Complete map of the potato genome reveals highly tandem replication gene clusters associated with important agronomic traits in complex regions

The potato genetics, breeding and cultivation innovation team and vegetable molecular design and breeding innovation team of the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, performed full sequence assembly of the genome of potato haplotype DM. A genome completion map (DM8.1) of telomere-to-telomere (T2T) containing 24 telomeres and 12 centromere complete sequences of potato haplotype DM was obtained, and a large number of gene clusters regulating important agronomic traits were identified in highly repetitive regions where the potato genome had not been fully assembled. The findings were recently published in Molecular under the title The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions Plant(IF=21.949).

 

The potato is the world's third largest food crop after wheat and rice, and its homotetraploid inheritance and high heterozygosity limit potato genetic breeding research. High-quality reference genomes are an important basis for potato genetic breeding research. The dihaploid DM1-3 516 R44 (DM) genome has been playing an important role as a reference genome in potato genomics, genetics and breeding research, and its genomic version has been improved to DM6.1 (Pham et al., 2020) over a decade since the original DM4.04 (PGSC, 2011), but there are still 161 gaps, and the telomere and centromeromere structure is still incomplete. What genetic information is hidden in these GAP regions and telomere and centromeric structures is unknown. With the development of third-generation sequencing technology, especially the combination of high-continuity ONT ultra-long sequencing and high-precision HIFI sequencing, it is expected to overcome the problem of difficult assembly of centromeres or highly repetitive regions. The gap-free genome is the ultimate goal of genome assembly, the basis for in-depth study of unique genes and variants (SV) in sequence regions such as centromeres, transposable factors (TEs), and segmental duplications (SDs). At present, only rice, Arabidopsis thaliana and watermelon with relatively small genomes have achieved the Gap-free genome.

 

In this study, Nanopore ONT Ultra-long reads and Hi-C mounting, combined with a variety of technical methods for gap closing, obtained a complete T2T genome map of potato haplotype DM containing 24 telomeres and 12 centromeres complete sequences (DM8.1).

 

First, ONT ultra-long reads were used for third-generation assembly and Hi-C mounting, and the genome version preDM8, which was significantly better than DM6.1, was obtained in terms of size, integrity and continuity The ntig N50 is twice as large as the DM6.1. The preDM8 genome contains only 25 gaps in 12 chromosomes, less than 161 in DM6.1, and the complete chromosome of chr05 is directly obtained. Secondly, 25 gaps in preDM8 were filled by iterative assembly, collinear comparison, long fragment amplification of target sequences, and HiFi sequencing. Among them, in the process of HiFi sequencing hole filling, primers were designed based on the sequence of 5 kb on both sides of the gap, the product was obtained by long-PCR amplification and sequenced, and iterative assembly was carried out by combining HiFi sequencing reads and sequence on both sides of the gap, and finally the gap-free genome of potato DM (DM8.1) was obtained.

 

The study further found that there are highly tandem repeating gene clusters in the unfilled gap of the genome DM6.1, and these genes regulate important agronomic traits in potato, including patatin, TPS, Cupin, Leucine-rich repeat and other genes. Among them, the tuber storage protein patatin gene was specifically amplified in the potato genome, and this amplification process continued during the process of potato speciation, domestication and breeding improvement. In addition to the large amplification of copy number, the gene function of patatin is also strongly positively selected. Transcriptome analysis showed that the vast majority of these highly amplified patatin genes were highly specific and highly expressed in potato tubers. Based on the above findings, it is speculated that the patatin gene plays a key role in potato crop domestication and tuber formation through dose amplification and functional evolution. The findings also suggest the potential feasibility of crop improvement by regulating the copy number/absolute dose of a single or small number of key genes.

 

The results of this study will promote our attention and understanding of highly repetitive sequence regions or highly repetitive structures in the genome; DM8.1, as the first genome completion map in nightshade crops, also provides a reference for the completion map assembly of other genomes; in addition, DM8.1 completion map will promote the rapid development of genetic breeding research of potatoes and other nightshade crops, which is of great significance.

 

Researcher Li Guangcun from the Potato Genetics, Breeding and Cultivation Innovation Team, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, and Cheng Feng, from the Vegetable Molecular Design and Breeding Innovation Team, are the co-corresponding authors of the paper, and Yang Xiaohui, associate researcher at the Institute of Vegetables, Shandong Academy of Agricultural Sciences, and Zhang Lingkui, a doctoral student at the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, are the first authors of this paper. Huang Sanwen, a researcher at the Chinese Academy of Tropical Agricultural Sciences and the Shenzhen Institute of Agricultural Genomics of the Chinese Academy of Agricultural Sciences, guided the study. The research was supported by the National Natural Science Foundation of China, Shandong Province Fine Seed Project, National Potato Industry Technology System, Central Public Welfare Scientific Research Institute Basic Scientific Research Funds Special Project, Chinese Academy of Agricultural Sciences Science and Technology Innovation Project and other projects.