Prakash Raj Timilsena, Eric K Wafula, Craig F Barrett, Saravanaraj Ayyampalayam, Joel R McNeal, Jeremy D Rentsch, Michael R McKain, Karolina Heyduk, Alex Harkess, Matthieu Villegente, John G Conran, Nicola Illing, Bruno Fogliani, Cécile Ané, J Chris Pires, Jerrold I Davis, Wendy B Zomlefer, Dennis W Stevenson, Sean W Graham, Thomas J Givnish, James Leebens-Mack, Claude W dePamphilis
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree...
2022: Frontiers in Plant Science