Phylotranscriptomics and genome size evolution in Leucaena (Fabaceae): Paleotetraploid genomic stability overshadows...

Advances in transcriptomic and reduced representation genomic sequencing are deepening our understanding of how hybridization, reticulation, and environmental variation impact species diversification and genome size. Leucaena is a useful system for exploring the genomic basis of allopatric and allopolyploid speciation events and the effect of environmental pressures on genome size across 30° of latitude. We investigate phylogenetic relationships, the roles of polyploidy and hybridization in speciation, and genome size evolution in the genus.

Using newly generated RNA-sequencing data for Leucaena, we applied reference-guided and de novo phylotranscriptomics to reconstruct nuclear and organellar phylogenies. We then used comparative genome sizes from 252 samples and phylogenetic methods to investigate genome size evolution broadly and the impacts of environmental variables specifically.

The phylogenetic results supported cladogenetic, rather than reticulate/hybrid, origins for most of the 19 paleotetraploid species. By contrast, gene tree data supported hybrid origins for octoploid Leucaena. The ancestral paleotetraploid genome size (1.52 pg/2 C) is relatively conserved among the paleotetraploids, rejecting our hypothesis associated with environmental variables significantly impacting genome sizes.

The phylogenetic results illustrate the complex interplay of intrinsic and external factors that impact speciation, including ancient whole-genome duplication (WGD), cladogenesis, secondary contact, and allopolyploidy. A weak relationship between genome size and environmental variables suggests that other factors, including paleotetraploid genomic stability, have constrained genome size variation following a WGD 16+ million years ago. The findings are consistent with a small but growing number of studies identifying groups with ancient WGDs that resist diploidization associated with gene and DNA loss.