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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Different biosynthesis patterns among flavonoid 3-glycosides with distinct effects on accumulation of other flavonoid metabolites in pears (Pyrus bretschneideri Rehd.).
Rui Zhai,Xiao-Ting Liu,Wen-Ting Feng,Sha-Sha Chen,Lingfei Xu,Zhigang Wang,Jiangli Zhang,Pengmin Li,Fengwang Ma +8 more
TL;DR: It is proposed that the strong accumulation of flavonoid 3-galactosides stimulated the biosynthesis of other flavonoids compounds in the red mutant and, therefore, caused systemic variation of flav onoid biosynthesis profiles between ‘Zaosu’ and its red mutant.
Journal ArticleDOI
PbCOP1.1 Contributes to the Negative Regulation of Anthocyanin Biosynthesis in Pear
Meng Wu,Min Si,Xieyu Li,Linyan Song,Jianlong Liu,Rui Zhai,Liu Cong,Rongrong Yue,Chengquan Yang,Fengwang Ma,Lingfei Xu,Zhigang Wang +11 more
TL;DR: It is hypothesized that PbCOP1.1 is an anthocyanin synthetic inhibitory factor of pear coloration, which is highly homologous with those of other species.
Journal ArticleDOI
Heterologous gene silencing induced by tobacco rattle virus (TRV) is efficient for pursuing functional genomics studies in woody plants
Yuanzhong Jiang,Shenglong Ye,Lijun Wang,Yanjiao Duan,Wanxiang Lu,Wanxiang Lu,Hong Liu,Di Fan,Faqi Zhang,Faqi Zhang,Keming Luo,Keming Luo +11 more
TL;DR: An effective heterologous VIGS system in woody plants based on tobacco rattle virus (TRV) vectors is presented and it is demonstrated that V. fordii as a heterOLOGous VigS system provides a valuable tool for functional genomic analysis in woodY plant species.
Journal ArticleDOI
Two Highly Similar Poplar Paleo-subgenomes Suggest an Autotetraploid Ancestor of Salicaceae Plants.
Yinzhe Liu,Jinpeng Wang,Weina Ge,Zhenyi Wang,Yuxian Li,Nanshan Yang,Sangrong Sun,Liwei Zhang,Xiyin Wang +8 more
TL;DR: This work produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation, and uncovered homologous blocks in the grape and poplar genomes and also between them.
Journal ArticleDOI
Genome-wide analysis characterization and evolution of SBP genes in Fragaria vesca, Pyrus bretschneideri, Prunus persica and Prunus mume.
TL;DR: The results recommended that the purifying selection might be leading force during the evolution process and dominate conservation of SBP genes in Rosacea species according to environmental selection pressure analysis.
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