Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition

Authors: ZHUANG, YONGBIN - Shandong Agricultural University; WANG, XUTONG - Purdue University; LI, XIANCHONG - Shandong University; HU, JUNMEI - Shandong University; FAN, LICHUAN - Shandong University; LANDIS, JACOB - Cornell University; Cannon, Steven; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology; JACKSON, SCOTT - University Of Georgia; DOYLE, JEFFREY - Cornell University; ZHANG, XIAN SHENG - Shandong University; ZHANG, DAIJAN - Shandong University; MA, JIANXIN - Purdue University

Submitted to: Nature Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2022
Publication Date: 3/14/2022
Citation: Zhuang, Y., Wang, X., Li, X., Hu, J., Fan, L., Landis, J.B., Cannon, S.B., Grimwood, J., Schmutz, J., Jackson, S.A., Doyle, J.J., Zhang, X., Zhang, D., Ma, J. 2022. Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. Nature Plants. 8: 233-244. https://doi.org/10.1038/s41477-022-01102-4.
DOI: https://doi.org/10.1038/s41477-022-01102-4

Interpretive Summary: Soybean, one of the most important crops globally for its protein and oil content, faces numerous challenges from insects, pathogens, and environmental stresses. A group of wild relatives of soybean, from Australia, may provide information to researchers to better understand how to improve soybean resilience to various stresses. This research reports the full genome sequences from six soybean relatives, all in the genus Glycine. All six of the newly sequenced species are perennial, and all are able to survive in challenging environments in their native ranges in Australia. This work also identifies genes that are highly conserved across the Glycine genus, as well as genes that are specific to one or several species. A gene involved in the transition between the perennial and annual life forms is also described. These results provide basic information that may be used for soybean improvement, particularly in light of increasing environmental challenges due to climate change.

Technical Abstract: Polyploidy and life strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and genetic bases of such transitions remain elusive. This report describes the assembled genomes of representative perennial species across the genus Glycine, including five diploids and a young allopolyploid. These genome sequences were used to construct a Glycine super-pangenome framework, by integrating 26 annual soybean genomes. The perennials exhibited greater genome stability than the annuals, and less abundant centromeric repeats. Biased subgenome fractionation has occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with preexisting local genomic differentiation. A gene annotated to modulate vegetative to reproductive phase transition was identified to have undergone adaptive evolution underlying the perenniality-annuality transition. This study provides insights into mechanisms of polyploid genome evolution, and provides resources for accessing the perennial gene pool for soybean improvement.