The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis

First author: Fengchao Jiang; Affiliations: Beijing Academy of Forestry and Pomology Sciences (北京林果科学院): Beijing, China

Corresponding author: Yuzhu Wang 

Apricots, scientifically known as Prunus armeniaca L, are drupes that resemble and are closely related to peaches or plums. As one of the top consumed fruits, apricots are widely grown worldwide except in Antarctica. A high-quality reference genome for apricot is still unavailable, which has become a handicap that has dramatically limited the elucidation of the associations of phenotypes with the genetic background, evolutionary diversity, and population diversity in apricot. DNA from P. armeniaca was used to generate a standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on Sequel SMRT Cells, generating a total of 16.54 Gb of PacBio subreads (N50 = 13.55 kb). The high-quality P. armeniaca reference genome presented here was assembled using long-read single-molecule sequencing at approximately 70× coverage and 171× Illumina reads (40.46 Gb), combined with a genetic map for chromosome scaffolding. The assembled genome size was 221.9 Mb, with a contig NG50 size of 1.02 Mb. Scaffolds covering 92.88% of the assembled genome were anchored on eight chromosomes. Benchmarking Universal Single-Copy Orthologs analysis showed 98.0% complete genes. We predicted 30,436 protein-coding genes, and 38.28% of the genome was predicted to be repetitive. We found 981 contracted gene families, 1324 expanded gene families and 2300 apricot-specific genes. The differentially expressed gene (DEG) analysis indicated that a change in the expression of the 9-cis-epoxycarotenoid dioxygenase (NCED) gene but not lycopene beta-cyclase (LcyB) gene results in a low β-carotenoid content in the white cultivar “Dabaixing”. This complete and highly contiguous P. armeniaca reference genome will be of help for future studies of resistance to plum pox virus (PPV) and the identification and characterization of important agronomic genes and breeding strategies in apricot.

杏子，拉丁名为Prunus armeniaca L，是一种核果，形态上类似于桃子或李子，并且遗传上也是近缘物种。作为最受欢迎的消费类水果之一，杏在全球除了南极洲以外的地区都很受欢迎。杏的参考基因组图谱仍未有报道，这严重限制了解析杏表型与遗传背景、演化多样性及群体多态性之间的关联。作者利用杏的DNA构建了一个标准的、插入片段大小一定的文库，平均DNA片段大小为20kb。通过Sequel SMRT Cells对文库进行了测序，产生了约为16.54Gb的PacBio subreads，其中N50大小为13.55kb。作者结合了约70×长read单分子测序、171×的Illumina reads以及遗传图谱构建了杏的高质量参考基因组。组装的杏基因组大小为221.9Mb，ContigN50长为1.02Mb。占基因组92.88%的Scaffolds能够被挂载到8条假染色体上。BUSCO分析显示杏基因组上包含了约98%的核心植物基因。作者预测了30436个蛋白编码基因，基因组的38.28%为重复序列。作者鉴定了981个收缩基因家族、1324个扩张基因家族以及2300个杏特异基因。差异表达基因分析显示白色栽培种“大白杏”果实中β-类胡萝卜素含量低的原因并不是因为番茄红素β-环化酶LcyB基因表达的改变所导致的，而是因为9-顺式-环氧类胡萝卜素双加氧酶NCED基因表达的改变。本文所报道的杏基因组将有助于将来对于李痘病毒的抗性育种，并且可用来鉴定重要的农艺相关基因，辅助制定适宜的育种策略。

通讯：王玉柱

研究方向：杏、李、核桃和柿等树种的资源收集评价、品种选育和生物学特性的研究工作。

doi: https://doi.org/10.1038/s41438-019-0215-6

Journal: Horticulture Research

Published date: November 18, 2019