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分阶段的二倍体基因组组装和泛基因组为研究苹果驯化的遗传历史提供了线索。

Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication.

机构信息

Boyce Thompson Institute, Ithaca, NY, USA.

US Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Unit, Geneva, NY, USA.

出版信息

Nat Genet. 2020 Dec;52(12):1423-1432. doi: 10.1038/s41588-020-00723-9. Epub 2020 Nov 2.

DOI:10.1038/s41588-020-00723-9
PMID:33139952
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7728601/
Abstract

Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.

摘要

苹果的驯化主要是通过种间杂交驱动的。在本研究中，我们报告了栽培苹果（Malus domestica cv. Gala）及其两个主要野生祖先 M. sieversii 和 M. sylvestris 的单倍型解析基因组。每个基因组的两个单倍型之间存在大量差异。基因组祖先推断表明，Gala 基因组中有23%来自杂交。对 91 个品系的深度测序确定了来自两个祖先之一的选择清除，与重要的驯化特征相关。苹果泛基因组的构建和分析揭示了数千个新基因，其中数百个基因来自其中一个祖先，并在栽培苹果中大量固定，表明通过杂交引入新基因/等位基因是苹果驯化的一个标志。最后，在 13 个发育阶段对 Gala 果实的转录组图谱进行分析，发现19%的基因表现出等位基因特异性表达，其中许多与果实品质有关。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/5d8581bcffc9/41588_2020_723_Fig8_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/49eeabcc8733/41588_2020_723_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/23b8923ef5e9/41588_2020_723_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/83d7446c8d2f/41588_2020_723_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/d16ea1af6667/41588_2020_723_Fig7_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/5d8581bcffc9/41588_2020_723_Fig8_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/49eeabcc8733/41588_2020_723_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/d4d943f88916/41588_2020_723_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/e9db182c3994/41588_2020_723_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/e9f6e4c4b271/41588_2020_723_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/23b8923ef5e9/41588_2020_723_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/83d7446c8d2f/41588_2020_723_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/d16ea1af6667/41588_2020_723_Fig7_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a85f/7728601/5d8581bcffc9/41588_2020_723_Fig8_ESM.jpg

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