Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 May 25;114(3):286-293.
doi: 10.1093/jhered/esad018.

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

Julia Harenčár  1 , Oscar M Vargas  2 , Merly Escalona  3 , Douglas W Schemske  4 , Kathleen M Kay  1
Affiliations

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

Julia Harenčár et al. J Hered. .

Abstract
in English, Spanish

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 2 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 2 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.

Costus es un género pantropical de monocotiledóneas herbáceas perennes; el clado neotropical de Costus se diversificó rápidamente en más de 60 especies en los últimos millones de años. Las especies de neotropicales de Costus tienen una rica historia de investigación evolutiva y ecológica que puede motivar e informar las investigaciones genéticas modernas. Aquí, presentamos los dos primeros ensamblajes de genoma a nivel de cromosoma en el género, C. pulverulentus y C. lasius, y comparamos brevemente su sintenía. El genoma de C. pulverulentus lo ensamblamos a partir de una combinación de datos de secuenciación de lectura corta, secuenciación de proximidad de cromatina CHiCago y Hi-C de Dovetail y su alineación con un mapa de ligamiento. Ensamblamos el genoma de C. lasius con lecturas largas HiFi de Pacific Biosciences y alineación con el genoma de C. pulverulentus. Estos dos ensamblajes son los primeros genomas publicados para plantas tropicales no cultivadas. Estos genomas solidifican Costus como un sistema modelo y que facilitarán la investigación sobre la base genética poco conocida de la diversificación de plantas tropicales.

Keywords: genome resources; herbaceous; monocot; synteny; tropical plant.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Geographic distributions and photos of each species. Location data are from the Vargas et al. (2020) supplement and represent expert-verified collection locations. Photos show a terminal inflorescence with a single open flower. Photo credits: C. lasius - KMK; C. pulverulentus - Rossana Maguiña.
Fig. 2.
Fig. 2.
Syntetic dotplot with the C. lasius genome assembly represented by the x axis and the C. pulverulentus genome assembly represented on the y axis. Dots represent matching sequences and where they are found along the genomes. Dot color represents alignment identity, or how well the sequences match between the genomes, with 1 representing a perfect match and 0 representing no match. Dark green represents sequences with alignment scores of 0.75 to 1, light green represents scores from 0.5 to 0.75 alignment identity, etc. We generated the plot with D-GENIES using Minimap 2 for alignment and selecting the “sort” and “hide noise” options. Access the interactive plot here.
See this image and copyright information in PMC

References

    1. Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC.. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019;20:224. - PMC - PubMed
    1. Argout X, Salse J, Aury J-M, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, et al. . The genome of Theobroma cacao. Nat Genet. 2011;43:101–108. - PubMed
    1. Ávila-Lovera E, Goldsmith GR, Kay KM, Funk JL.. Above- and below-ground functional trait coordination in the neotropical understory genus Costus. AoB PLANTS. 2022;14:plab073. - PMC - PubMed
    1. Bartlett ME, Specht CD.. Evidence for the involvement of GLOBOSA-like gene duplications and expression divergence in the evolution of floral morphology in the Zingiberales. New Phytol. 2010;187:521–541. - PubMed
    1. Bizzarri L, Baer CS, García-Robledo C.. DNA barcoding reveals generalization and host overlap in hummingbird flower mites: implications for the mating rendezvous hypothesis. Am Nat. 2022;199:576–583. - PubMed

Publication types