Key points are not available for this paper at this time.
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 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 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 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 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 Pellicer see Nic Lughadha et al., 2016). At the higher taxonomic levels, representation currently stands at 15% of genera (2118 out of c. 14 000), as well as 63% of families (262 out of 416) and 94% of orders (58 out of 62) recognized by APG IV (2016), illustrating the need to continue to prioritize efforts to fill taxonomic gaps, particularly at the genus and family levels, in future research. There are two major lineages beyond angiosperms whose representation in the database has improved significantly from the previous release, namely monilophytes (increasing the number of species with data from 101 to 246), and algae (increase from 253 to 445 species). Nevertheless, given the number of species recognized in these two groups (> 11 000 monilophytes and > 20 000 algae), phylogenetic representation is still extremely low, especially for many of the monophyletic groups of algae. With respect to monilophytes, not only has the taxonomic coverage increased, but the new data now include the first reported example of extreme genomic obesity beyond angiosperms. This arises from the Hidalgo et al. (2017b) report of a giant genome in the whisk-fern Tmesipteris obliqua, whose genome size of 146 500 Mb/1C is over twice the size of the previous record holder (i.e. 71 221 Mb in Psilotum nudum), thereby extending the range of C-values in monilophytes from 94-fold to 196-fold). This new value closely rivals the gigantic genome of the angiosperm Paris japonica (1C = 148 851 Mb; Pellicer et al., 2010), which is the largest so far reported for any eukaryote (Hidalgo et al., 2017a; Fig. 2). Another relatively underexplored group from a genome size perspective is the algae, which comprise several evolutionarily distinct lineages, some with closer affinities to animals than plants (e.g. those belonging to Heterokonta, such as diatoms, and the brown algae (Phaeophyta)). They are often neglected because of the methodological challenges they pose when estimating genome size (Voglmayr, 2007; Mazalová et al., 2011). Evolutionary relationships among many algal lineages are still controversial, but recent phylogenetic studies provide strong support for three of the streptophyte algal lineages (i.e. Charophyceae, Coleochaetophyceae and Zygnematophyceae) forming a monophyletic group that is sister to land plants (Embryophyta) (Wickett et al., 2014; Gitzendanner et al., 2018). Thus, data on the size of these algal genomes are critical for providing insights into the evolutionary implications of genome size diversity before the colonization of land. Despite data still being sparse (i.e. six Charophyceae, four Coleochaetophyceae and 49 Zygnematophyceae species), the new estimates in the database highlight considerable genome size variation. While Charophyceae (1882–19 208 Mb/1C) and Coleochaetophyceae (343–1348 Mb/1C) have genomes that fall within the range encountered in bryophytes (i.e. 156–19 560 Mb/1C), which include the sister group to all vascular plants, larger genomes are found in Zygnematophyceae, including the largest for any algal lineage reported so far: the polyploid desmid Microasterias rotata (= 31 723 Mb/1C). Such a large genome extends beyond those so far encountered in bryophytes and highlights that the potential for genome size expansion is not restricted to vascular land plants (Fig. 2). At the other end of the scale, the Chlorophyta and Rhodophyta include the smallest genomes reported for any free-living photosynthetic organism (12.46 Mb/1C in the green chlorophyte Ostreococcus tauri and 13.20 Mb/1C in the rhodophyte Galdieria sulphuraria; these genome sizes fall within the values reported for some bacterial genomes, and are considered to represent the bare limits of life for free-living photosynthetic eukaryotes; Peers Sun et al., 2017; Vurture et al., 2017). More recently, a mapping-based genome size estimation approach has been reported (MGSE; Pucker, 2019) that infers genome size from short-read sequencing data by mapping reads to a highly contiguous assembly, and assuming a random fragmentation of DNA when preparing it for sequencing (i.e. equal distribution of reads over the complete sequence). Although these bioinformatic methods might appear to be promising alternatives to flow cytometry, it is noted that they often give genome size estimates that are lower than those from flow cytometry. The causes of such bias are currently unclear. Further, it is not known whether such approaches are even applicable to the many plants which are polyploid, highly repetitive and/or are particularly large, as all these features are likely to present challenges to the underpinning assumptions of the bioinformatic pipelines (Sun et al., 2017; Vurture et al., 2017). Instead, these observations highlight the urgent need for appropriate comparative analyses to be conducted across the diversity of plant genomes which compare bioinformatic and flow cytometry estimates determined from the same specimen. Only then will we be able to shed light on the underlying causes generating the discrepancies, and hence their reliability. Given these potential limitations, genome size estimates derived from such methods have not yet been included in the Plant DNA C-values database. Nevertheless, we will continue to monitor the development of these and related approaches for consideration in future releases of the Plant DNA C-values database. We thank Emmeline Johnston for her help in collating and entering all the genome size data into the database, as well as all those authors who have kindly provided data through their publications that have been incorporated into the database. We are also grateful to Eduardo Toledo and his IT team at the Royal Botanic Gardens, Kew for their help in upgrading the webpage interface and enabling the new release to go live. JP and IJL contributed equally to conceiving and writing this letter.
Pellicer et al. (Mon,) studied this question.