Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry
Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry
复制标题
四倍体蓝莓的单倍型相基因组和植物营养素途径的进化
DOI：
10.1093/gigascience/giz012
复制
发表时间：
2019-03-01
期刊：
影响因子：
9.2
通讯作者：
Edger, Patrick P.
中科院分区：
文献类型：
--
作者：
Colle, Marivi;Leisner, Courtney P.;Edger, Patrick P.
摘要背景高丛蓝莓（Vaccinium corymbosum）因其独特的风味和促进健康的植物营养素组成而长期被消费。然而，由于缺乏足够的基因组资源和对编码关键性状的潜在遗传学的了解有限，提高蓝莓果实品质的育种工作受到了极大的阻碍。高丛蓝莓的基因组在很大程度上由于其多倍体性质和基因组大小而特别具有挑战性。结果在这里，我们提出了一个染色体规模和单倍型相的基因组组装的品种“德雷珀”，它具有最高的抗氧化剂水平之间的多样性面板的71个品种和13个野生越橘种。我们利用这个基因组，结合基因表达和代谢产物的数据测量整个水果的发展，以确定候选基因参与生物合成的重要植物营养素之间的其他代谢产物与上级水果品质。全基因组分析表明，多倍体和串联基因重复修饰了参与关键植物营养素生物合成的各种途径。此外，基因表达分析暗示存在时空特异性显性表达的亚基因组，包括在果实发育期间。结论这些结果和参考基因组将作为指导未来高丛蓝莓重要农艺性状基因组使能育种的宝贵资源。
Abstract Background Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size. Findings Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar “Draper,” which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. Conclusions These findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.