, Ye Tao, Hui Chen, Ya‐Nan 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, Lin-Lin Xu, Yuan Li, Xing Liu, Qingsong Li, Jiahui Shen, Junyi Wang, Robert E. Paull, Jeffrey L. Bennetzen, Jun Wang, Shaoling Zhang
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 194× coverage. 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, C3'H, 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.