A reference quality genome assembly and investigation of whole genome duplication in the mimosoid legume leucaena trichandra

Authors: BAILEY, DONOVAN - New Mexico State University; STRICKLER, SUSAN - Chicago Botanical Garden; KOENEN, ERIK - University Of Zurich; RINGELBERG, JENS - University Of Edinburgh; BANGA, KITTI - New Mexico State University; LOPEZ, MIKE - New Mexico State University; IIOBA, OGO - New Mexico State University; REYNOLDS, GILLIAN - Montana State University; Nageswara Rao, Madhugiri; TRUJILLO, JOSHUSA - Purdue University; STRAUB, SHANNON - Hobart And William Smith Colleges; WEITEMIER, KEVIN - Oregon State University; CRONN, RICHARD - Us Forest Service (FS); HUGHES, COLIN - University Of Zurich; LISTON, AARON - Oregon State University

Submitted to: International Botanical Congress
Publication Type: Abstract Only
Publication Acceptance Date: 5/15/2024
Publication Date: 7/21/2024
Citation: Bailey, D.C., Strickler, S.R., Koenen, E.J., Ringelberg, J.J., Banga, K., Lopez, M., Iioba, O., Reynolds, G.L., Nageswara Rao, M., Trujillo, J.T., Straub, S.C., Weitemier, K.A., Cronn, R., Hughes, C.E., Liston, A. 2024. A reference quality genome assembly and investigation of whole genome duplication in the mimosoid legume leucaena trichandra. International Botanical Congress, July 21-27, 2024. Madrid, Spain.

Interpretive Summary:

Technical Abstract: Previous phylogenetic and evolutionary work on the mimosoid legume genus Leucaena has inferred a complex history that included an ancient whole genome duplication (WGD) prior to the diversification of 19 diploidized divergently related species. Inter subclade hybridization events among a subset of these 19 species resulted in the formation of five independent allotetraploid species, some of which are important multipurpose trees in tropical agroforestry systems. Here we use whole genome sequencing from long- and short-read data to assemble a reference genome for the putatively diploidized species L. trichandra, the putative parent of four of the five Leucaena allotetraploids. The genome is used 1) in comparative genomic analyses to investigate the relative quality of the genome and the associated annotations, 2) to clarify WGD relevant events and the diploid, tetraploid, and/or octoploid nature of Leucaena species, and 3) to investigate the role of methylation and chromatin structure on gene expression following an ancient WGD. The comparative genomic analyses show that the chromosome-scale assembly captures contiguous gene space well and that the annotation file is comprehensive. Despite the modest genome sizes observed in Leucaena, our results conflict with the prior conclusion of extensive genic diploidization following a stem lineage WGD. This lack of diploidization suggests that Leucaena comprises 19 tetraploid species and five allooctoploid species as well as several other putatively hybrid lineages. The inferred combination of ancestral subgenomes contributing to the stem lineage WGD is also apparently complex, with three potentially distinct subgenomes representing the observed genomic diversity. Lastly, we discuss the impact of cytosine methylation and chromatin structure on the fate of duplicated genes and their expression following the ancient WGD.