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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Genome Re-Sequencing of Diverse Sweet Cherry (Prunus avium) Individuals Reveals a Modifier Gene Mutation Conferring Pollen-Part Self-Compatibility
TL;DR: Phylogenetic, evolutionary and gene expression analyses revealed that MGST may have undergone lineage-specific evolution, and the encoded protein may function differently from the corresponding proteins encoded by GST orthologs in other species, including members of the subfamily Maloideae (Rosaceae).
Journal ArticleDOI
Characterization of DNA methyltransferase and demethylase genes in Fragaria vesca
TL;DR: A regulatory role of DNA methylation in the turning stage of non-climacteric fleshy fruit and responses to environment stimuli is indicated, and would facilitate functional studies of DNA epigenetic modification in the growth and development ofnon-clinacteric fruits.
Journal ArticleDOI
Arguments for standardizing transposable element annotation in plant genomes
TL;DR: It is argued that the lack of focus dedicated to the fine-scale characterization of repeat fractions and the absence of consistent methods for their annotation impede the ability to critically understand the influence of TEs on the epigenome with implications in gene expression and non-Mendelian inheritance.
Journal ArticleDOI
Genetic mapping of polygenic scab (Venturia pirina) resistance in an interspecific pear family
Kyungho Won,Héloïse Bastiaanse,Yoon Kyeong Kim,Jang Hoon Song,Sam Seog Kang,Han Chan Lee,Kang Hee Cho,Lester Brewer,Gagandeep Singla,Susan E. Gardiner,David Chagné,Vincent G. M. Bus +11 more
TL;DR: In this article, PEAR1×PEAR2 derived from European (Pyrus communis) and Asian (P. pyrifolia and P. ussuriensis) pears was infected with three single-spore isolates of V. pirina using droplet inoculation technique.
Journal ArticleDOI
A de novo genome assembly of the dwarfing pear rootstock Zhongai 1
Chunqing Ou,Fei Wang,Jiahong Wang,Song Li,Yanjie Zhang,Ming Fang,Ma Li,Yanan Zhao,Shuling Jiang +8 more
TL;DR: The assembled genome of ‘Zhongai 1’ will help identify genes involved in dwarfism, early flowering, stress tolerance, and commercially desirable fruit characteristics and will be a valuable resource and reference for future pear breeding, genetic improvement, and comparative genomics among related species.
References
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