Abstract
We present the whole genome sequences of Dryas alaskensis, D. ajanensis, and D. integrifolia from plants collected from interior Alaska. We performed deep Illumina sequencing of a single leaf of each voucher. The sequence reads were then de novo assembled and conserved regions across all preassemblies were used to join contigs in a finishing step. The raw and assembled data is publicly available via Genbank.
Keywords: dryas, genomes
Introduction
Mountain Avens (Dryas spp. Rosaceae) is a circumpolar genus of about fifteen species of wind-dispersed, self-incompatible dwarf shrubs that are distributed throughout the Arctic and Alpine regions of the northern hemisphere (Springer and Parfitt 2015; http://www.itis.gov). Dryas is primarly referenced as a classic palynological indicator of past climate (i.e. Younger Dryas stadial). As an abundant and charismatic floristic element of arctic ecosystems, species of Dryas are the official plants of the Northwest Territories, Canada and Iceland.
Here we present the first genome assemblies for three species of Dryas occurring in interior Alaska. The taxonomy of Dryas is in desperate need of taxonomic revision. The nomenclature we use here follows the Flora of North America (Springer and Parfitt 2015).
Dryas alaskensis Porsild (DAL) grows in Alaska and the Yukon Territories and D. ajanensis ssp. beringensis Jurtzev (DAJ) occurs from the Northwest Territories into Chukotka Autonomous Okrug, Russia. The ecology of DAL and D. ajanensis ssp. beringensis (DAJ) has been carefully studied to understand how they have persisted in sympatry. The two species are readily distinguished by differences in leaf size and leaf pubescence as well as microhabitat, with DAL occupying moist, ‘snowbed’ sites and DAJ occupying dry, rocky, exposed, ‘fellfield’ sites (McGraw and Antonovics 1983). The species have distinct flowering times and significant genetic differentiation as interpreted from allozyme (Max, Mouchaty, and Schwaegerle 1999) and genotyping by sequencing data (Stasinski et al. 2021). The third species, D. integrifolia Vahl., is widely distributed in Alaska, Canada, and the Russian fareast.
A genome for the other North American species, Dryas drummondii was published in 2018 as part of an investigation into the biology of nitrogen fixation in root nodules (Griesmann et al. 2018). These genome assemblies will add to the growing resources available to study this phenomenon as well as the taxonomy, ecology, evolution, and conservation of Dryas plants.
Methods
Leaf tissue from wild plants was extracted using the Qiagen Plant DNAeasy kit according to the manufacturer’s instructions. A paired-end sequencing library was constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The library was sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150 bp format. The resulting fastq files were trimmed of adapter/primer sequence and low-quality regions with Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled by SPAdes v2.5 (Bankevich et al. 2012) followed by a finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).
Results and Data Availability
Raw sequence reads and assembled genomes were deposited to Genbank’s SRA and Genomes submission pipelines.
| species | genome size | N50 | SRA | genome |
|---|---|---|---|---|
| Dryas alaskensis | 204,362,168 | 13.449 KB | SRR14834469 | JAOTQX000000000 |
| Dryas integrifolia | 211,994,740 | 15.434 KB | SRR14834464 | JAOTRM000000000 |
| Dryas octopetala | 228,063,777 | 11.214 KB | SRR14835741 | JAOTQF000000000 |
Funding
Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa.
Dawson White is supported by the Grainger Bioinformatics Center at the Field Museum and an NSF Postdoctoral Fellowship in Biology, award 2010821.
REFERENCES
- Bankevich Anton, Nurk Sergey, Antipov Dmitry, Gurevich Alexey A., Dvorkin Mikhail, Kulikov Alexander S., Lesin Valery M., et al. 2012. “SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.” Journal of Computational Biology 19 (5): 455–77. 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bolger Anthony M., Lohse Marc, and Usadel Bjoern. 2014. “Trimmomatic: A Flexible Trimmer for Illumina Sequence Data.” Bioinformatics 30 (15): 2114–20. 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Griesmann Maximilian, Chang Yue, Liu Xin, Song Yue, Haberer Georg, Crook Matthew B., Billault-Penneteau Benjamin, et al. 2018. “Phylogenomics Reveals Multiple Losses of Nitrogen-Fixing Root Nodule Symbiosis.” Science 361 (6398): eaat1743. 10.1126/science.aat1743. [DOI] [PubMed] [Google Scholar]
- Kieras M, O’Neill K, and Pirro S. 2021. Zanfona, a Genome Assembly Finishing Tool for Paired-End Illumina Reads. https://github.com/zanfona734/zanfona.
- Max Karen N., Mouchaty Suzette K., and Schwaegerle Kent E.. 1999. “Allozyme and Morphological Variation in Two Subspecies of Dryas Octopetala (Rosaceae) in Alaska.” American Journal of Botany 86 (11): 1637–44. 10.2307/2656800. [DOI] [PubMed] [Google Scholar]
- McGraw JB, and Antonovics J. 1983. “Experimental Ecology of Dryas Octopetala Ecotypes: I. Ecotypic Differentiation and Life-Cycle Stages of Selection.” Journal of Ecology 71 (3): 879. 10.2307/2259599. [DOI] [Google Scholar]
- Springer Joshua C., and Parfitt Bruce D.. 2015. “Dryas.” In Flora of North America North of Mexico [Online], edited by Flora of North America Editorial Committee 1993+. New York and Oxford: Oxford University Press. http://www.efloras.org/florataxon.aspx?flora_id=1&taxon_id=110971. [Google Scholar]
- Stasinski Lance, White Dawson M., Nelson Peter R., Ree Richard H., and Meireles José Eduardo. 2021. “Reading Light: Leaf Spectra Capture Fine-scale Diversity of Closely Related, Hybridizing Arctic Shrubs.” New Phytologist 232 (6): 2283–94. 10.1111/nph.17731. [DOI] [PMC free article] [PubMed] [Google Scholar]