Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Ministry of Agriculture, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China.
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
Plant Biotechnol J. 2020 Feb;18(2):581-595. doi: 10.1111/pbi.13226. Epub 2019 Aug 12.
China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide-binding site (NBS)-type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR-NBS-LRR (TNL)-type genes, which represented the greatest number of TNL-type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism-related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high-quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.
中国是东方梨的起源和进化中心。豆梨是中国原产的野生种，分布于北方地区，广泛用作砧木。在这里，我们报道了使用 PacBio 测序、BioNano 图谱和染色体构象捕获（Hi-C）测序相结合的综合策略对 P. betuleafolia-Shanxi Duli 进行从头组装的结果。基因组组装大小为 532.7 Mb，contig N50 为 1.57 Mb。总共注释了该基因组的 59552 个蛋白质编码基因和 247.4 Mb 的重复序列。豆梨的扩张基因在次生代谢中显著富集，这可能解释了该物种对环境的高度适应性。直系同源基因的比对分析表明，在东方梨的驯化过程中，果实大小、糖代谢和运输以及光合作用效率发生了正选择。在豆梨基因组中鉴定了 573 个核苷酸结合位点（NBS）-型抗病基因类似物（RGA），其中 150 个是 TIR-NBS-LRR（TNL）-型基因，这代表了已发表的蔷薇科基因组中 TNL 型基因数量最多，解释了该野生种的强抗病性。风味代谢相关基因的研究表明，花色苷还原酶（ANR）代谢途径影响梨果实的涩味，山梨醇转运蛋白（SOT）跨膜转运可能是影响可溶性有机物积累的主要因素。该高质量的豆梨基因组为利用野生梨进行基础梨研究和育种提供了宝贵的资源。
