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

Abstract

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 & Lowry, 2011) as well as extinct ones (Laane & Hoiland, 1986; 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 & Kumar Sharma, 1969; Schlarbaum & Tsuchiya, 1984; 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 & Mayrose, 2014). Due to their significance and the relative ease by which chromosome numbers can be obtained, it is not surprising that chromosome number is the most extensively and consistently recorded cytological property in most plant families and genera (Guerra, 2008). These data have been documented along the years in an array of journal manuscripts, printed books (Löve & Löve, 1948; Darlington & Wylie, 1955; Fedorov, 1969) and, more recently, in the form of online databases (Goldblatt & Johnson, 1979; Watanabe, 2002; Bennett & Leitch, 2011). To date, the most comprehensive data source is the Index to Plant Chromosome Numbers (IPCN; Goldblatt & Johnson, 1979), which provides reference point to original chromosome counts reported in the literature. IPCN was initially established at the University of California Berkeley in the 1950s and was later maintained by Canada Department of Agriculture, Missouri Botanical Garden, and currently by the International Association for Plant Taxonomy (IAPT). A large portion of the counts referenced during 1979–2006, the years that IPCN has been housed in the Missouri Botanical Garden, can be accessed and searched online. Counts reported in more recent years are currently published under IAPT/IOPB Chromosome Data series (Marhold, 2006) but are not stored within a central, easily searched, database. In addition to IPCN, several other online data sources are available, most of which are dedicated to either a specific geographical region (Slovakia – Marhold et al., 2007; 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 sci