Publications

Background High-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported.

Results Here, we perform the pan-3D genome analysis using Hi-C sequencing data from 27 soybean accessions and comprehensively investigate the relationships between 3D genomic variations and structural variations (SVs) as well as gene expression. We find that intersection regions between A/B compartments largely contribute to compartment divergence. Topologically associating domain (TAD) boundaries in A compartments exhibit significantly higher density compared to those in B compartments. Pan-3D genome analysis shows that core TAD boundaries have the highest transcription start site (TSS) density and lowest GC content and repeat percentage. Further investigation shows that non-long terminal repeat (non-LTR) retrotransposons play important roles in maintaining TAD boundaries, while Gypsy elements and satellite repeats are associated with private TAD boundaries. Moreover, presence and absence variation (PAV) is found to be the major contributor to 3D genome variations. Nevertheless, approximately 55% of 3D genome variations are not associated with obvious genetic variations, and half of them affect the flanking gene expression. In addition, we find that the 3D genome may also undergo selection during soybean domestication.

Conclusion Our study sheds light on the role of 3D genomes in plant genetic diversity and provides a valuable resource for studying gene regulation and genome evolution.

Keywords Pan-3D genome, Structural variations, Non-LTR retrotransposons, Gypsy elements, Satellite repeats, PAV

In eukaryotic cells, the distal cis-regulatory genomic sequences are usually thousands to millions of base pairs away from the transcription start sites of genes. The interactions between these sequences and the genes they controlled are regulated by the three-dimensional (3D) genome organization in the nucleus. In the past decade, high-throughput methods have been used to help map 3D organization, identify multiple 3D genome structures, and investigate the functional role of 3D genome organization in gene regulation. However, the relationship between 3D genome structure and function in soybean is not completely understood. Here we review recent progress in this field and discuss several future directions to improve functional genome study and breeding in soybean.

As one of the most important crops to supply majority plant oil and protein for the whole world, soybean is facing an increasing global demand. Up to now, vast multi-omics data of soybean were generated, thereby providing valuable resources for functional study and molecular breeding. Nevertheless, it is tremendously challenging for researchers to deal with these big multi-omics data, particularly considering the unprecedented rate of data growth. Therefore, we collect the reported high-quality omics, including assembly genomes, graph pan-genome, resequencing and phenotypic data of representative germplasms, transcriptomic and epigenomic data from different tissues, organs and accessions, and construct an integrated soybean multi-omics database, named SoyOmics (https://ngdc.cncb.ac.cn/soyomics). By equipping with multiple analysis modules and toolkits, SoyOmics is of great utility to facilitate the global scientific community to fully use these big omics datasets for a wide range of soybean studies from fundamental functional investigation to molecular breeding.

Soybean provides more than half of the oilseeds and more than a quarter of protein worldwide. It is estimated that the production of soybean has to be doubled by 2050 to meet the needs of the rapidly increasing consumption of soybean seeds along with a continuously increasing population. As such, development of a genotyping platform with high throughput, high efficiency and high precision but low-cost is urgently needed to accelerate soybean functional study and molecular design breeding.

Soybean is one of the most important crops worldwide. A high-quality reference genome will facilitate its functional analysis and molecular breeding. Previously, we de novo assembled a high-quality Chinese soybean genome Gmax_ZH13. However, due to technical limitations at the time when we generated Gmax_ZH13, a large number of small contigs were not anchored onto chromosomes. Therefore, we here build a new golden reference genome for Zhonghuang 13 consisting of 20 nearly complete chromosomes by adding more single-molecule real time (SMRT) sequencing reads. Furthermore, we add large RNA-seq and smRNA-seq datasets for improving the annotation of its protein coding genes.