HZAU’s Group of Cotton Genetic Improvement (GCGI) has published its latest academic paper on the international journal Molecular Biology and Evolution. The team presented the first modern evaluation of the observed genome expansion in the lineage leading to K2, and provided evidence for an evolutionary understanding of higher-order chromatin structure organization in Gossypium following activation of LTR retrotransposon amplification.
With the reported reference-grade genome assemblies for three species of cotton ranging three-fold in genome size, namely Gossypium rotundifolium (K2), G. arboretum (A2), and G. raimondii (D5), the research sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants, and provides a topological basis for functional analysis of non-coding genomic sequences in complex genomes.
The Gossypium genus contains around 52 species divided into eight monophyletic groups (designated A to G and K) and a single allotetraploid clade (AD1 to AD7). Notably, the largest diploid genomes belong to the K genome clade, whose large size is similar to the tetraploid cotton genomes and is about three-fold larger than the smallest species. These characteristics make cotton an excellent system for studying the evolutionary mechanism and consequences germane to genome size expansion. Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants.
This group applied Oxford Nanopore Technologies to assemble genomes of three cotton species, which resulted in 3,593 contigs comprising 2.44 Gb in G. rotundifolium, 1,173 contigs comprising 1.62 Gb in G. arboretum, and 366 contigs comprising 0.75 Gb in G. raimondii. The analysis of full-length LTRs in the three genomes suggested that the insertion time peak of LTR retrotransposons in K2 was found at 4.5-5 MYA, while A2 had a more recent amplification peak at 0.6-1 MYA.
The chromatin interaction analysis assisted us in discovering approximately 17% of syntenic genes exhibited chromatin status change between active (“A”) and inactive (“B”) compartments, and TE amplification was associated with the increase of the proportion of A compartment in gene regions in K2 and A2 relative to D5. Of note is the finding that 60% of genomic length of TAD boundaries were covered by Gypsy LTR retrotransposons in K2 as young LTR retrotransposons had higher expression levels than the ancient ones in the three genomes. These criteria contribute to the evolutionary models of A/B compartment switching, lineage-specific TE amplification, and lineage-specific TAD organization, displayed as below.
The co-first authors of the paper comprise Prof. Wang Maojun and Dr. Li Jianying. The co-corresponding authors consist of Prof. Zhang Xianlong, Wang Kunbo, researcher from the Institute of Cotton Research of Chinese Academy of Agricultural Sciences, and Prof. Jonathan F. Wendel from Iowa State University. This work was funded by National Transgenic Plant Research of China (2016ZX08005-001) and National Natural Science Foundation of China (31922069).
Source: http://news.hzau.edu.cn/2021/0512/60231.shtml
Article: https://doi.org/10.1093/molbev/msab128
Translated by: Yan Xiruo
Supervised by: Pan Buhan
