Online resources for chromosome number databases

Abstract

Available online resources for animal and plant chromosome number databases are surveyed and briefly discussed.

Keywords:

• bioinformatics
• cytotaxonomy
• world wide web

Introduction

The first chromosome counts were published in 1882 by Eduard Strasburger (1844–1912) and included several data concerning mostly some genera of vascular plants, but also salamanders (Garbari et al. 2012). This happened before the coining of the term chromosome itself (“chromosom”) by Wilhelm Waldeyer in 1888 (“If the term I propose is practically applicable it will become familiar, otherwise it will be soon sink into oblivion”; Battaglia 2009) and well before the discovery of DNA as “giant hereditary molecule” in 1927 by Nikolai Koltsov (Soyfer 2001).

Today, besides morphological data, chromosome number (CN) is the most widespread and the cheapest systematic character, while karyotype structure details, karyotype asymmetry, chromosome painting, genome size and molecular systematics have a much narrower coverage in scientific literature (Bennett and Leitch 2010; Guerra 2012; Siljak-Yakovlev and Peruzzi 2012; Peruzzi and Eroğlu 2013).

CNs can vary among and within taxonomic groups of living organisms, and in more than 130 years a lot of data has accumulated in literature, stimulating the production of databases, either hard-printed (especially in the last century) or online.

Currently, the known CN in organisms ranges from 2n = 2 in the ant Myrmecia pilosa to 2n = 1440 in the psilophyte fern Ophioglossum reticulatum (Ruffini Castiglione and Cremonini 2012).

In recent years, many CN databases have been made publicly available online, as well as databases dealing with other karyological parameters, such as genome size (Garcia et al. 2013; Vallès et al. 2013) and rDNA loci (Garcia et al. 2012; Roa and Guerra 2012). This work aims to summarize the available online resources providing access to just CNs, and has also served as the basis for a recent comparative study among animal and plant groups (Peruzzi et al. 2014).

Online animal CN databases

Chromosomes of Russian mammals

Available at http://www.bionet.nsc.ru/labs/chromosomes/intr_engl.htm (Graphodatsky et al. 2000 onwards). It stores CNs and other karyological data, such as karyotypes and FISH, of mammals, with 2758 different chromosome counts. The database consists in a series of tables in HTML format. Each record includes provenance and bibliographic reference.

Chromorep: a reptiles chromosomes database

Available at http://chromorep.univpm.it/ (Olmo and Gelo Signorino 2012). It deals with CNs of reptiles and hosts 1731 different chromosome counts along with other karyological data such as localization of nucleolar organizer regions, sex chromosomes, and several type of banding; for each record appropriate references are provided. The data are accessed through a search page.

Online plant CN databases

A karyological survey of Asclepiadoideae, Periplocoideae and Secamonoideae, and evolutionary considerations within Apocynaceae s.l.

Available at www.bio.uni-bayreuth.de/planta2/research/Aschrom/ASCHROM.pdf. It deals with the eudicot family Apocynceae and was the subject of a scientific publication dealing more generally with an information system about this family (Liede-Schumann and Meve 2006). The database consists in a large table in .pdf format with 837 different chromosome counts.

BSBI cytology search form

Available at rbg-web2.rbge.org.uk/BSBI/cytsearch.php. It deals with British Isles vascular flora. The database is searchable, but the query mask is not user friendly.

Chilean plants cytogenetic database

Available at www.chileanpcd.com (Jara-Seguel and Urrutia 2011 onwards). It deals with Chilean vascular flora and hosts 243 different chromosome counts. It was the subject of a scientific publication presenting the initiative (Jara-Seguel and Urrutia 2012). The database consists in a long table on a web page.

Chrobase.it – CNs for the Italian flora

Available at www.biologia.unipi.it/chrobase (Bedini et al. 2010 onwards). It deals with Italian vascular flora and hosts 3817 different CNs (as of 8 January 2014). It was the subject of publications presenting the initiative and summarizing the data (Bedini et al. 2012a, 2012b), as well as of others comparing CN variation in a phylogenetic (Bedini et al. 2012c), and in a geographic framework involving the comparison of the Italian dataset with those available from New Zealand (Peruzzi et al. 2011), Slovakia and Poland (Peruzzi et al. 2012). The database is searchable, continuously updated and open to collaboration of other scientists.

Chromosome counts for Malvaceae

Available at www.malvaceae.info/Biology/Chromosomes.php (Hinsley 2009). It deals with Malvaceae and hosts 943 different chromosome counts. The database consists in a long list published as a web page.

CN database – PLANTS

Available at http://chromosomes.binoz.uj.edu.pl//chromosomes/ (Góralski et al. 2009 onwards). It deals with the Polish vascular flora and hosts 1854 different chromosome counts. The data were used for publications concerning CN variation and polyploidy of Polish angiosperms (Gacek et al. 2011), comparison between alien and native taxa (Góralski et al. 2014), and comparison of CN variability among Italian, Slovak and Poland flora (Peruzzi et al. 2012). The database is searchable through an easy query mask.

“Flora” section of Biocat

Available at http://biodiver.bio.ub.es/biocat/index.jsp. It deals with Spanish vascular flora, but also includes chromosome counts from elsewhere. It was the subject of a scientific publication presenting the initiative (Simon et al. 2001). The database is searchable, but the query mask is not user friendly.

Flora of North America

Available at www.efloras.org/flora_page.aspx?flora_id=1. It deals with North American vascular flora, but the data are nested within the taxa description and not searchable, so it cannot be properly considered a CN database.

Karyological database of the genus Cardamine

Available at http://www.cardamine.sav.sk/. It deals with the genus Cardamine (Brassicaceae, eudicots) and was the subject of a scientific publication presenting the initiative (Kučera et al. 2005). The database is searchable.

Karyological database of ferns and flowering plants of Slovakia

Available at www.chromosomes.sav.sk/ (Marhold et al. 2007a). It deals with the vascular plants of Slovakia and was also published as a hard-print book (Marhold et al. 2007b). It hosts 3493 different chromosome counts, and the data were also used for a comparison of CN variability among Italian, Slovak and Poland floras (Peruzzi et al. 2012). The database is searchable.

Index to CNs in Asteraceae

Available at www.lib.kobe-u.ac.jp/products/e-index.html. It deals about Asteraceae (eudicots). The database is searchable.

Index of CNs of indigenous New Zealand vascular plants

Available at: www.landcareresearch.co.nz/publications/researchpubs/chromosome2008.pdf. It deals with New Zealand vascular flora and is based mainly on two published sources (Dawson 2000; Dawson et al. 2000). It hosts 2520 different CNs; the data were used for a comparison of CN variability among New Zealand and the nearly Antipodean Italian flora (Peruzzi et al. 2011). The database consists in a large table in .pdf format.

Index to plant CNs

Available at http://www.tropicos.org/Project/IPCN. It deals with worldwide plants and represents the online searchable transposition of the book series Index to Plant CNs, published from 1981 to 2010 (Goldblatt 1981, 1984, 1985, 1988; Goldblatt and Johnson 1991, 1994, 1996, 2000, 2003, 2006, 2010), indexing the data published worldwide in the period 1975–2006. The database is searchable, but, unfortunately the online material starts from 1979 (i.e. the first book, covering the period 1975–1978, is not covered). Moreover, recently the Missouri Botanical Garden has decided to discontinue the publication of this book series and to stop updating this very important database. The IAPT (International Association of Plant Taxonomists) is currently maintaining this important resource online and up to date (K. Marhold, pers. comm.).

Prota4U

Available at www.prota4u.org/. It deals with tropical African plants. The database is searchable, but the chromosome data are nested within other kinds of information and cannot be easily extracted.

Published chromosome counts in Hieracium

Available at www.botanischestaatssammlung.de/projects/chrzlit.html (Schuhwerk 2012). It deals with the genus Hieracium (Asteraceae, eudicots) and hosts 361 different chromosome counts. The database consists in a long list on a web page.

Worldwide database of published CNs in Onosma

Available at http://www.onosma.eu/database/. It deals with the genus Onosma (Boraginaceae, eudicots). The database is searchable.

A further relevant plant database, which was online for some years in the early 2000s, is PhytoKaryon (Bareka et al. 2008), hosting more than 45,000 chromosome counts. This database, at the moment not available to the scientific community, will hopefully go again online soon (G. Kamari, pers. comm.).

Knowledge of CNs in plants is continuously increasing: just in the last year, several studies were published with massive CN data (Chung et al. 2013; Dolatyari et al. 2013; Kaplan et al. 2013; Krahulcova et al. 2013; Kuo 2013; Malik and Gupta 2013; Moyetta et al. 2013; Ranjbar and Mahmoudi 2013; Wang et al. 2013; Zaveska Drabkova 2013; Correia-da-Silva et al. 2014; Rani, Jeelani, et al. 2014; Rani, Kumari, et al. 2014). The direct insertion of such data in online and constantly updated databases would much benefit the scientific community.