The Plant DNA C‐values database (release 7.1): an updated online repository of plant genome size data for comparative studies

Abstract

In recent decades, interest in plant genome size (i.e. the total amount of DNA in the unreplicated haploid nucleus; Greilhuber et al., 2005) has been growing exponentially as the biological, evolutionary and ecological significance of this key biodiversity trait is increasingly recognized (e.g. see reviews by Greilhuber & Leitch, 2013; Pellicer et al., 2018). Such interest is no doubt, in part, underpinned by the staggering diversity of genome sizes encountered within land plants (e.g. especially angiosperms which show a range of c. 2400-fold; Pellicer et al., 2010) and the considerable diversity in some algal clades, with the most variable being in the Chlorophyta clade of green algae, which have a range of 274-fold. Certainly, it is now clear that genome size can have an impact at many scales, from influencing gene and genome dynamics (e.g. Dodsworth et al., 2015) to playing a role at the whole-plant level, influencing, for example, plant growth strategies, plant community composition, plant–animal interactions, evolutionary trajectories and ecosystem dynamics (e.g. Suda et al., 2015; Guignard et al., 2016, 2019; Simonin & Roddy, 2018). In the era of fast-evolving high-throughput-sequencing technologies, C-values also provide baseline information necessary for estimating whole-genome sequencing costs, as these are directly linked to the size of the genome (e.g. Li & Harkess, 2018). Although genome size data have been accumulating in the literature since 1951 when the first estimate for a plant was published (Ogur et al., 1951), for many years such data remained scattered across the literature or compiled into lists available only in hard copy (e.g. Bennett & Smith, 1976; Bennett et al., 2000). This made the search to determine whether a particular genome size was available slow and tedious. Release 1 of the Plant DNA C-values database in 2001 contributed significantly to overcoming such a bottleneck and helped to revolutionize the field by facilitating large-scale comparative phylogenetic analyses across different plant groups (e.g. Leitch & Bennett, 2002; Soltis et al., 2003). Since then, six updates have been released, culminating in the latest, which went live in April 2019 (Leitch et al., 2019) and which collates data from 1067 original publications and personal communications. The new release of the Plant DNA C-values database (https://cvalues.science.kew.org/) contains genome size data for 12 273 species – increasing the number of species represented by 44% (i.e. an additional 3763 new species) since the last update in 2012 (Bennett & Leitch, 2012; Garcia et al., 2014). The vast majority of data are for angiosperms, with estimates for 10 770 species. However, the database also contains C-values for all other major land plant groups, with data for 421 gymnosperms, 303 pteridophytes (comprising 246 ferns (monilophytes) and 57 lycophytes) and 334 bryophytes (209 mosses, 102 liverworts and 23 hornworts). Data are also available for 445 ‘algae’, comprising species belonging to evolutionarily distinct higher-order lineages (i.e. Rhodophyta, Chlorophyta, and the streptophyte green algae within Kingdom Plantae, and Phaeophyta and Heterokonta within the Stramenopiles). The new user-friendly interface of the database has a range of searching and output options so that the user can extract and display specific information as required. For example, queries can be made using the whole database, or limited to specific taxonomic lineages and levels (e.g. families, genera). In addition, more detailed searches can be made by specifying certain criteria (e.g. restricting searches to defined genome size ranges, ploidal levels, chromosome numbers, higher taxonomic groups, life cycles etc.). The new release also includes predictive typing in the taxonomy boxes (i.e. family, genus and species levels). Although the species names given in the original publications are always kept, the family affiliations for the angiosperms follow those of the most recent Angiosperm Phylogeny Group (APG IV) update (Angiosperm Phylogeny Group, 2016). Where more than one estimate has been reported for a species, by default the output of a query will just display the prime genome size estimate, which represents the most consistent value obtained under best-practice methods (as originally defined by Bennett & Smith, 1976). Nevertheless, all data published for a given species in the database can be accessed by changing the search parameters to display ‘all estimates’. Although we encourage efforts to generate novel data in underexplored groups, we are now committed to include, wherever possible, only C-values that have been estimated using best-practice protocols (e.g. Doležel et al., 2007; Pellicer & Leitch, 2014). In brief, the original publications (or authors) should provide information about the method used for genome size estimation (with flow cytometry currently recommended as best practice), the number of replicates made, a clear indica