The genome of the pear (Pyrus bretschneideri Rehd.)

被引:823
作者
Wu, Jun [1 ]
Wang, Zhiwen [2 ]
Shi, Zebin [3 ]
Zhang, Shu [2 ]
Ming, Ray [4 ]
Zhu, Shilin [2 ]
Khan, M. Awais [5 ]
Tao, Shutian [1 ]
Korban, Schuyler S. [5 ]
Wang, Hao [6 ]
Chen, Nancy J. [7 ]
Nishio, Takeshi [8 ]
Xu, Xun [2 ]
Cong, Lin [2 ]
Qi, Kaijie [1 ]
Huang, Xiaosan [1 ]
Wang, Yingtao [1 ]
Zhao, Xiang [2 ]
Wu, Juyou [1 ]
Deng, Cao [2 ]
Gou, Caiyun [2 ]
Zhou, Weili [2 ]
Yin, Hao [1 ]
Qin, Gaihua [1 ]
Sha, Yuhui [2 ]
Tao, Ye [2 ]
Chen, Hui [1 ]
Yang, Yanan [1 ]
Song, Yue [1 ]
Zhan, Dongliang [2 ]
Wang, Juan [2 ]
Li, Leiting [1 ,4 ]
Dai, Meisong [3 ]
Gu, Chao [1 ]
Wang, Yuezhi [3 ]
Shi, Daihu [2 ]
Wang, Xiaowei [2 ]
Zhang, Huping [1 ]
Zeng, Liang [2 ]
Zheng, Danman [5 ]
Wang, Chunlei [8 ]
Chen, Maoshan [2 ]
Wang, Guangbiao [2 ]
Xie, Lin [2 ]
Sovero, Valpuri [9 ]
Sha, Shoufeng [1 ]
Huang, Wenjiang [1 ]
Zhang, Shujun [3 ]
Zhang, Mingyue [1 ]
Sun, Jiangmei [1 ]
机构
[1] Nanjing Agr Univ, Ctr Pear Engn Technol Res, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Jiangsu, Peoples R China
[2] BGI Shenzhen, Shenzhen 518083, Peoples R China
[3] Zhejiang Acad Agr Sci, Inst Hort, Hangzhou 310021, Zhejiang, Peoples R China
[4] Univ Illinois, Dept Plant Biol, Urbana, IL 61801 USA
[5] Univ Illinois, Dept Nat Resources & Environm Sci, Urbana, IL 61801 USA
[6] Univ Georgia, Dept Genet, Athens, GA 30602 USA
[7] Univ Hawaii, Dept Trop Plant & Soil Sci, Honolulu, HI 96822 USA
[8] Tohoku Univ, Grad Sch Agr Sci, Aoba Ku, Sendai, Miyagi 9818555, Japan
[9] Univ Illinois, Dept Crop Sci, Urbana, IL 61801 USA
[10] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark
基金
中国国家自然科学基金;
关键词
F-BOX GENE; DE-NOVO; IDENTIFICATION; PROGRAM; INCOMPATIBILITY; PREDICTION; ALIGNMENT; SEQUENCE; PHYLOGENIES; FINDER;
D O I
10.1101/gr.144311.112
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 194x 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, similar to 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 similar to 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.
引用
收藏
页码:396 / 408
页数:13
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