等位基因定义的同源多倍体甘蔗基因组 Saccharum spontaneum L.

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

机构信息

Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, 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. 2018 Nov;50(11):1565-1573. doi: 10.1038/s41588-018-0237-2. Epub 2018 Oct 8.

DOI:10.1038/s41588-018-0237-2

PMID:30297971

Abstract

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.

摘要

现代甘蔗是多倍体种间杂种，结合了甜高粱的高含糖量、抗逆性和再生能力。对一个单倍体甘蔗 AP85-441 的测序，促进了 32 个假染色体的组装，这些假染色体由 8 个同源组组成，每组 4 个成员，包含 35525 个有定义等位基因的基因。甘蔗属中基本染色体数从 10 减少到 8 是由 2 条祖先染色体的裂变引起的，随后发生了到 4 条染色体的易位。令人惊讶的是，80%与抗病性相关的核苷酸结合位点编码基因位于 4 条重排染色体上，51%位于重排区。对 64 个甘蔗属基因组的重测序发现，在重排区存在平衡选择，保持了其多样性。现代甘蔗中的导入甘蔗属染色体在 AP85-441 基因组中随机分布，表明不同甘蔗属品系中的同源物之间存在随机重组。等位基因定义的甘蔗属基因组为加速甘蔗改良提供了新的知识和资源。