Add plant genome size (Kew Plant DNA C-values)

Joins plant genome-size data from the Kew Plant DNA C-values database (Pellicer & Leitch 2020) to a taxify() result by looking up accepted_name. The 1C DNA amount is a per-species median. The chromosome number and ploidy level are the base cytotype, with the range across a species' cytotypes in the _min / _max columns.

Usage

add_kew_cvalues(x, cols = NULL, verbose = TRUE)

Arguments

x

A data.frame returned by taxify().

cols

Which columns to attach: NULL (default) the curated set, "all" every column the source carries, or a character vector of names. See enrichment_cols.

verbose

Logical. Default TRUE.

Value

The same data.frame with additional columns. The default set:

cval_genome_size_1c_pg

Genome size (1C DNA amount, picograms).

cval_chromosome_2n

Somatic chromosome number (2n), base cytotype.

cval_ploidy_x

Ploidy level, base cytotype.

cols = "all" also attaches the per-species min/max/n spread of each value, plus per-species provenance:

cval_original_reference

The paper(s) the values were measured in, joined by "; " where a species carries records from several.

cval_estimation_method

The method(s) used, in the source's codes: FC:PI and other FC: variants are flow cytometry with the named stain, Fe is Feulgen densitometry. The two are not interchangeable, so a species measured by both reports both.

Details

Source: Kew Plant DNA C-values database, release 7.1 (Royal Botanic Gardens Kew), CC BY. Vascular plants.

References

Pellicer J, Leitch IJ (2020) The Plant DNA C-values database (release 7.1): an updated online repository of plant genome size data for comparative studies. New Phytologist 226:301-305.

Examples

if (FALSE) { # \dontrun{
# Downloads the enrichment on first use.
taxify("Zea mays", backbone = "gbif") |>
  add_kew_cvalues()
} # }