The genome of the pear (Pyrus bretschneideri Rehd.)
- Jun Wu1,11,
- Zhiwen Wang2,11,
- Zebin Shi3,11,
- Shu Zhang2,11,
- Ray Ming4,11,
- Shilin Zhu2,11,
- M. Awais Khan5,
- Shutian Tao1,
- Schuyler S. Korban5,
- Hao Wang6,
- Nancy J. Chen7,
- Takeshi Nishio8,
- Xun Xu2,
- Lin Cong2,
- Kaijie Qi1,
- Xiaosan Huang1,
- Yingtao Wang1,
- Xiang Zhao2,
- Juyou Wu1,
- Cao Deng2,
- Caiyun Gou2,
- Weili Zhou2,
- Hao Yin1,
- Gaihua Qin1,
- Yuhui Sha2,
- Ye Tao2,
- Hui Chen1,
- Yanan Yang1,
- Yue Song1,
- Dongliang Zhan2,
- Juan Wang2,
- Leiting Li1,4,
- Meisong Dai3,
- Chao Gu1,
- Yuezhi Wang3,
- Daihu Shi2,
- Xiaowei Wang2,
- Huping Zhang1,
- Liang Zeng2,
- Danman Zheng5,
- Chunlei Wang8,
- Maoshan Chen2,
- Guangbiao Wang2,
- Lin Xie2,
- Valpuri Sovero9,
- Shoufeng Sha1,
- Wenjiang Huang1,
- Shujun Zhang3,
- Mingyue Zhang1,
- Jiangmei Sun1,
- Linlin Xu1,
- Yuan Li1,
- Xing Liu1,
- Qingsong Li1,
- Jiahui Shen1,
- Junyi Wang2,
- Robert E. Paull7,
- Jeffrey L. Bennetzen6,
- Jun Wang2,10,12 and
- Shaoling Zhang1,12
- 1Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China;
- 2BGI-Shenzhen, Shenzhen 518083, China;
- 3Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- 4Department of Plant Biology,
- 5Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois 61801, USA;
- 6Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
- 7Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii 96822, USA;
- 8Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan;
- 9Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA;
- 10Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
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↵11 These authors contributed equally to this work.
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.
Footnotes
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↵12 Corresponding authors
E-mail slzhang{at}njau.edu.cn
E-mail wangj{at}genomics.org.cn
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.144311.112.
Freely available online through the Genome Research Open Access option.
- Received June 15, 2012.
- Accepted November 6, 2012.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.