DOI: 10.5061/dryad.mpg4f4rbp
title: A chromosome-level genome assembly of the beavertail cactus, Opuntia basilaris

description: Few genomic resources currently exist for the American endemic family
 Cactaceae, a group of around 1850 species, which are world-renowned for
 their amazing growth forms and succulent habits. These icons of arid
 landscapes across the Americas are threatened in many parts of their
 range, including in parts of California, and developing more comprehensive
 genomic data will aid efforts to better understand and preserve these
 plants. We sequenced and assembled the genome of the beavertail cactus,
 Opuntia basilaris, which is represented by three varieties in California,
 one of which is threatened, and another endangered. The genome assembly
 has a BUSCO complete score of 98.1%, and a total scaffold length of 980
 Mb, with a scaffold N50 length of 83 Mb. The genome size of
 diploid O. basilaris is markedly smaller than other diploid
 members of Cactaceae that have been assembled to date. This is the first
 nuclear genome sequenced in subfamily Opuntioideae and the most complete
 nuclear genome for Cactaceae to date and will lay the foundation for
 future genomic work across the biologically and taxonomically complicated
 prickly pear cacti.
description: # A Chromosome-level Genome Assembly of the Beavertail Cactus, *Opuntia
 basilaris* Dataset DOI: [10.5061/dryad.mpg4f4rbp](10.5061/dryad.mpg4f4rbp)
 ## Description of the data and file structure Data represent supplemental
 figures and tables associated with the publication of a chromosome-level
 assembly genome of *Opuntia basilaris* var. *basilaris* (Cactaceae). ###
 Files and variables #### File:
 SupplementaryFigure1.dcOpuBasi1.hifi.readlength.distribution.png
 **Description:** Read length distribution. #### File:
 SupplementaryFigure2.IRplusOutput.dcOpuBasi1.chloroplast.pdf
 **Description:** Map of inverted repeats in chloroplast genome. #### File:
 SupplementaryFigure3.blobtools\_dcOpuBasi1.NCBI.a\_ctg.snail.png
 **Description:** Snailplot of alternative genome assembly. #### File:
 Supplementary\_Tables.xlsx **Description:** List and description of
 removed contaminants. Tables correspond to Blobtools output per
 haplotype. The tables show information per contig related to coverage,
 length, GC content and taxonomic assignment. Table 1. is Primary
 haplotype/haplotype 1 Table 2. Alternate haplotype/haplotype 2. Table 3.
 Summary of the removed contaminants based on contamination screening upon
 submission to NCBI. Output is the  summary of the FCS:GX contamination
 screening pipeline. ## Code/software Assembly scripts and other data for
 the analyses presented can be found at the following GitHub repository:
 [www.github.com/ccgproject/ccgp_assembly](http://www.github.com/ccgproject/ccgp_assembly) ## Access information Other publicly accessible locations of the data: Data generated for this study are available under NCBI BioProject PRJNA777201. Raw sequencing data for sample *Fawcett & Madeiros 1504* (NCBI BioSample SAMN41564419) are deposited in the NCBI Short Read Archive (SRA) under SRR30989401 for PacBio HiFi sequencing data, and SRR30989399, SRR30989400 for the Omni-C Illumina sequencing data. GenBank accessions for both primary and alternate assemblies are GCA_043229145.1 and GCA_043229025.1; and for genome sequences JBFLFP000000000 and JBFLFQ000000000. The GenBank genome assembly for the chloroplast genome is CM091650. The voucher specimen is deposted in the Jepson herbarium (JEPS) at UC Berkeley.