Chromosome numbers and polyploidy events in Korean non-commelinids monocots: A contribution to plant systematics

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Korean J. Pl. Taxon. 2018;48(4):260-277

Publication date (electronic) : 2018 December 31

doi : https://doi.org/10.11110/kjpt.2018.48.4.260

Tae-Soo JANG, Hanna WEISS-SCHNEEWEISS¹

Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea

¹Department of Botany and Biodiversity Research, University of Vienna, A-1030 Vienna, Austria

^*Author for correspondence: jangts@cnu.ac.kr

Received 2018 June 04; Revised 2018 September 09; Accepted 2018 December 16.

Abstract

Chromosome numbers and the incidence of polyploidy in non-commelinids monocot species native to Korea

All available chromosome numbers and base chromosome numbers for Korean non-Commelinids monocots were obtained from the Chromosome Counts Database (CCDB, version 1.45; http://ccdb.tau.ac.il/Angiosperms/, accessed on 2018 May 22) (Rice et al., 2015) following APG IV classification system (Angiosperm Phylogeny Group IV) (Appendix 1) (The Angiosperm Phylogeny Group, 2016). Due to the scarcity of available data on chromosome numbers and ploidy levels variation in Korean Commelinids including Arecales, Commelinales, Poales, and Zingiberales (The Angiosperm Phylogeny Group, 2016), these were excluded from the current analyses.

The systematic ranking of taxa adopted in this study was mainly based on the recent online resources for monocot plants (http://emonocot.org/), the World Checklist of Selected Plant Families (http://wcsp.science.kew.org), the Missouri Botanical Garden Tropicos Database (http://www.tropicos.org/), and the nomenclature was adopted from the most accepted taxonomic treatment for the species based on the Korean Plant Names Index Committee (http://www.nature.go.kr/kpni/index.do) (Appendix 1).

The genome size values and ploidy level inferences in Korean non-Commelinids monocots were retrieved from the Plant DNA C-values database (http://www.kew.org/cvalues/, accessed on 2018 May 22) (Bennett and Leitch, 2012). The data on number and chromosomal localization of rDNA loci (5S and 35S rDNA) in Korean non-Commelinids monocots obtained applying fluorescent in situ hybridization were retrieved from the third release of the plant rDNA database (Vitales et al., 2017; http://www.plantrdnadatabase.com/, accessed on 2018 May 22).

Chromosome numbers are reported for 252 taxa (232 species, 2 subspecies, and 18 varieties) of Korean monocots, with the exception of Commelinids, due to the scarcity of published chromosome numbers for this very speciose this group (Appendix 1). Base chromosome numbers and ploidy levels variation is given for each taxon in Appendix 1. The chromosome numbers reported for Korean non-Commelinids monocots vary between 2n = 2x = 10 in Paris verticillata M. Bieb. and 2n = 40x = 400 in Dioscorea japonica Thunb. (Appendix 1). To date, the documented chromosome numbers in angiosperms vary from 2n = 4 (e.g., Ornithogalum tenuifolium Delaroche in Hyacinthaceae) to 2n = 640 (Sedum suaveolens Kimnach in Crassulaceae), although most species possess between 2n = 14 and 2n = 40 chromosomes (Guerra, 2008; Weiss-Schneeweiss and Schneeweiss, 2013). The base chromosome numbers of analyzed Korean species vary from x = 5 in the genus Paris L. to x = 30 in the genus Hosta Tratt. (Appendix 1). Not only interspecific base chromosome number variation is found in thirteen genera analyzed here (Acorus L., Arisaema Mart., Alisma L., Hydrocharis L., Potamogeton L., Lycoris Herb., Asparagus Tourn. ex L., Polygonatum Mill., Scilla L., Iris Tourn. ex L., Cephalanthera Rich., Gastrodia R. Br., Fritillaria Tourn. ex L.) (Appendix 1) but also intraspecific base chromosome number variation is found within several species (x = 9, 11, 12 in Acorus calmus L.; x = 13, 14 in Arisaema amurense Maxim.; x = 13, 14 in Arisaema peninsulae Nakai; x = 13, 14 in most of taxa in the genus Potamogeton L.; x = 9, 10 in Polygonatum falcatum A. Gray; x = 10, 11 in Polygonatum humile Fisch. ex Maxim.; x = 9, 10, 11 in Polygonatum involucratum (Franch. & Sav.) Maxim.; x = 8, 9 in Scilla scilloides (Lindl.) Druce) (Appendix 1). The incidence of both interspecific (x = 5, 6, 7 in Lotus/Fabaceae: Grant, 1991; x = 9, 10, 11, 12, 13, 14 in Melampodium/Asteraceae: Blöch et al., 2009; x = 3, 4, 5, 6 in Crepis/Asteraceae: Babcock and Jenkins, 1943) and intraspecific base chromosome number variation (x = 5, 6, 7: Prospero autumnale complex: Jang et al., 2013; x = 8, 9: Scilla scilloides complex: Choi et al., 2008) have quite frequently been reported in angiosperms (Husband et al., 2003). Due to very low levels of phenotypic variation and thus lack of diagnostic morphological characters for species delimitations in some taxonomically intricate plant groups (often treated as species complexes), more detailed karyological investigations of the chromosome number variations and karyotype structure are needed for correct interpretation of taxonomic and evolutionary patters as well as classifications of angiosperms in general, but also specifically of monocot species native in Korea in global world-wide context.

Two general types of polyploids can be distinguished, autopolyploids and allopolyploids. Allopolyploids originate via hybridization of at least two different taxa, thus carrying different multiplied sets of chromosomes, while autopolyploids result from multiplication of entire chromosome sets within one taxon, typically species. Thus, both hybridization and polyploidization may play an important role in creating new species diversity in angiosperms (Guerra, 2008; Soltis and Soltis, 2009; Husband et al., 2013; Weiss-Schneeweiss and Schneeweiss, 2013). In this study, the incidence of polyploidy has frequently been reported in Araceae Juss., Hydrocharitaceae Juss, Juncaginaceae Rich., Amaryllidaceae J. St.-Hil., Asparagaceae Juss., Dioscoreaceae R. Br., Liliaceae Juss., Melanthiaceae Batsch ex Borkh., Smilacaceae Vent. (Appendix 1). Analyses of ploidy levels distribution among these groups indicated that diploids (ca. 44%) and tetraploids (ca. 14%) prevail, with triploids (ca. 6%), pentaploids (ca. 2%), and hexaploids (ca. 4%) being found less frequently (Fig. 1, Appendix 1). Polyploidy is less frequent in Orchidaceae than in other families of Korean non-Commelinids monocots (Appendix 1), in agreement with previous reports for this region (Goldblatt, 1980; Ko et al., 2009; Rice et al., 2015, references therein). Despite the relatively high incidence of polyploidy in Korean non-Commelinids monocot flora and ease of inferring more recent polyploidy events based purely on increase of chromosome numbers, the clear inference of the mode of polyploids origin and inferences of the patterns of their post-polyploidization genome evolution are non-trivial and thus are not attempted here. These require rigorous phylogenetic analyses of the genera harboring polyploids to infer putative parental species and subsequent molecular cytogenetic analyses as well as genome size measurements to infer the patterns of their genome evolution. Such data are available only for a handful of selected monocot taxa (Appendix 1) and thus, more indepth and group-oriented molecular cytological analyses are required to assist and guide species delimitation and interpretation of phylogenetic relationships and evolutionary patterns among Korean monocots (Choi et al., 2008; Jang et al., 2013; Jang and Weiss-Schnneeweiss, 2015).

Fig. 1.

Distribution of ploidy level variation containing two to eight ploidy levels in non-Commelinids monocot species occurring in Korea (representing their worldwide distribution).

Genome size variation in non-commelinids monocots species native to Korea (in worldwide context)

The dynamics of genome size variation in a group of related diploid taxa can be very high despite lack of change in chromosome number. Genome size increase is, however, directly correlated to polyploidization, particularly recent one. Genome size changes in the absence of chromosome number changes are attributed to differential accumulation of various types of repetitive DNA elements (Leitch and Leitch, 2013). The range of genome sizes of Korean monocots falls within that reported in the Plant DNA C-values database which ranges from 0.061 pg/1C of DNA in Genlisea tuberosa Rivadavia, Gonella & A. Fleischm. (Fleischmann et al., 2014) to 152.33 pg/1C of DNA in Paris japonica Franch. (Pellicer et al., 2010). The 1C-values of species studied here differ nearly 150-fold and range from 0.3 pg in Spirodela polyrrhiza (L.) Schleid. (Araceae) to 44.5 pg in Trillium kamtschaticum Pall. ex Pursh (Melanthiaceae) (Fig. 2, Appendix 1). In general, the broad range of variation of genome sizes in flowering plants correlates with the differences of total karyotype length and incidence of polyploidy, but also correlates with other factors, like the life cycle types (annual/perennial) (Bennett, 1972; Chumová et al., 2015).

Fig. 2.

Distribution of genome size variation in non-Commelinids monocot species occurring in Korea (representing their worldwide distribution).

Patterns of genome evolution: the use of molecular cytogenetics and phylogenetic analyses in Plant Systematics

Extensive studies of chromosome numbers (including polyploidy incidence) and genome sizes in evolutionary context, aiming to elucidate the genome dynamics and often aiding taxonomic classifications have often been carried out in plants of agricultural importance or in model plants (Gong et al., 2012; Renny-Byfield et al., 2013; Novák et al., 2014; Zhang et al., 2014). However, recent advances in the advent of NGS technologies that enable large amounts of DNA sequence data to be generated in a single sequencing run at low cost, wild plants groups are now also amenable for in-depth genomic analyses. Such studies often address the evolution of polyploid complexes and focus on genome evolution in comparative context (e.g., polyploid and its lower-ploidy parental taxa) (Table 1) (Novák et al., 2010; Dodsworth et al., 2015; Weiss-Schneeweiss et al., 2015; McCann et al., 2018). These approaches allow for rapid identification of numerous types of DNA repeats providing new chromosomal markers that can be used in molecular cytological analyses applying in situ hybridization (fluorescence and genomic in situ hybridization; FISH and GISH, respectively) and thus, contributing to better understanding of the evolution of plant genomes (Table 1) (Renny-Byfield et al., 2010; Emadzade et al., 2014; Novák et al., 2014; Zhang et al., 2014; Jang and Weiss-Schneeweiss, 2015). Repetitive DNA fraction of plant genomes is composed of tandem repeats encompassing satellite DNAs, microsatellites and rDNAs (5S and 35S ribosomal RNA genes) as well as dispersed repeats represented by mobile genetic elements, known also as transposable elements. The latter comprise class I retroelements and class II DNA transposons (Weiss-Schneeweiss et al., 2015). In-depth analyses of repeatomes have recently been demonstrated to be informative for inferences of phylogenetic relationships in plants (Table 1) (Dodsworth et al., 2015, 2017; McCann et al., 2018).

Table 1.

Summary of the chromosome numbers, ploidy level variation, and numbers of 5S and 35S rDNA signals in non-Commelinids monocot species occurring in Korea (representing their worldwide distribution)

Molecular cytogenetic mapping of the nuclear ribosomal RNA genes encoding for 35S (18S-5.8S-25S) and 5S rDNAs have proved useful for identifying the patterns and dynamics of chromosomal changes in closely related species groups (Jang et al., 2013, 2016a; Vitales et al., 2017). The distribution of rDNA loci has been reported for some Korean monocots, as summarized in Table 1 (data retrieved from Plant rDNA Database; http://www.plantrdnadatabase.com/, 2018 May 22). The number and localization of rDNA loci in diploids and polyploids was intensively studied in selected genera of Alismatales (Wan et al., 2012), Asparagales (Hizume, 1994; Hizume and Araki, 1994; Lee et al., 1999; Do et al., 1999, 2001; Remon-Büttner et al., 1999; Kim et al., 2004; Hayashi et al., 2005; Lim et al., 2007; Deng et al., 2012; Son et al., 2012), and Liliales (Sultana et al., 2010). A survey of rDNA loci numbers reported for Korean monocots indicated that rDNA loci number can vary at the interspecific level in the genera Allium, Lilium, and Potamogeton (between 2 and 6) (Table 1) regardless of chromosome number and ploidy level variation between species, as show for many other plant groups (Table 1, Appendix 1). The rDNA loci number variation within species or among closely related taxa have often been shown to be correlated with geographic and/or populational factors (e.g., Jang et al., 2016a). Thus, the localization of rDNA loci analyzed in comparative context aids not only the analyses of chromosomal structural changes, but when interpreted in phylogenetic context (e.g., Jang et al., 2013, 2016b), it also allows broader conclusions with implications for taxonomy. Monocot genomes are often more dynamically evolving than those of the dicots. Thus, further cytogenetic analyses of selected groups of Korean monocots will be undertaken to shed light into their genome evolution and evolutionary relationships. Such analyses should and will certainly include also populations and relatives from other geographical areas to allow for more robust conclusions to be drawn.

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