Costus pulverulentus genome annotations

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 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.

Methods
To create a draft annotation for the C. pulverulentus genome, we mapped a transcriptome of C. pulverulentus (GenBank accession SRX7544604, Vargas et al. 2020) to the draft genome using PASApipeline (Haas et al., 2003). To search for potential gene functions in our draft annotation, we queried our mapped transcripts against a protein database (GO; Harris et al., 2004) using EnTAP (Hart et al., 2020). Matching protein names and functions were added as annotation notes in the .gff3 annotation file generated with PASA using a custom python script available with the annotation files in this repository.