The Chromosome Counts Database (CCDB) – a community resource of plant chromosome numbers

For nearly a century, biologists, and botanists in particular, have been interested in the determination and documentation of chromosome numbers for extant taxa (reviewed in Goldblatt Masterson, 1994). These data have been widely used to evaluate the evolutionary pattern of chromosome number change and to estimate the base chromosome number of clades of interest. Chromosome numbers have also been extensively utilized as an important phylogenetic character in the context of cytotaxonomy (Chatterjee Schlarbaum Guerra, 2012). Perhaps the most influential use of chromosome number data has been in the inference of major genomic events such as whole genome duplications (polyploidy), as well as changes in single chromosome numbers (e.g. dysploidy). Early researchers analyzed the distribution of chromosome numbers within a group of interest and employed various threshold techniques to estimate ploidy levels for the analyzed taxa (Stebbins, 1938; Grant, 1963; Goldblatt, 1980). More recently, phylogenetic information was incorporated into the analyses, allowing researchers to infer transitions in chromosome numbers along branches of the tree using either the maximum parsimony principle (Schultheis, 2001; Hansen et al., 2006; Ohi-Toma et al., 2006; Wood et al., 2009) or by using a probabilistic evolutionary model within the likelihood paradigm (Mayrose et al., 2010; Cusimano et al., 2012; Glick Darlington Fedorov, 1969) and, more recently, in the form of online databases (Goldblatt Watanabe, 2002; Bennett Goldblatt Poland – Góralski et al., 2009 onwards) or to a certain taxonomic group (e.g. Hieracium – Schuhwerk, 1996; Asteraceae – Watanabe, 2002). The amount of chromosome counts that exist to date is extensive, and searching the large number of resources that contain such information is a daunting task, particularly when a large number of taxa is examined. Consequently, many researchers search for chromosome number information only through the largest online database(s), while smaller but nonetheless valuable sources are ignored. This usually results in missing data for some of the species in question, which may lead to erroneous conclusions drawn from the analysis. Obviously, a large accessible database that unifies all currently known databases, including both printed and online sources, would be of great value to the botanical community and would make the task of data collection much easier. In addition, such a central resource would enable researchers to add new counts as soon as they are being reported, facilitating the task of data sharing. Here, we present the Chromosome Counts Database (CCDB), as a community resource of plant chromosome numbers. The database incorporates data from dozens of sources, more than doubling the amount of data available within any single resource. The online database additionally enables researchers to add new counts or to comment on existing data entries, thereby facilitating data sharing. The extensive amount of data currently available in CCDB further allowed us to analyze the patterns of chromosome number distribution among major plant groups. We estimate the percentage of plant species exhibiting intraspecific variation in chromosome numbers as well as in their ploidy levels. Chromosome counts were collected from a large number of electronic resources, older chromosome counts compendiums in the form of printed books, and an array of miscellaneous sources such as floras, monographs and other scientific manuscripts. The full list of resources is given in Table 1. Data from these sources were collected using the following procedures: Data from several online databases were retrieved directly from the database curator via personal communication in the form of comma-separated value (CSV) files. These include data from the Plant DNA C-values database (Bennett obtained from Ilia Leitch) and Chromosome number database of Polish plants (Góralski et al., 2009 onwards; obtained from Grzegorz Góralski). Other online chromosome counts databases were downloaded and processed using Perl/Python scripts. The following online sources were retrieved: IPCN (Goldblatt volumes 1 and 2 (Kumar Moore, 1970, 1971, 1973, 1974, 1977). The IPCN volume for the years 1975–1978 (Goldblatt, 1981) was also parsed but counts were inserted into the database only in case the online IPCN database did not already contain them. In addition to dedicated chromosome counts databases and hard copy books, a large number of other sources exist that contain information regarding the chromosome number for a given taxon. These resources include floras, monographs and an array of scientific manuscripts. However, automatic retrieval of chromosome number data from such resources is not a trivial task because the data are organized in a source-specific manner (e.g. the botanical description of a given species as appears in its relevant flora obtained through http://www.efloras.org). Hence, the downloading and processing of each data source were performed using dedicated Perl/Python scripts written specifically for each data source, followed by a manual verification of hundreds of records. As mentioned above, we preferred to maximize data accuracy over data completeness and therefore some fraction of the data available in these sources was not used. Thousands of chromosome counts were acquired from online floras – eflora accessed 20 October 2013 (http://www.efloras.org), Flora Iberica accessed 20 June 2013 (http://www.floraiberica.es), and from the Interactive flora of NW Europe accessed 20 June 2013 (http://wbd.etibioinformatics.nl/bis/flora.php). In addition to floras, chromosome counts that appear within several Systematic Botany Monographs were retrieved (Saunders, 2000; Bohs, 2001; Freire-Fierro, 2002; Aldasoro et al., 2004; Zuloaga et al., 2004; Thompson, 2005; Wagner et al., 2005; Meudt, 2006; Miller Solanaceae – Colchicaceae – et al., – & 2014). 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