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 Jung Chen,Takeshi Nishio,Xun Xu,Lin Cong,Kaijie Qi,Xiaosan Huang,Wang Yingtao,Xiang Zhao,Juyou Wu,Cao Deng,Caiyun Gou,Weili Zhou,Hao Yin,Qin Gaihua,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,Chun-Lei Wang,Maoshan Chen,Guangbiao Wang,Xie Lin,Valpuri Sovero,Shoufeng Sha,Wenjiang Huang,S. L. Zhang,Mingyue Zhang,Jiangmei Sun,Linlin Xu,Yuan Li,Xing Liu,Qingsong Li,Jiahui Shen,Junyi Wang,Robert E. Paull,Jeffrey L. Bennetzen,Jun Wang,Shaoling Zhang +59 more
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TLDR
In this article, a high-quality draft genome sequence of the diploid P. bretschneideri Rehd was provided for de novo assembly of a highly heterozygous genome of this size with highly repetitive DNA sequences.Abstract:
Pear, the third most important temperate fruit species after grape and apple, belongs to the subfamily Pomoideae in the family Rosaceae. The majority of cultivated pears are functional diploids (2n = 34). As a popular fruit in the world market, pear has widespread cultivation on six continents, with major production in China, the United States, Italy, Argentina, and Spain (Supplemental Fig. 1). Pears are among the oldest of the world's fruit crops, with >3000 yr of cultivation history (Lombard and Westwood 1987), likely originating during the Tertiary period (65–55 million years ago [MYA]) in the mountainous regions of southwestern China and, from there, spreading on to both the East and West (Rubtsov 1944; Zeven and Zhukovsky 1975). Central Asia and eastern China are identified as two subcenters of genetic diversity for pear (Vavilov 1951). The Pyrus genus is genetically diverse with thousands of cultivars, but it can be divided into two major groups, Occidental pears (European pears) and Oriental pears (Asiatic pears). At least 22 primary species are well-recognized in Pyrus; however, only a few species, including Pyrus bretschneideri, Pyrus pyrifolia, Pyrus ussuriensis, Pyrus sinkiangensis, and Pyrus communis, have been utilized for fruit production.
Herein, we report on a high-quality draft genome sequence of the diploid P. bretschneideri Rehd. cv. ‘Dangshansuli’ (also known as ‘Suli’), the most important commercial Asiatic pear cultivar grown in the world (>4 million tons per year), having >500 yr of cultivated history in China. Pear is highly heterozygous due to self-incompatibility and interspecies compatibility. The genome is known to have an abundance of repetitive DNA sequences. In this study, a novel combination of BAC-by-BAC (bacterial artificial chromosome) strategy, with Illumina sequencing technology, is used for the first time for de novo assembly of a highly heterozygous genome of this size with highly repetitive DNA sequences. This has demonstrated that a complex plant genome sequence can be assembled and characterized using these technologies without the availability of a physical reference. Additionally, we also report on primary factors contributing to genome size differences between pear and apple, both belonging to the subfamily Pomoideae; chromosomal evolution of Rosaceae; and genes controlling valuable traits of pear, including self-incompatibility, lignified stone cells in flesh of fruit (unique to pear), sugar, and aroma.read more
Citations
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Journal ArticleDOI
Construction of a high-density bin-map and identification of fruit quality-related quantitative trait loci and functional genes in pear
Meng Qin,Leiting Li,Jugpreet Singh,Manning Sun,Bing Bai,Siwei Li,Jiangping Ni,Jiaying Zhang,Xun Zhang,Jiaming Li,Kaijie Qi,Shaoling Zhang,Awais Khan,Jun Wu +13 more
TL;DR: In this paper , the authors performed whole-genome sequencing of six pear cultivars and their 176 F1 progeny to identify genome-wide single-nucleotide polymorphism (SNP) markers for constructing a high-density bin-map of pear.
Journal ArticleDOI
De novo assembly, functional annotation, and marker development of Asian pear (Pyrus pyrifolia) fruit transcriptome through massively parallel sequencing.
TL;DR: These Pyrus pyrifolia transcriptome data provide a rich resource for the discovery and identification of new genes and will be important resources for the future development of a linkage map or of marker-assisted breeding programs for the Asian pear.
Journal ArticleDOI
Characterizing the expression of translation elongation factor gene EF1α in pear ( Pyrus ) fruit: evaluation of EF1α as a housekeeping gene
TL;DR: The expression analysis based on the high-throughput sequencing and sequence differences typing provided a high resolution to distinguish the expression among the members of pear EF1α and indicates that any two genes having complementary expression patterns can be used as a reference for qPCR analysis with the high stability of their mean expression value.
Book ChapterDOI
Genetic and Physical Mapping of the Apple Genome
Yuepeng Han,Schuyler S. Korban +1 more
TL;DR: Strategies for establishing genetic and physical maps of the apple genome along with the details of these findings will be presented.
Journal ArticleDOI
An integrated database of wood-formation related genes in plants
TL;DR: To create this database, collected plant genome data published in other online databases and predicted all cell wall and wood formation related genes using BLAST and HMMER, and provides an integrative platform for gene inquiry, downloading and analysis.
References
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