Vol. XIX Issue 1 / Communication 6 - Journal of Basic & Applied Genetics

Vol. XXIX Issue 1
Communication 6

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /><title>Untitled Document</title></head><body>ARTÍCULOS ORIGINALESChilean plants cytogenetic database: coverage, features  and usagesBase de datos citogenéticos de plantas Chilenas: cobertura, características y usos Pedro Jara-Seguel1,2, Jonathan Urrutia-Estrada31 Departamento de Ciencias Biológicas y Químicas  2 Núcleo de Estudios Ambientales (NEA), Facultad de Recursos Naturales,  Universidad Católica de Temuco, Rudecindo Ortega 2950, Temuco-Chile  3 Laboratorio de Invasiones Biológicas, Facultad de Recursos Naturales,  Universidad de Concepción, Casilla 160-C, Concepción-Chile.  * Corresponding author: <a href="mailto:pjara@uct.cl">pjara@uct.cl</a>Fecha de recepción: 23/01/2017  Fecha de aceptación de versión final: 10/02/2018<hr />ABSTRACTChilean Plants Cytogenetic Database (CPCD) is a resource available on line in electronic format, which provides a cytogenetics catalogue  for continental and insular Chilean vascular plants. In this report, we made reference to the CPCD, discussing aspects on its coverage, features and  usages. Currently, the database stores cytogenetic information for 247 species, 107 genera, and 55 families belonging to Pteridophyta, Pinophyta,  and Magnoliophyta.Key words: Chromosome number; Karyotype; Chilean Plants.RESUMENLa Base de Datos Citogenéticos de Plantas Chilenas (CPCD) es un recurso disponible en formato electrónico en línea, que provee de un  catálogo citogenético para plantas vasculares de Chile continental e insular. En esta comunicación hacemos referencia a la CPCD, discutiendo  aspectos sobre su cobertura, rasgos y usos. Actualmente, la base de datos contiene información citogenética para 247 especies, 107 géneros y 55  familias pertenecientes a Pteridophyta, Pinophyta y Magnoliophyta.Palabras clave: Número cromosómico; Cariotipo; Plantas chilenas.<hr /> INTRODUCTION The electronic databases have taken relevance in biological investigation from the beginning of the genomic revolution. The most used databases -the so-called GenBank- are a tool related to the molecular biology but with multiple applications in different fields of the biological sciences. These databases contain public available nucleotide sequences and protein translation for more than 260,000 species (Benson et al., 2013). Other available databases most related to cytology store information on genome size (or DNA C-values) for a high number of Eukaryote species including plants, animals, fungi, and algae (more than 10,000 species according to Gregory et al., 2006). In the specific case of plants, current reports estimate that the only existing electronic catalogue on genome sizes comprises data for more than 8,000 species of around the world (Bennett and Leitch, 2016). Thus, this database provides a truly comprehensive catalogue on plant genome size, and represents a much-needed resource for cytogeneticists, with innumerable applications that have been broadly discussed in the literature (Bennett and Leitch, 2005; Leitch et al., 2005; Peruzzi et al., 2009; Roa and Pires de Campos Telles, 2017).  Regarding on line resources for plant chromosomes, fourteen cytogenetic databases in electronic format are available around the world (Peruzzi and Bedini, 2014). For all of them, data have been obtained from different bibliographic sources, being chromosome number (2n, n) the main presented character. Chilean plants have a scarce representation in most databases, even though many species have been included during the last decades in the Index to Plant Chromosome Number (IPCN, Goldblatt and Johnson, 2006), together with species from other latitudes. This low representation of Chilean plants in databases makes it difficult to conduct literature reviews aimed to explain tendencies on chromosome evolution in a wide geographic scale, including species from continental and insular Chile. It is important to remark that continental Chile is a mosaic of environments along its latitudinal configuration, having more than 4,000 km in length from 18° S to 56° S, with marked climatic North to South gradients. In addition, the longitudinal gradient of Chile is marked by differences in altitudes (up to 6,000 m.a.s.l.) which originate a variation of microclimates and, thus, of environments, many of which are favorable for plant growth. Of this territory, 55% is covered by vegetation with 45% of floristic endemism. In addition, insular Chile is also an interesting mosaic with 320 km2 in surface, and an endemism that varies between 64% and 87% (Villagrán and Hinojosa, 2005; CONAF, 2013; Urbina-Casanova et al., 2015). Therefore, cytogenetic studies on spatial scale on the Chilean flora are of relevance to analyze tendencies on genome variation along geographic gradients. The first review reporting the state of the art on cytogenetic of Chilean angiosperms emphasized on these matters as well as on the difficulties encountered to compile the information, specifically for data documented in the oldest literature (Jara-Seguel and Urrutia, 2012). At present, theoretical and/or empirical investigations on different fields of biology (i.e., cytogeography, genomics, taxonomy, evolution, and/or palaeobotany) require the data to be readily available and compiled from diverse sources. Thus, at present, databases constitute a valuable resource in which the information can be easily accessible to the scientific community (Gregory et al., 2006; Jara-Seguel and Urrutia, 2012; Roa and Pires de Campos Telles, 2017).  In this communication we make reference to the Chilean Plants Cytogenetic Database (CPCD, Jara-Seguel and Urrutia, 2016), and discuss aspects on its coverage, features and uses.COVERAGE, FEATURES AND USAGESThe CPCD provides the first electronic catalogue exclusive for the Chilean flora, and was launched for the first time in September 2010, with 101 recorded species. Since then, two updates were made, the first in March 2011, which increased the number of species to 163 (release 2.0), and the second in June 2016, in which this number was increased to 247 (release 3.0). The latter number of species represents almost 4.8% of the Chilean Vascular Plants. The adscription of the species to families and/or genera was based on the classification given in the original source cited in the references. The CPCD assembles information obtained from 88 bibliographic sources covering 55 years of investigation on the topic. In total, CPCD contains information for 247 species representing 107 genera and 55 families belonging to Pteridophyta, Pinophyta, and Magnoliophyta. As remarkable contribution, the database includes a wide gamma of cytogenetic characters [chromosome number, karyotype morphology, banding patterns (C, Ag-NOR, CMA3 and DAPI), nuclear DNA content (C-value) and/or fluorescent in situ hybridization (rDNA 5S, 18S, 28S)], which is advantageous regarding other databases focused only on chromosome numbers or rDNA chromosome location. Moreover, all bibliographic references are appended to the cytogenetic data of each species. Several statistical details on the database coverage are summarized in <a href="#tab1">Table 1</a>. <a name="tab1" id="tab1"></a>Table 1. Cytogenetic data for each plant division recorded in the Chilean Plants Cytogenetic Database (CPCD) and the current percentage of species representation in the database regarding to the total Chileanvascular flora. <img src="https://sag.org.ar/jbag/wp-content/uploads/2019/11/XXIX1a06tab1.jpg" width="555" height="159" /> (1) Based in Rodríguez (1995). (2) Based in Marticorena (1990).The cytogenetic data comprised in the CPCD increases the potential applications of the accumulated knowledge on genome structure and diversity of Chilean native plants, focused on relevant cytogenetic characters. In general, it is remarkable that the higher number of species included in the database (196 continental species) are representative of discontinuous latitudinal strips localized between 18° S and 53° S, and most of them (192 species) are found within the Chilean Hotspots (Myers et al., 2000). Nevertheless, cytogenetic data of species that inhabit in the Juan Fernández Archipelago and Isla de Pascua are also included (51 insular species).  The database is a comprehensive, ordered, easily accessible and useful catalogue for experimented and incipient cytogeneticist interested in cytogenetic aspects of Chilean plants or for comparative investigations with cofamilial members that inhabit other geographic regions. The database is of free access, and the traffic has increased steadily since its launching in September 2010, with more than 7,400 visitors belonging to 46 countries of around the world. From the time of launching and on, the database has been cited in seven publications, some of them analyzing tendencies on chromosome number variation of global or local floras (Jara-Seguel and Urrutia, 2012; Peruzzi et al., 2012; Rice et al., 2015), and others discussing the usefulness of databases assembling data on plant rDNA chromosome localization or genome size (García et al., 2012; Dagher- Kharrat et al., 2013). Recently, CPCD has been included in the largest community resource of plants chromosome numbers at the worldwide level (see CCDB, Rice et al., 2015), which may increase its visibility and use. It is also listed as an on line resource for chromosome numbers among other 17 databases available around the world (Peruzzi and Bedini, 2014). In fact, the data on Chilean plants pooled in the CPCD not only have been used to analyze tendencies, but have also served as substrate to propose new quantitative methods to analyze large data sets of chromosome numbers of animals and plants (see Peruzzi et al., 2014). Thus, the CPCD is a valuable tool for generating knowledge in different cytogenetic fields.FUTURE PROSPECTSThe CPCD could be annually or biannually updated, as new cytogenetic information may published or obtained from old sources. However, for continuously being an important source of information for cytogeneticists and/ or taxonomists, it is necessary to increase the number of cytogenetic studies in all taxonomic divisions that represent the Chilean plant biodiversity.ACKNOWLEDGEMENTSTo Núcleo de Estudios Ambientales (NEA), Universidad Católica de Temuco, for funding the current implementation of the Chilean Plants Cytogenetic Database (CPCD). Our gratefulness to the authors cited in the database for theirvaluable contribution to the knowledgeof the Chilean flora. BIBLIOGRAPHY 1. Bennett M., Leitch I. (2005) Plant genome size research: A field in focus. Ann. Bot. 95 (1): 1-6. 2. Bennett M., Leitch I. (2016) Plant DNA C-values database. URL: <a href="http://data.kew.org/cvalues/" target="_blank">http://data.kew.org/cvalues/</a> (Viewed: January 08, 2018). 3. Benson D., Cavanaugh M., Clark K., Karsch-Mizrachi I., Lipman D., Ostell J., Sayers E. (2013) GenBank. Nucleic Acids Res. 42: 36-42. 4. Conaf (2013) Por un Chile forestal sustentable. Corporación Nacional Forestal, Santiago, Chile. 5. Dagher-Kharrat M., Abdel-Samad N., Douaihy B., Bourge M., Firdlender A., Siljak-Yakovlev S., Brown S. (2013) Nuclear DNA C-values for biodiversity screening: Case of the Lebanese flora. Plant Biosyst. 147 (4): 1128-1237. 6. Garcia S., Garnatje T., Kovarík A. (2012) Plant rDNA database: ribosomal DNA loci information goes online. Chromosoma 121 (4): 389-394. 7. Goldblatt P., Johnson D. (2006) Index to Plant Chromosome Numbers 2001-2003. Syst. Bot. 106: 1-242. 8. Gregory R., Nicol J., Tamm H., Kullman B., Kullman K., Leitch I., Murray B., Kapraun D., Greilhuber J., Bennett M. (2006) Eukaryotic genome size databases. Nucleic Acids Res. 35: 332-338. 9. Jara-Seguel P., Urrutia J. (2012) Cytogenetics of Chilean Angiosperms: Advances and prospects. Rev. Chil. Hist. Nat. 85: 1-12. 10. Jara-Seguel P., Urrutia J. (2016) Chilean Plants Cytogenetic Database. URL: <a href="http://www.chileanpcd.com/" target="_blank">http://www.chileanpcd.com/</a>. (Viewed: January 15, 2018). 11. Leitch I., Soltis D., Soltis P., Bennett M. (2005) Evolution of DNA amounts across Land Plants (Embryophyta). Ann. Bot. 95: 207-217. 12. Marticorena C. (1990) Contribución a la estadística de la flora vascular de Chile. Gayana Bot. 47 (3-4): 85-113. 13. Myers N., Mittermeier R., Mittermeier C., Fonseca G., Kent J. (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853-858. 14. Peruzzi, L., Bedini, G. (2014) Online resources for chromosome number databases. Caryologia 67(4): 292-295. 15. Peruzzi L., Caparelli K., Bedini G. (2014) A new index for the quantification of chromosome number variation: An application to selected animal and plant groups. J. Theor. Biol. 353: 55-60. 16. Peruzzi L., Góralski G., Joachimiak A., Bedini G. (2012) Does actually mean chromosome number increase with latitude in vascular plants? An answer from the comparison of Italian, Slovak and Polish floras. Comp. Cytogen. 6 (4): 371-377. 17. Peruzzi L., Leitch I., Caparelli K. (2009) Chromosome diversity and evolution in Liliaceae. Ann. Bot. 103: 459-475. 18. Rice A., Glic L., Abadi S., Einhorn M., Kopelman N., Salman-Minkov A., Mayzel J., Chay O., Mayrose I. (2015) The Chromosome Counts Database (CCDB) – a community resource of plant chromosome numbers. New Phytol. 206: 19-26. 19. Roa F., Pires de Campos Telles M. (2017) The Cerrado (Brazil) plant cytogenetics database. Comp. Cytogen. 11 (2): 285-297. 20. Rodríguez R. (1995) Pteridophyta. In: Marticorena C., Rodríguez R. (Eds.) Flora de Chile. Ediciones Universidad de Concepción, Concepción, Chile, pp. 119-350. 21. Urbina-Casanova R., Saldivia P., Scherson R. (2015) Consideraciones sobre la sistemática de las familias y los géneros de plantas vasculares endémicos de Chile. Gayana Bot. 72 (2): 272-295.22. Villagrán C., Hinojosa L. (2005) Esquema biogeográfico de Chile. In: Llorente-Bousquets J., Morrone J. (Eds.) Regionalización biogeográfica en Iberoamérica y tópicos afines. Ediciones de la Universidad NacionalAutónoma de México, México, pp. 551-577.</body></html>