Internal transcribed spacer (ITS) and genetic variations in Lilium native to Korea

Abstract

Internal transcribed spacers (ITS) of nuclear ribosomal DNA cistrons were studied in wild Lilium species native to Korea and compared with those species in the genus distributed in other countries to investigate the phylogenetic relationships among Lilium species. Sequence analysis data of Lilium plants collected from China and Japan were also included to study the inter-and intra-specific relationships in the genus. Lilium species formed a monophyletic clade and were separated in two clusters that belonged to the section Sinomartagon and Martagon. The phylogenetic relationships of Lilium species inferred from the ITS sequences using the maximum likelihood method were highly congruent with previous studies of cytogenetic evidence and classification (Comber, 1949) based on the morphological characters. The length of ITS1 and ITS2 regions in Lilium species native to Korea was uniform, however, nucleotide polymorphisms were noted. A region with a conserved sequence was observed from position 330-340 among all the species. Comparison of the sequence analysis of Lilium accessions native to different countries revealed the presence of six insertions/deletions (indels) and 121 substitutions (transitions and transversions) in both regions of ITS1 and ITS2. Indels were responsible for variation of ITS length in different accessions. The sequences of Lilium species collected from each country had less variations than those of species collected from different countries. Sequences variations in both ITS regions suggested that they could be used for assaying genetic diversity in Lilium at the inter-and intra-specific level.Additional key words: lily, nuclear ribosomal DNA, phylogeny, sequence polymorphism Hort. Environ. Biotechnol. 52(5):502-510. 2011.The ribosomal RNA genes (45S rDNA) of higher eukaryotes are part of repeat units arranged in tandem arrays within the nucleolar organizer regions (NORs), which typically are about 10 kb (Heslop-Harrison, 2000). Each repeat unit of 45S rDNA consists of individual 18S, 5.8S, and 26S rRNA genes, which are separated from the next repeat unit by the intergenic spacer region (IGS) (Apples and Honeycutt, 1986). Within each repeat, the coding regions of these three genes are separated by internal transcribed spacers (ITS) that flank the 5.8S rRNA gene (Gründler et al., 1991;Wanzenböck et al., 1997).The coding regions of these rRNA genes show a little sequence divergence between closely related species, whereas the ITS regions show higher rate of divergence that is useful for inferring phylogenies of closely related species and populations in a given species. The length and sequence of ITS regions are believed to be fast evolving and, therefore, may be variable. In angiosperms, ITS sequences vary in length from approximately 500-700 bp (Baldwin et al., 1995). Because of their relatively high rate of mutations, ITS regions are useful for studying inter-or intra-specific genetic variations (Delgado-Salinas et al.

LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species

“…In our IRAP analysis, the Martagon lilies formed an out-group cluster to support the Lighty's proposal (Lighty 1968(Lighty , 1969. Sequence variation in the internal transcribed spacers (ITS) of rDNA also showed the Martagon lilies were in the out-group to other lilies that are growing in Korea (Sultana et al 2011). Among the Sinomartagon lilies, the out-grouping of L. lancifolium from other Asiatic lilies is also interesting.…”

Re-emergence of Lilium callosum Sieb. et Zucc. in Taiwan after a fire allows propagation and renews the possibility of conservation

“…Information of ITS sequences has been published for different L . callosum populations collected from Japan (Dubouzet and Shinoda 1999 ; Nishikawa et al 1999 , 2001 ), South Korea (Sultana et al 2011 ; Lee et al 2011 ), and China (Du et al 2014 ). Sequence-related amplified polymorphism (SRAP) markers (Li et al 2011 ) and rbcL and matK gene sequences were also used to analyze phylogenetic relationships between Lilium species, including L .…”

“…In comparison with different origins of L . callosum , plants from Korea, Japan and China were placed into different groups, and this may be attributed to the considerable divergence in lengths and sequences of ITS1 and ITS2 (Sultana et al 2011 ). Pelkonen and Pirttilä ( 2012 ) also constructed a phylogenetic tree of the main species and sections of the Lilium .…”

Genetic diversity assessment of lily genotypes native to Korea based on simple sequence repeat markers

“…Molecular marker studies in Lilium are not advanced compared to other plant species because of their large genome sizes. Molecular studies of wild Lilium species has been increasing and the reported molecular markers are ISSR (Xi et al 2012), SRAP (Robarts and Wolfe 2014), RAPD (Huang et al 2009), and ITS (Kumari et al 2018;Sultana et al 2011) to explore diversity of wild Lilium species. So, molecular techniques are required to systematically study of wild Lilium species in depth.…”