Genome assemblies and comparison of two Neotropical spiral gingers: Costus pulverulentus and C. lasius

Abstract

The spiral gingers (Costus L.) are a pantropical genus of herbaceous perennial monocots; the Neotropical clade of Costus radiated rapidly in the past few million years into over 60 species. The Neotropical spiral gingers have a rich history of evolutionary and ecological research that can motivate and inform modern genetic investigations. Here, we present the first two chromosome-level genome assemblies in the genus, for C. pulverulentus and C. lasius, and briefly compare their synteny. We assembled the C. pulverulentus genome from a combination of short-read data, Chicago and Dovetail Hi-C chromatin-proximity sequencing, and alignment with a linkage map. We annotated the genome by mapping a C. pulverulentus transcriptome and querying mapped transcripts against a protein database. We assembled the C. lasius genome with Pacific Biosciences HiFi long reads and alignment to the C. pulverulentus genome. These two assemblies are the first published genomes for non-cultivated tropical plants. These genomes solidify the spiral gingers as a model system and will facilitate research on the poorly understood genetic basis of tropical plant diversification.

Repeated loss of floral scent in independent transitions from bee to hummingbird pollination in spiral gingers

“…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). We assembled a reference genome for C. allenii (bee) to generate a dataset of two hummingbird- and two bee-pollinated species.…”

“…Of the three species for which we generated RNAseq data, an unannotated genome was previously available for C. lasius (Harenčár et al 2023). In this study we also generated a genome assembly for C.allenii .…”

“…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.…”

“…(Martin 2011). We then mapped the reads from all three species to both the Costus allenii and Costus lasius genome (Harenčár et al 2023). We ran 2pass mapping using STAR (Dobin et al 2013).…”

“…Traits including small flower size, the absence of nectar guides, and brightly colored floral bracts are all predictive of hummingbird pollination (Kay and Grossenbacher 2022). The combination of recent genomic resources, a well-resolved phylogeny, and the possibility of collecting samples both in the field and in greenhouses, makes Costus a powerful system to study the evolution of convergence on hummingbird pollination (Vargas et al 2020; Kay and Grossenbacher 2022; Harenčár et al 2023).…”