Exploring Structural Plastome Evolution in Asterales: Insights from Off-Target Hybrid Enrichment Data on the Small Single-Copy Region.

The massive increase in the amount of plastid genome data have allowed researchers to address a variety of evolutionary questions within a wide range of plant groups. While plastome structure is generally conserved, some angiosperm lineages exhibit structural changes. Such is the case of the megadiverse order Asterales, where rearrangements in plastome structure have been documented. This study investigates the possibility of recovering plastid loci from off-target reads obtained through hybrid enrichment techniques. Our sampling includes 63 species from the eleven currently recognized families in Asterales derived from previously published studies. We assembled and annotated complete and partial plastomes using custom pipelines and estimate phylogenomic relationships. We retrieved plastid information from 60 of the 63 sampled species including a complete plastome from Tithonia tubaeformis (Asteraceae), circular partial (with gaps) plastomes from seven species, and non-circular partial plastomes from other 52 species. We focused on the small single-copy region because it could be recovered for over 29 species. Within the small single-copy region, we assessed intron losses and presence of putative pseudogenes. Comparative genomics revealed a relocated fragment of ~ 6500 bp in two Campanulaceae lineages (i. e. subfamily Lobelioideae and Pseudonemacladus oppositifolium), involving the genes rbcL, atpB, atpE, trnM-CAU, and trnV-UAC. Obtained phylogenetic hypotheses were congruent across the applied methods and consistent with previously published results. Our study demonstrates the feasibility of recovering plastid information, both complete and partial, from off-target hybrid enrichment data and provides insights on the structural plastome changes that have occurred throughout the evolution of the order Asterales.