带苞菠萝基因组与克隆繁殖作物的驯化。

The bracteatus pineapple genome and domestication of clonally propagated crops.

机构信息

FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.

Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

出版信息

Nat Genet. 2019 Oct;51(10):1549-1558. doi: 10.1038/s41588-019-0506-8. Epub 2019 Sep 30.

DOI:10.1038/s41588-019-0506-8

PMID:31570895

Abstract

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.

摘要

对源自南美洲的克隆繁殖作物（如菠萝）的驯化，曾被假设为“单步操作”。我们对 Ananas comosus var. bracteatus CB5 进行了基因组测序，将 513Mb 组装成 25 条染色体，包含 29412 个基因。对 CB5、F153 和 MD2 的基因组比较揭示了纤维生产、颜色形成、糖积累和果实成熟的基因组基础。我们还重新测序了 89 个 Ananas 基因组。品种“ Smooth Cayenne”和“Queen”表现出古老和近期的混合，而“新加坡西班牙”支持驯化的单步操作。我们鉴定了 25 个选择压力区域，包括一个含有一对串联重复的菠萝蛋白酶抑制剂的强选择压力区域。F153 中四个自交不亲和的候选基因连锁，但在自交亲和的 CB5 中没有功能。我们的研究结果支持克隆繁殖作物驯化过程中，有性重组和单步操作的共存。这项工作为探索其他克隆繁殖作物的有性和无性驯化轨迹提供了指导。