The genetic mechanisms underlying the convergent evolution of pollination syndromes in the Neotropical radiation of Costus L.

Abstract

Selection together with variation in floral traits can act to mold floral form, often driven by a plant’s predominant or most effective pollinators. To investigate the evolution of traits associated with pollination, we developed a phylogenetic framework for evaluating tempo and mode of pollination shifts across the genus Costus L., known for its evolutionary toggle between traits related to bee and bird pollination. Using a target enrichment approach, we obtained 957 loci for 171 accessions to expand the phylogenetic sampling of Neotropical Costus. In addition, we performed whole genome resequencing for a subset of 20 closely related species with contrasting pollination syndromes. For each of these 20 genomes, a high-quality assembled transcriptome was used as reference for consensus calling of candidate loci hypothesized to be associated with pollination-related traits of interest. To test for the role these candidate genes may play in evolutionary shifts in pollinators, signatures of selection were estimated as dN/dS across the identified candidate loci. We obtained a well-resolved phylogeny for Neotropical Costus despite conflict among gene trees that provide evidence of incomplete lineage sorting and/or reticulation. The overall topology and the network of genome-wide single nucleotide polymorphisms (SNPs) indicate that multiple shifts in pollination strategy have occurred across Costus, while also suggesting the presence of previously undetected signatures of hybridization between distantly related taxa. Traits related to pollination syndromes are strongly correlated and have been gained and lost in concert several times throughout the evolution of the genus. The presence of bract appendages is correlated with two traits associated with defenses against herbivory. Although labellum shape is strongly correlated with overall pollination syndrome, we found no significant impact of labellum shape on diversification rates. Evidence suggests an interplay of pollination success with other selective pressures shaping the evolution of the Costus inflorescence. Although most of the loci used for phylogenetic inference appear to be under purifying selection, many candidate genes associated with functional traits show evidence of being under positive selection. Together these results indicate an interplay of phylogenetic history with adaptive evolution leading to the diversification of pollination-associated traits in Neotropical Costus.

The convergent evolution of hummingbird pollination results in repeated floral scent loss through gene downregulation

“…For this, we need genome data to allow us to determine the number of TPS genes in each species. There are currently three publicly available Costus genomes: C. bracteatus (bee), C. lasius (hummingbird) , and C. pulverulentus (hummingbird) (Valderrama et al 2022; Harenčár et al 2023). To generate a dataset of two hummingbird- and two bee-pollinated species, we assembled an additional high-quality reference genome for bee-pollinated C. allenii (Table S1 for assembly statistics, Figure S3 to see alignment with C. lasius genome).…”

“…For this, we need genome data to allow us to determine the number of TPS genes in each species. There are currently three publicly available Costus genomes: C. bracteatus (bee), C. lasius (hummingbird) , and C. pulverulentus (hummingbird) (Valderrama et al 2022; Harenčár et al 2023). Costus lasius and C. pulverulentus represent two independent transitions to hummingbird pollination (Kay and Grossenbacher 2022).…”

“…In this study we also generated a genome assembly for C.allenii . In addition, previously published genomes are available for both C. bracteatus and the more distantly-related C. pulverulentus (Valderrama et al 2022; Harenčár et al 2023). We started by processing RNAseq data as evidence for annotations.…”

Balancing read length and sequencing depth: Optimizing Nanopore long‐read sequencing for monocots with an emphasis on the Liliales

“…One modification we made to the standard SDS protocol was a chloroform-isoamyl alcohol cleanup step, which is standard in most CTAB protocols (Doyle and Doyle, 1987). While this step is not necessary for Illumina sequencing following SDS extractions (Valderrama et al, 2020(Valderrama et al, , 2022, the chloroform cleanup greatly improves the A 260 /A 280 and A 260 /A 230 values recorded with the NanoDrop to levels closer to pure DNA (A 260 /A 280 between 1.8-2.0; A 260 /A 230 between 2.0-2.2), which are necessary for good Nanopore sequencing runs. The final step in our DNA cleaning process was the Qiagen DNeasy PowerClean Pro Cleanup Kit, which removes inhibitory substances in the extracted DNA, including polysaccharides and lipids.…”

“…The final step in our DNA cleaning process was the Qiagen DNeasy PowerClean Pro Cleanup Kit, which removes inhibitory substances in the extracted DNA, including polysaccharides and lipids. Although this step does fragment the DNA, sometimes by as much as half (N50 of ~20 kbp to ~10 kbp), the total output per flow cell is boosted 2-3×, as was seen in the long-read sequencing of Costus L. (Landis et al, unpublished data;Valderrama et al, 2022). Performing a second elution of the DNA from the spin column allows for a greater recovery of DNA.…”