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J. Agr. Sci. Tech. (2019) Vol. 21(4): 1005-1021

Phylogenetic Affinities of Wild and Cultivated Ornithogaloideae Based on ITS and trnL–F DNA Sequences by Extended Sampling from Iran

K. Riahi Rad1, A. Babaei1*, V. Mozaffarian2, and D. Potter3

ABSTRACT

The taxonomic classification of subfamily Ornithogaloideae has been a subject of considerable controversy in recent decades. is a relatively large in Ornithogaloideae including valuable ornamental and medicinal . These wild ornamentals, which are introduced into agriculture recently, are becoming increasingly popular as cut flowers, pot plants, and for gardening. This is the first molecular phylogenetic study that includes 10 of the 13 Ornithogalum native to Iran. The aims of the present study were to use ITS and trnL-F sequences to explore phylogenetic relationships and to evaluate genetic resources of Ornithogaloideae naturally occurring in Iran, with an increased sampling of species to be compared to previous phylogenetic studies. In the present study, the combined tree resulted in the best-resolved phylogenetic relationships at the generic level. The results of Maximum Likelihood and Bayesian analysis of molecular data were compared to those from hierarchical cluster analysis of morphological characters. Based on the results, all specimens collected in Iran across all previously recognized taxonomic genera in Ornithogaloideae were placed in Ornithogalum stricto and Loncomelos, which is in line with the morphological analysis. Divergent placements of multiple specimens of a single species in L. brachystachys, O. orthophyllum, and O. sintenisii are attributed to the possibility of past hybridization events, although incomplete lineage sorting and ITS paralogy cannot be overlooked. Increased understanding of naturally occurring variation among wild Ornithogalum populations of Iran and the phylogenetic relationships of wild and cultivated species of Ornithogaloideae could contribute to important opportunities to introduce new ornamentals and improve the agricultural performance of ornamental varieties.

Keywords: Molecular , Nuclear and DNA sequences, Ornithogalum,

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INTRODUCTION (Martínez-Azorín et al., 2011). Manning Forest et al. (2009) extensively studied the possible classifications within this subfamily Ornithogalum L. belongs to subfamily based on plastid molecular sequences, and Ornithogaloideae of Hyacinthaceae, a family of about 700-900 species of bulbous plants mainly finally proposed three tribes (Dipcadieae, Ornithogaleae, and Albuceae), with only four distributed through Africa, Europe, and south- west Asia, with one small genus found in South genera, L., Dipcadi Medik., Ornithogalum L. and Pseudogaltonia Kuntze. America (¨) (APG II 2003). The They divided genus Ornithogalum into four taxonomic classification of this subfamily remains a subject for speculation in recent years subgenera i.e. Galtonia Decne., Aspasia Salisb., Avonsera Speta., and Ornithogalum. Although ______1Department of Horticulture Science, Tarbiat Modares University, Tehran, Islamic Republic of Iran. 2Research Institute of Forests and Rangelands, Tehran, Islamic Republic of Iran. 3Department of Plants Science, University of California Davis, Davis, USA. *Corresponding author; e-mail: [email protected]

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Galtonia, Avonsera, and Aspasia were irritant and relaxant and as a food additive homogeneous in morphology, Ornithogalum (Nazifi et al., 2010). Recently, some studies (with seven sections) was extremely suggested Ornithogaloideae species contain heterogeneous. Moreover, in to make O. compounds that exhibit cytotoxic properties section Ornithogalum monophyletic, Manning against a variety of malignant tumor cells et al. (2009) included Loncomelos Raf. [O. (Asadi et al., 2014). Despite this potential subgenus Beryllis (Salisb.) Baker] within this importance, the genetic resources available genus, therefore, constructing a within this subfamily are still largely morphologically heterogeneous aggregate unexploited (Anderson, 2006). which is difficult to define with regard to other Iran is recognized as one of the 34 hotspots of sections. In the most recent classification on the biodiversity in the world basis of the phylogenetic analyses based on (http://www.biodiversityhotspots.org/xp/Hotspo plastidial and nuclear DNA regions by ts). It is also a country with high diversity of Martínez-Azorín et al. (2011), 19 monophyletic bulbous plants. More than 200 species of genera are accepted within Ornithogaloideae: bulbous plants from different families grow in Albuca, Avonsera, Battandiera Maire., Cathissa Iran (Farahmand and Nazari, 2015), including Salisb., Coilonox Raf., Dipcadi, Eliokarmos 15 species of Ornithogalum (Rechinger, 1995; Raf., Elsiea F.M.Leight., Ethesia Raf., Maroufi, 2010; Heidaryan, 2011; Bidarlord and Galtonia, Honorius Gray, Loncomelos, Ghahremaninejad, 2016). Baker (1872) Melomphis Raf., Neopatersonia Schonland, traditionally placed these species in 3 Nicipe Raf., Ornithogalum, Pseudogaltonia, subgenera: O. subgen. Beryllis (Salisb) Baker Stellarioides Medik., and Trimelopter Raf. In (= Loncomelos), O. subgen. Ornithogalum their study, the Loncomelos was sister to (Syn.: Subgen Heliocharmos Baker) (= the monophyletic Ornithogalum s. str., which Ornithogalum s. str.), and O. subgen. Caruelia provides easy morphological circumscription (Parl) Baker (= Melomphis p. p.) (Rechinger, for both groups. As pointed out by Müller 1995). Doblies and Müller Doblies (1996) dividing Although there are several published studies genus Ornithogalum based on the DNA about the phylogenetic and morphological molecular sequences seems to be by far the characterization of Ornithogaloideae around the better taxonomic solution than including Albuca world, to date there are no published studies of and other genera into Ornithogalum, which phylogenetic affinities for Ornithogaloideae makes a huge taxonomic ‘dustbin’. species native to Iran. Placing Iranian species in Several species of Ornithogaloideae such as a phylogenetic context should improve our Eliokarmos thyrsoides (Jacq.) Raf. and E. understanding of the extent and distribution of dubius (Houtt.) Mart.-Azorín, M.B.Crespo & their biodiversity, which, in turn, should have Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 Juan have been developed as cut flowers (Luria important implications for germplasm selection et al., 2000) and pot plants (Anderson 2006). in breeding programs aimed at development of Also, Ornithogalum Umbellatum L., these species as ornamental and medicinal Loncomelos pyramidale (L.) Raf. and Honorius plants. nutans (L.) Gray. are used in gardens and In the present study, we aimed to use nuclear Melomphis arabica (L.) Raf. and Galtonia (ITS) DNA and plastid (trnL–F) sequences to: saundersiae (Baker) Mart.-Azorín, M. B. (a) Explore phylogenetic relationship of the Crespo & Juan as cut flowers (Plančić et al., cultivated and wild Ornithogaloideae species, 2015). On the other hand, many plants from this with increased sampling of species native to subfamily have been used for various medicinal Iran compared to previous studies; (b) Evaluate purposes, while several species are implicated generic and infrageneric of 3 genera in livestock poisoning (Watt and Breyer- of Ornithogaloideae from Iran; and (c) Evaluate Brandwijk 1932, Botha et al., 2000). For genetic resources of this genus in Iran in order example, O. cuspidatum Bertol. is used in to provide important information for plant Iranian traditional medicine to treat respiratory breeders interested in generating new and inflammatory diseases (Samavati et al., Ornithogaloideae cultivars for medicinal and 2010). Furthermore, it has been used as an anti- ornamental purposes.

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MATERIALS AND METHODS (Table 2). The datasets were subjected to a hierarchical cluster analysis using Ward’s method and squared Euclidean distances Plant Material (Version 9.3.1; SAS Institute Inc, Cary, NC).

Young leaves of 50 specimens representing 10 Sequence Generation species of Ornithogalum, Loncomelos and Melomphis were collected through 50 localities in Iran (Table 1). The samples were labeled and The trnL intron and trnL–F spacer (the trnL–F immediately placed in liquid nitrogen. The region; hereafter trnL–F) were amplified as a coordinates of the readings were determined by single fragment using primers c and f (Taberlet et the Global Positioning System (GPS). The map al., 1991). ITS was amplified using ITS6 and for geographical distribution of collected ITS9 primers (Potter et al., 2007). A total samples was generated from GPS data using volume of 50 µL was used in the PCR ArcGIS Desktop (ESRI, Inc.) (Figure 1a-b). amplification process as follows: 2 µL dNTP, 5 Samples were stored at -80°C till DNA µL 10X PCR buffer (Qiagen, USA), 1 µL (10 extraction. DNA was extracted using the DNeasy µM) of forward and reverse primers (each), 1 µL Plant Mini Kit (Qiagen, USA) according to the of MgCl2 (25 mM), 0.5 µL of Taq DNA manufacturer's recommendations. The Polymerase, 38.5 µL deionized water and 1 µL identification of taxa was made by an expert of DNA template plus 1 µL DMSO for ITS botanist [Mozafarian (PhD)], Research Institute amplification. PCR amplifications were of Forests and Rangelands, Tehran, Iran) and performed with an initial 5 min at 95 °C, deposited in the herbarium of Iranian Biological followed by 35 cycles of 1 minute at 95°C, 1 Research Center. Voucher numbers are shown in minute at 50°C, 1 minute at 72°C, followed by a Table S2. final 7 minutes at 72°C. PCR products were subjected to gel electrophoresis and were cleaned up using a QIAquick Gel Extraction Kit (Qiagen, Morphological Characters USA). Purified PCR products were directly sequenced in both forward and reverse All plants chosen for DNA extraction were directions, using the corresponding primers. The morphologically described and 26 morphological sequencing process was performed using ABI characters were used for a hierarchical cluster 3730 Capillary Electrophoresis Genetic analysis. Of these, 11 were continuous (including Analyzers. Sequencher 5.4 ( Codes plant, scape and length; leaves and Corporation, Ann Arbor, MI, USA) was used to flower number; leaves, perigone and length assemble complementary strands. The Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 and width) while the remaining 15 were discrete sequences’ identities were confirmed by comparison with various published sequences Table 1. Populations included in the phylogenetic analyses of the genus Ornithogalum L. collected in Iran. Subfamily Genus Species name Samples number Loncomelos kurdicum Bornm. 1 Loncomelos Loncomelos arcuatum (Stev.) Speta 4 Loncomelos brachystachys (C. Koch.) Hort. Gorenk. ex Schult. f. 12 Loncomelos bungei Boiss. 1 Ornithogaloideae Ornithogalum oligophyllum E. D. Clarke. 1 Ornithogalum orthophyllum Ten. 5 Ornithogalum Ornithogalum sintenisii Freyn. 11 Ornithogalum neurostegium Boiss. & C. I. Blanche ex Boiss. 3 Ornithogalum cuspidatum (Bertol.) Griseb. 9 Melomphis Melomphis persica (Hausskn. ex Bornm.) Mart.-Azorín, M. 3 B. Crespo & Juan

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Persian Gulf

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(b) Figure 1. Geographical distribution of collected samples (a) and hierarchical cluster analysis of morphological characters (b) using Ward’s method.

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Table 2. Discrete morphological characters included in the analysis of genus Ornithogalum in Iran. Characters Descriptor state Characters Descriptor state 1. Leaves color Chartreuse 1 9. Petal stripe color Without strip 0 Electric lime 2 Dandelion 1 Bright green 3 Dark yellow 2 Bitter lemon 4 Fluorescent yellow 3 Green 5 Green 4 Dark olive green 6 Deep green 5 Deep green 7 10. Petal stripe width Without strip 0 2. Leaves tip shape Semi _lanceolate 0 Narrow 1 lanceolate 1 Semi_wide 2 Wide 3 3. Leaves position Erect 0 Wider 4 Non erect 1 4. Margin of leaves Non_wavy 1 11. color Dandelion 1 Slightly wavy 2 Dark yellow 2 Wavy 3 Brown 3 5. Leaves shape Wide linear 1 Dark brown 4 Semi wide linear 2 Dark chocolate 5 Linear 3 12. Anther color Creamy 1 Narrowly linear 4 Yellow 2 Very narrowly linear 5 Deep lemon 3 6. Leaves longer than No 0 Dark yellow 4 inflorescence Equal 1 Yes 3 13. Bulb color Creamy 1 Eggshell 2 7. Inflorescence Non_compact 1 Canary 3 compaction Compact 2 Corn 4 Compressed and 3 Citrine 5 compact 8. color Snow 1 14. Scale style Semi_ contiguous 1 Conditioner 2 Semi_free 2 Milk 3 Free 3 Cream 4 Blond 5 15. Erect scape Yes 1 No 0

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available in GenBank. Consensus sequences (Table S2). The majority of available trnL–F for each specimen were deposited in sequences in Genbank were short (300-500 bp); GenBank; accession numbers are listed in in order to avoid large proportions of missing supplementary data (Table S2). data, we did not include the sequences under 908 bases in length in our trnL–F and combined data Phylogenetic Reconstruction analyses. In combination with sequences generated by this study, 112 sequences from 93 taxa for ITS, Bowiea volubilis Harv. ex Hook. f. was selected and 70 sequences from 44 taxa for trnL–F were as the out-group based on Martínez-Azorín et al. included in the following analyses. The collected (2011). The Ornithogaloideae was used as a sequences were first aligned using MUSCLE query to search the non-redundant (nr) dataset of (Edgar, 2004) through MEGA7 (Kumar et al., GenBank in order to obtain additional ingroup 2016) followed by manual adjustments. Aligned sequences (Searched on 1st of May, 2017) sequences were then analyzed using jModeltest 2

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v2.1.7 (Darriba et al., 2012) to estimate the best examined taxa yielded data useful for substitution model based on AIC, cAIC, and phylogenetic evaluation. Six of these sequences BIC. The estimated model was then passed on to when aligned to others were missing a part of the RAxML v8.2.8 (Stamatakis, 2014) under 5.8S rDNA region; thus, we determined these as default algorithm (Option: -fd) to generate a pseudogenes (Hřibová et al., 2011). After the maximum likelihood tree. Model parameters exclusion of these pseudogene sequences, 26 and equilibrium base frequencies were sequences for ITS and 33 sequences for trnL–F estimated by RAxML. Four parallel searches regions remained from the original 50 genotypes. were conducted in order to avoid selecting a For ITS, the resulting alignment contained 691 tree lodged on a local optimum. Bootstrap positions (with 448 variable and 316 parsimony- values were calculated from 100 replicates, informative sites). For trnL–F, the resulting and corresponding coefficients were alignment contained 1,089 positions (with 169 variable and 97 parsimony-informative sites). indicated above each branch. For the combined analysis, the resulting The Bayesian analysis was conducted with alignment contained 1682 positions (with 481 MrBayes 3.1.2 (Huelsenbeck and Ronquist, variable and 267 parsimony-informative sites). 2005). The Markov Chain Monte Carlo chains 6 6 Moreover, jModeltest2 (Darriba et al., 2012) were run for 20×10 for ITS and 10×10 found GTR+I+G for ITS, GTR+G for trnL–F generations for trnL–F and combined trees and and GTR+G for combined tree to be the best setting the ‘burnin’ at 50,000 for ITS and 25,000 model based on AIC, cAIC, and BIC. In for trnL–F and combined trees. We used the Maximum Likelihood analysis, RAxML with Markov Chain Monte Carlo method within a estimated parameters (α= 1.450162 and I= Bayesian framework to estimate the posterior 0.272202 for ITS, α= 0.309291 for trnL–F and probabilities of the phylogenetic trees (Larget α= 0.299892 for combined tree) generated the and Simon, 1999) using the 50% majority rule. most likely phylogeny with the likelihood score of -6203.766527 for ITS, -3006.911030 for RESULTS trnL–F and -8064.615813 for combined tree. In all three of our trees, all of the Iranian native species appeared in a single large clade. In the Morphological Characters ITS and combined trees, the clade was strongly supported (1.00 PP; 100% BS), while in the On the basis of the morphological analysis, trnL–F tree, the clade was weakly supported (69 including 26 characters, the species of PP; 50% BS) (Figures 2, 3, and 4). Loncomelos [= O. subgen. Beryllis (Salisb) Baker] and Melomphis [= O. subgen. Caruelia

Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 ITS tree (Parl) Baker] were grouped together in one clade. Melomphis persica (Hausskn. ex Bornm.) Mart.- Azorín, M. B. Crespo & Juan, the sole member The ITS tree includes two main . The first of Melomphis (= O. subgenus Caruelia) included one comprises Ornithogalum, Honorius, in our study, was placed as sister to Loncomelos Loncomelos, Cathissa, Melomphis, Nicipe and kurdicum Bornm.. Ornithogalum s. str. [= O. Elsiea (Clade A), which includes two main sub- subgen. Ornithogalum (Syn.: Subgen clades. The first sub-clade contains Heliocharmos Baker)] was placed as sister to Ornithogalum and Honorius and the second one Loncomelos and Melomphis. In the includes Loncomelos plus 3 specimens of M. morphological character tree, multiple persica. The Iranian species are nested in clade individuals of a single species clustered together. A within genera Ornithogalum, Honorius and 3.2. Phylogenetic Relationships amongst Loncomelos. The genus Nicipe forms a Ornithogaloideae Species Based on DNA monophyletic clade sister to the clade comprising Sequences Ornithogalum, Honorius and Loncomelos. The Despite difficulties in amplification and species of Cathissa, Melomphis and Elsiea do sequencing, PCR amplicons were successfully not form monophyletic clades. obtained for all the samples, and for most

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Figure 2. Bayesian inference analysis obtained from ITS sequences in the phylogenetic analysis of Ornithogaloideae. Sequences specified with bold words are generated by this study. The new proposed generic circumscription of the present study for Iranian species is shown on the right side. Posterior probabilities and bootstrap percentages are shown next to nodes. The generic treatment by Martínez-Azorín et al. (2011) is followed for the studied samples.

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Figure 3. Bayesian inference analysis obtained from trnL-F sequences in the phylogenetic analysis of Ornithogaloideae. Sequences specified with bold words are generated by this study. The new proposed generic circumscription of the present study for Iranian species is shown on the right side. Posterior probabilities and bootstrap percentages are shown next to nodes. The mentioned genera in this tree are accepted by Martínez- Azorín, Crespo et al. (2011). The species not studied by Martínez-Azorín et al. (2011) are shown in checkered.

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Figure 4. Bayesian inference analysis obtained from the combination of ITS and trnL–F sequences in the phylogenetic analysis of Ornithogaloideae. Sequences specified with bold words are generated by this study. The new proposed generic circumscription of the present study for Iranian species is shown on the right side. Posterior probabilities and bootstrap percentages are shown next to nodes. The mentioned genera in this tree are accepted by Martínez-Azorín et al. (2011).

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The first sub-clade in clade A includes trnL–F Tree Ornithogalum and Honorius. In this sub-clade, O. sintenisii specimens do not form a In the trnL–F tree one main clade can be monophyletic group and are placed in three distinguished and successively sister groups different sub-clusters; one includes 3 specimens appear in that large clade. According to our and the other one includes O. sintenisii.1. The results, the trnL–F analysis reveals a large clade sequence of the specimen obtained from (0.69 PP; 50% BS) for the Iranian native species GenBank, which was also collected in Iran included in this study. The trnL–F tree follows (Martínez-Azorín et al., 2011), and the the ITS tree arrangement where Ornithogalum, specimens collected in this study are resolved Honorius and Loncomelos are placed in one into two distant clades. The four specimens of clade. In this tree, Ornithogalum and O. orthophyllum Ten. collected in Iran form a Loncomelos cannot be identified as sub-cluster and are placed distant from the monophyletic. Also, in this tree, different specimen obtained from GenBank, which is specimens of each species do not form based on a collection from Italy (Martínez- monophyletic groups. All members of Azorín et al., 2011). O. neurostegium Boiss. & Ornithogalum s. str., except O. oligophyllum.1 C. I. Blanche ex Boiss. is placed as sister to the and O. orthophyllum.5, grouped in one clade. rest of species in Ornithogalum. Two The specimens of L. brachystachys are placed in specimens of O. cuspidatum formed a sub- different sister clades as are 3 specimens of M. cluster sister to O. oligophyllum E. D. Clarke. persica. The other sister clade shows a close (Figure 2). relationship between L. kurdicum and L. The second sub-clade in clade A includes arcuatum which form a well-supported cluster Loncomelos plus 3 specimens of Melomphis. (1.00 PP; 100% BS). Furthermore, the trnL–F persica. Seven specimens of L. brachystachys tree reveals the same relationship as ITS tree are also placed in this sub-clade, but in different between L. brachystachys.12 and O. sub-clusters; three specimens of L. orthophyllum.5 specimens (1.00 PP; 99% BS). brachystachys including 2, 5, and 7, formed one Different specimens of O. sintenisii form a sub-cluster, and three other specimens of L. monophyletic group (95 PP; 78% BS) and brachystachys including 8, 3, and 10, formed different specimens of O. cuspidatum are placed another sub-cluster. L. brachystachys.12 plus O. in sister clades. Eliokarmos is recovered as orthophyllum.5 are placed on a well-supported monophyletic (1.0 PP; 100% BS) and sister to sub-cluster (1.0 PP; 98% BP) which is sister to the rest of genera in the main clade. The other L. bungei Boiss.1. All 3 specimens of M. genera are placed as sister clades to this main persica formed a small well-supported (1.0 PP; clade. 100% BP) sub-cluster (Figure 2) which is sister Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 to L. arcuatum Steven. (85 PP; 67% BP). Finally, L. kurdicum is sister to all of these taxa Combined Tree (67 PP; 98% BP). Clade B includes Albuca, Coilonox, Stellarioides, Trimelopter, Dipcadi, The combined tree, including 59 taxa, reveals Battandiera, Neopatersonia, Eliokarmos, that the specimens included in this study are Galtonia, Ethesia and Avonsera. This clade is clearly divided into 2 main clades. The first main further divided into two main sub-clades. The clade in the combined tree, Clade A, includes first one comprises genera Albuca plus Ornithogalum, Honorius, Loncomelos, Cathissa, Coilonox, which are sisters to Stellarioides, and Melomphis, Nicipe, Eliokarmos, Ethesia and finally Trimelopter falls as sister to this clade. Galtonia. There is a well-supported main sub- Also, Dipcadi and Battandiera form sister clade (1.0 PP; 100% BP) comprising clades and Neopatersonia falls as sister to the Ornithogalum, Honorius and Loncomelos. In this latter. The second sub-clade includes clade, these three genera are divided in two main Eliokarmos as monophyletic. Galtonia and sub-clades which include all Iranian species. The Ethesia are sister to Eliokarmos. second sub-clade in clade A includes Eliokarmos, Ethesia and Galtonia. Clade B, the

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second main clade, comprises Coilonox, Albuca, as Ornithogalum and Loncomelos, Stellarioides and Dipcadi. respectively. Furthermore, O. subgenus Within clade A, specimens of M. persica form Caruelia, represented by M. persica in this study, a moderately supported sub-cluster (97 PP; 73% formed a small cluster and was placed in a nested BP) which is found as sister to O. oligophyllum. position within Loncomelos. Lonomelos brachytachys.12 and O. The nested position of Honorius within orthophyllum.5 are found in the same position as Ornithogalum (1.0 PP; 94% BS) and also the in the trnL–F and ITS trees within a well- sister relationship of these two genera with supported sub-cluster (1.0 PP; 100% BP). The Loncomelos clade (1 PP; 98% BP) in our ITS phylogenetic relationships among the rest of the tree (Figure 2) is similar to that in the ITS tree species and specimens in the combined tree are reported by Martínez-Azorín et al., (2011). In generally similar to those in the ITS tree (Figure our ITS tree, all sampled taxa of Ornithogalum 2). from Iran fell in the clades corresponding to Ornithogalum s. str. and Honorius, which together formed a strongly supported clade (1.0 DISCUSSION PP; 94% BS). Furthermore, the Iranian Loncomelos species were placed in a clade, The New Proposed Generic similar to the results of Martínez-Azorín et al. Circumscription for Iranian Species (2011). Melomphis persica appeared as an within Ornithogaloideae: independent clade and nested within Loncomelos in our ITS tree. In contrast, the trnL–F tree generated in this study revealed the nested As traditionally treated by Baker (1872), this position of Ornithogalum within Loncomelos subfamily is considered as one genus and with a sister relationship to Honorius (0.62 PP; consists of 9 subgenera, 3 of which occur in Iran: 50% BS) (Figure 3) and justified segregation of O. subgen. Beryllis (Salisb) Baker, O. subgen. the latter genus from Ornithogalum. The Ornithogalum (Syn.: subgen Heliocharmos phylogenetic study by Manning et al. (2009) Baker), and O. subgen. Caruelia (Parl) Baker revealed the same relationship. Like ITS tree, the (Rechinger, 1995). According to the most recent trnL–F tree included M. persica in Loncomelos. classification (Martínez-Azorín et al., 2011), 19 The combined tree (Figure 4) justified monophyletic genera are accepted within segregation of Ornithogalum, Loncomelos and subfamily Ornithogaloideae. These 19 genera are Honorius and placed them in three different well characterized morphologically, and are clades. In our combined tree, M. persica again circumscribed in such a way that allows easy was placed within the Loncomelos clade. definition and makes easier subsequent Melomphis persica is clearly differentiated from Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 attribution of a taxon to a given genus. In the Loncomelos by the morphology of the new arrangement, Martínez-Azorín et al. (2011) , and gynoecium, which are treated the species traditionally included in O. more similar to M. arabica; on the other hand, it subgenus Beryllis in 4 different genera including is similar to Loncomelos in some morphological Loncomelos, Nicipe, Stellarioides, and characters like plant height, leaf number, leaf Trimelopter, the species traditionally included in length, flower number, perigone length and O. subgenus Ornithogalum in genus width, and bulb length, width, and color. The Ornithogalum and the species traditionally phylogenetic placement of M. persica and its included in O. subgenus Caruelia in genera morphological characters could reflect a possible Melomphis and Eliokarmos. hybrid origin from a cross between M. arabica The species traditionally classified by Baker and some eastern Loncomelos species. However, (1872) in O. subgenus Ornithogalum and O. a wider sampling of related taxa is needed to subgenus Beryllis include Eurasian and North improve our knowledge of phylogenetic African species. In our morphological analysis, relationships within these genera. The topology each of these subgenera formed a monophyletic of our combined tree is similar to that obtained group. As Martínez-Azorín et al. (2011) noted, by Martínez-Azorín et al. (2011). these two subgenera are clearly differentiated by the morphology of inflorescences, capsules, and

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Our results support the classification of all Relationships at the Species Level for Iranian species of Ornithogaloideae in Iranian Species Ornithogalum s. str. and Loncomelos. The ITS, trnL–F and combined trees reveal that Iranian species were placed in clades corresponding to Divergent placement of multiple specimens of a Ornithogalum, Loncomelos, and Honorius clades single species is found in L. brachystachys, O. and clearly are divided into 2 main clades in the orthophyllum and O. sintenisii. In the ITS tree, ITS and combined trees (Figures 2 and 4) which seven specimens of L. brachystachys were is in line with the morphological analysis (Figure placed in three different sub-clusters. In this 1). Genus Honorius, represented by H. nutans, regard, the bio-geographical distribution of each segregated in different ways from these two group has a peculiar pattern. Specimens from genera in different trees. In the trnL–F and northwestern Iran (L. brachystachys.2, 5, 7) combined trees Loncomelos clade did not form a formed the first sub-cluster and specimens from monophyletic group where O. oligophyllum was southwestern Iran formed the second sub-cluster placed within this genus. This conflict suggests (L. brachystachys. 8, 3, 10). The third sub-cluster the possibility of past hybridization events in O. included L.brachystachys.12 and O. oligophyllum. However, further studies are orthophyllum.5. Based on morphological data, needed to confirm its final position. Despite this the first and second sub-clusters grouped misplacing, which may reflect hybridization together but are morphologically diagnosable by event in this species, we consider the combined scape length, which is longer in L. tree as the most informative phylogenetic tree in brachystachys.2, 5, 7. Karyotypic differences this study (Figure 4) and it justifies segregation among the species and ecotypes of Ornithogalum of Ornithogalum, Loncomelos and Honorius. have been observed (Anderson, 2006). Five Furthermore, combination of ITS and trnL–F cytotypes were documented among L. sequences resulted in a phylogenetic tree that brachystachys specimens collected in five supports the monophyly of genera previously different locations of Iran, with the chromosome described on the basis of molecular data and numbers 2n= 12, 2n= 16, 2n=22, 2n= 24 and morphological characters as shown by Martínez- 2n=30 (Heidaryan, 2011). However, we do not Azorín et al. (2011). Honorius, Ornithogalum, have the cytotypes for the specimens we Loncomelos, Melomphis, Nicipe, Elikarmos, sampled. Ethesia, Galtonia, Coilonox, Albuca, Within Ornithogalum, considerable divergence Stellarioides, Dipcadi are segregated as proper of specimens of a single species was found for O. genera on the basis of last classification by sintenisii. The specimens of this species were Martínez-Azorín et al. (2011). The phylogenetic placed in quite different positions; 4 specimens relationships of genus Cathissa are not fully which are collected for this study were placed in Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 resolved in this tree, maybe because of the lack the same sub-clade of clade A in the ITS tree but of trnL–F sequences in this tree for the related in different positions. O. sintenisii.4, O. taxa and genera. The most important cultivated sintenisii.6 and O. sintenisii.11 formed one sub- horticultural species include E. thyrsoides, E. cluster distant from O. sintenisii.1. However, this dubius, O. umbellatum, H. nutans, M. arabica relationship reflects the clear morphological and G. saundersiae. Similar to the most recent divergence in morphology. In the morphological study by Martínez-Azorín et al. (2011), our analysis, different specimens of O. sintenisii phylogenetic tree based on ITS tree placed were placed in two sister clades. O. sintenisii.1 Melomphis, Ornithogalum, Honorius in the first was placed in a clade sister to O. sintenisii.4, O. main clade (clade A) and Eliokarmos and sintenisii.6 and O. sintenisii.11 clade (Figure 1). Galtonia in the second main clade (clade B). O. sintenisii.1 is defined morphologically by Also, our combined tree derived from ITS and smaller plant size and more numerous flowers in trnL–F sequences is similar to the combined tree comparison with O. sintenisii.4, O. sintenisii.6 derived from ITS, trnL–F, matK and rbcL and O. sintenisii.11. The specimen obtained from sequences in Martínez-Azorín et al. (2011) GenBank, which was also collected in Iran study, both of which placed all five of these (Martínez-Azorín et al., 2011), was placed far genera in clade A. from these 4 specimens. Potential conflict may arise within a single dataset as a result of

1016 Phylogenetic of Wild and Cultivated Ornithogaloideae ______

extended paralogy (Catalán et al., 2004). brachystachys.12 and O. orthophyllum.5. If they Pseudogene copies of ITS sequences, were hybrids between L. brachystachys and O. accumulating quite a few mutations in O. orthophyllum species, we would expect sintenisii.1, and misidentification of the phylogenetic trees based on their cpDNA specimen used from the GenBank are all valid on sequences to place them in a clade with their theoretical grounds to cause divergent maternal parent, while trees based on nuclear ITS placements of the O. sintenisii sequences. Thus, sequences might place both species in a clade this divergence remains a subject for speculation with the paternal parent. Thus, if they are and requires more studies. hybrids, the maternal parent must be a third In the ITS tree, the four specimens of O. species, presumably one not sampled in this orthophyllum collected in Iran formed a sub- study. A final possibility would be to consider cluster and placed distant from the specimen each of them as a new species. However, before obtained from GenBank, which is based on a taking such a step, further investigations are collection from Italy (Martínez-Azorín et al., required to understand their identities. 2011). O. orthophyllum is a poorly-known However, conflict between the trnL–F, ITS floristic species and was treated in different ways and combined trees in the placement of the as a for other species or defined as different specimens of each species may reflect other species (Herrmann, 2002). This is a native the possibility of past hybridization events species to Italy and at the latest checklist of the (Catalán et al., 2004), although incomplete vascular flora native to Italy it is recognized a lineage sorting and ITS paralogy cannot be different species from the previous statements overlooked (Catalán et al., 2004). Also, (Bartolucci et al., 2018). Unfortunately, we did pseudogene copies of ITS sequences and not have access to trnL-F sequences of the chromosome duplication events may have an specimen collected in Italy. Further studies are impact on the nuclear ITS sequences used in the required to distinguish final position of these phylogenetic reconstruction leading to the specimens. In both the ITS and trnL–F trees as divergent placements of different members of the well as the combined tree, L. brachystachys.12 species observed here (Marinho et al., 2014). A and O. orthophyllum.5 formed a well-supported final possible explanation would be the sub-clade and were placed in the same position misidentification of the specimens used to in the Loncomelos clade, apart from the generate the sequences we obtained from remaining specimens of related species. Genbank or collected samples for this study. Morphological clustering does not explain the close relationship between these 2 specimens in Distribution of Wild and Cultivated the phylogenetic trees based on sequence data. In morphological clustering, L. brachystachys.12 Species of Ornithogaloideae Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 falls as sister to the rest of L. brachystachys specimens and O. orthophyllum.5 falls as sister Ornithogaloideae are distributed in Africa, Asia- to the rest of O. orthophyllum specimens (Figure Temperate (which includes Iran), and Europe 1). On the other hand, both of these specimens (Eastern, Middle Northern, Southeastern, are characterized by their pale color in Southwestern). The natural habitats of the wild comparison with the rest of related specimens. species of Ornithogalum and Loncomelos range Their special color in morphological characters from dry semi-desert areas to marshy wetlands could provide evidence to consider them as and riverbanks, to mountaintops (Anderson, natural mutants. The conflict between 2006). Species of these genera have also been morphological and genetic results for these two introduced and naturalized in Africa (northwest specimens may be due to interspecific coast of Africa), Asia-Tropical, Europe (Eastern hybridization, which is reported in this genus and Northern), Australia (South Australia, (van Raamsdonk, 1985; Griesbach et al., 1993; Western Australia), and North America Joung and Roh, 2004). We have compared ITS (Manning et al., 2003; Manning et al., 2009; and trnL–F trees to identify topological eMonocot, 2017; Royal Botanic Gardens, 2017; incongruences that may indicate hybridization The Global Biodiversity Information Facility, events involved in the origin of L. 2017). Our results followed those of Martínez-

1017 ______Riahi Rad et al.

Azorín et al. (2011), where the first main clade in guide future breeding initiatives involving ITS and combined trees includes all north Ornithogalum. African and Eurasian taxa of Ornithogalum, Honorius, Loncomelos, Melomphis and Cathissa ACKNOWLEDGEMENTS plus the eastern and southern African species that correspond to Elsiea and Nicipe. The second main clade comprises Albuca, Coilonox, This research was financially supported by Stellarioides, Trimelopter, Dipcadi, Battandiera, Tarbiat Modares University as a grant awarded Neopatersonia, Eliokarmos, Galtonia, Ethesia for PhD study to Khadijeh RiahiRad. Additional and Avonsera, which mainly occur in Africa. support was provided by funding from the University of California Davis, Agricultural Experiment Station. We are grateful to Mostafa CONCLUSIONS Joodaki (Tarbiat Modares University) who helped with collecting samples and laboratory This is the first phylogenetic study employing procedures, Mahmoud Kiani (Amol University nuclear ITS and plastid trnL–F sequences to of Special Modern Technologies) for his examine the phylogenetic diversity of several contribution by giving many helpful insights; Kai Ornithogaloideae species collected from a Battenberg (UC Davis) who provided valuable broad range of climatic conditions of Iran with assistance in Maximum likelihood analysis, Dr. the goals of improving our understanding of Kazempour and Dr. Pedram (Tarbiat Modares relationships among these species within University) in Bayesian analysis. Ornithogaloideae, and comparing molecular diversity of these populations in Iran. Following REFERENCES the concept of Martínez-Azorín et al. (2011) classification, we put the species of O. subgenus Ornithogalum collected in Iran in 1. Anderson, N. O. 2006. Flower Breeding and Ornithogalum and the species of O. subgenus Genetics: Issues, Challenges and Opportunities Beryllis collected in Iran in Loncomelos on the for the 21st Century, SSBM. basis of phylogenetic and morphological 2. APG II, A. 2003. "An Update of the evidence. Additionally, the inclusion of the only Angiosperm Phylogeny Group Classification member of Melomphis included in this study, for the Orders and Families of Flowering M. persica, within genus Loncomelos in the Plants: APG II." Bot. J. Linn. Soc., 141(4): morphological clustering and trees based on 399-436. phylogenetic analysis of molecular data requires 3. Asadi, H., Orangi, M., Shanehbandi, D., a wider sampling of related taxa to improve the Babaloo, Z., Delazar, A., Mohammadnejad, L.,

Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 Shahneh, F.Z., Valiyari, S. and Baradaran, B. status of our knowledge of phylogenetic 2014. "Methanolic Fractions of Ornithogalum relationships among these genera. Better Cuspidatum Induce Apoptosis in PC-3 Prostate understanding of the complex phylogenetic Cancer Cell Line and WEHI-164 relationships that exist within Ornithogaloideae Fibrosarcoma Cancer Cell Line." Adv. species contributes important information about Pharma. Bull., 4(Suppl. 1): 455-458. their evolutionary history and helps to improve 4. Baker, J. G. 1872. "Revision of the Genera and our knowledge for developing effective Species of Scilleæ and Chlorogaleæ." Bot. J. conservation, utilization, and management Linn. Soc., 13(68): 209-266. practices. Improved understanding of naturally 5. Bartolucci, F., Peruzzi, L., Galasso, G., occurring variation among wild Ornithogalum Albano, A., Alessandrini, A., Ardenghi, N., populations of Iran and the phylogenetic Astuti, G., Bacchetta, G., Ballelli, S. and Banfi, relationships among wild and cultivated E. 2018. "An Updated Checklist of the species, as revealed in this study, could provide Vascular Flora Native to Italy." Pl. Biosyst., important opportunities to introduce new 152(2): 179-303. ornamental plants or improve the agricultural 6. Bidarlord, M. and Ghahremaninejad, F. 2016. performance of modern ornamental varieties. Ornithogalum boissieri (), a New Also, these results offer the opportunity to Species from the Talesh Mountains, Iran. Ann. Bot. Fenn. BioOne, 53 (1–2): 69-72.

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7. Botha, C., Schultz, R., Van der Lugt, J. and 19. Kumar, S., Stecher, G. and Tamura, K. 2016. Archer, C. 2000. "A Krimpsiekte-Like MEGA7: Molecular Evolutionary Genetics Syndrome in Small Stock Poisoned by Analysis Version 7.0 for Bigger Datasets. Mol. Ornithogalum toxicarium Archer & Archer." Biol. Evol., 33 (7): 1870–1874. J. S. Afr. Vet. Assoc., 71(1): 6-9. 20. Larget, B. and Simon, D. L. 1999. Markov 8. Catalán, P., Torrecilla, P., Rodrıguez, J. A. L. Chain Monte Carlo Algorithms for the and Olmstead, R. G. 2004. Phylogeny of the Bayesian Analysis of Phylogenetic Trees. Mol. Festucoid Grasses of Subtribe Loliinae and Biol. Evol., 16(6): 750-759. Allies (Poeae, Pooideae) Inferred from ITS 21. Luria, G., Watad, A., Cohen-Zhedek, Y. and and trnL–F Sequences. Mol. Phylogenet. Evol., Borochov, A. 2000. Growth and Flowering of 31(2): 517-541. Ornithogalum dubium. VIII International 9. Darriba, D., Taboada, G. L., Doallo, R. and Symposium on Flower 570, Cape Town, Posada D. 2012. jModelTest 2: More Models, . 12. New Heuristics and Parallel Computing. Nat. 22. Manning, J. C., Forest, F., Devey, D. S., Fay, Methods, 9(8): 772-772. M. F. and Goldblatt, P. 2009. A molecular 10. Edgar, R. C. 2004. MUSCLE: Multiple Phylogeny and a Revised Classification of Sequence Alignment with High Accuracy and Ornithogaloideae (Hyacinthaceae) Based on High throughput. Nucl. Acids Res., 32(5): an Analysis of Four Plastid DNA Regions. 1792-1797. Taxon., 58(1): 77-107. 11. eMonocot. 2017. EMonocot: An Online 23. Manning, J. C., Goldblatt, P. and Fay, M. F. Resource for Monocot Plants, Ornithogalum 2003. A Revised Generic Synopsis of L.. From: http://e- Hyacinthaceae in Sub-Saharan Africa, Based monocot.org/taxon/urn:kew.org:wcs:taxon:282 on Molecular Evidence, Including New 876. Combinations and the New 12. Farahmand, H. and Nazari, F. 2015. Pseudoprospereae. Edinburgh J. Bot., 60(03): Environmental and Anthropogenic Pressures 533-568. on Geophytes of Iran and the Possible 24. Marinho, R. C., Mendes-Rodrigues, C., Balao, Protection Strategies: A Review. J. Hortic. Sci. F., Ortiz, P. L., Yamagishi-Costa, J., Bonetti, Technol., 2(2): 111-132. A. M. and Oliveira, P. E. 2014. Do 13. Griesbach, R., Meyer, F. and Koopowitz, H. Chromosome Numbers Reflect Phylogeny? 1993. Creation of New Flower Colors in New Counts for Bombacoideae and a Review Ornithogalum via Interspecific Hybridization. of Malvaceae sl. Am. J. Bot., 101(9): 1456- J. Am. Soc. Hortic. Sci., 118(3): 409-414. 1465. 14. Heidaryan, F. 2011. Biosystematic Study of 25. Maroufi, H. 2010. Two New Plant Species Genus Ornithogalum in Iran. PhD. Islamic from Kurdistan Province, West of Iran. J. Bot., Azad University. (in Persion) 16(1): 76-80. 15. Herrmann, N. 2002. Biological Flora of 26. Martínez-Azorín, M., Crespo, M. B., Juan, A. Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 Central Europe: Ornithogalum angustifolium” and Fay, M. F. 2011. Molecular Phylogenetics nom. prov., Syn. pp O. orthophyllum ssp. of Subfamily Ornithogaloideae kochii= O. kochii Parl., O. gussonei Ten. Flora. (Hyacinthaceae) Based on Nuclear and Plastid 197(6): 409-428. DNA Regions, Including a New Taxonomic 16. Hřibová, E., Čížková, J., Christelová, P., Arrangement. Ann. Bot., 107(1): 1-37. Taudien, S., de Langhe, E. and Doležel, J. 27. Müller Doblies, U. and Müller Doblies, D. 2011. The ITS1-5.8 S-ITS2 Sequence Region 1996. Revisionula Incompleta Ornithogalorum in the Musaceae: Structure, Diversity and Use Austro‐Africanorum (Hyacinthaceae). Feddes in Molecular Phylogeny. PLoS One, 6(3): Repert., 107(5‐6): 361-548. e17863. 28. Nazifi, E., Movafeghi, A., Nazemiyeh, H., 17. Huelsenbeck, J. and Ronquist, F. 2005. Asnaashari, S., Moghadam, S. B. and Delazar, MrBayes, Version 3.1. 2. Available from the A. 2010. Phytochemical Analysis of Essential Authors: http://morphbank. ebc. uu. Oils from Different Plant Parts of se/mrbayes3/info. php. Ornithogalum cuspidatum Bertol. Pharma. 18. Joung, Y. H. and Roh, M. 2004. Paternity Sci., 16(1): 37-46. Determination of Ornithogalum Seedlings 29. Plančić, M., Božin, B., Kladar, N., Rat, M. and Using DNA Markers. J. Hortic. Sci. SrĎenović, B. 2015. Phytochemical Profile and Biotechnol., 79(2): 316-321. Biological Activities of the Genus

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مطالعه روابط فیلوژنی گونههای وحشی و اهلی زیرخانواده Ornithogaloideae بر اساس توالیهای ITS و trnL–F با توسعه نمونه برداری از ایران

ک. ریاحی راد، ع. بابایی، و. مظفریان، و د. پتر

چکیده Downloaded from jast.modares.ac.ir at 3:22 IRST on Monday September 27th 2021 طبقِبٌذی زیرخاًَادُ Ornithogaloideae در طی دِّّای اخیر بِ هعالِ هْوّی در علن تاکعًََهی تبذیل ؼذُ اظت.Ornithogalum یک جٌط بسرگ در زیرخاًَادُ Ornithogaloideae هی- باؼذ؛ ٍ حاٍی گیاّاًی با ارزغ زیٌتی ٍ دارٍیی هیباؼذ. ایي گیاّاىِ زیٌتیِ ٍحؽی، کِ اخیرا بِ صٌعت گیاّاى زیٌتی هعرفی ؼذُاًذ، بِ گیاّاى زیٌتی هحبَبی بِ عٌَاى گلّای ؼاخِ بریذُ، گیاّاى گلذاًی ٍ جْت کؽت ٍ کار در باغّا تبذیل ؼذُاًذ. هطالعِ حاضر اٍلیي هطالعِ فیلَشًتیکی جْتِ هطالعِ 01 گًَِ از گیاّاًی کِ تحت عٌَاى جٌط Ornithogalum در ایراى هعرفی ؼذُاًذ هیباؼذ. کاربرد تَالیّای trnL_F ٍ ITS جْت درک رٍابط فیلَشًتیکی گًَِّای هختلف ایي جٌط، ارزیابی هٌابع شًتیکی ایي زیرخاًَادُ با گعترغِ ًوًَِبرداری از ایراى در هقایعِ با هطالعاتِ قبلی از اّذاف ایي هطالعِ هیباؼذ. در هطالعِ حاضر، بْتریي رٍابط فیلَشًتیکی در ظطح جٌط از درخت ترکیبی قابل اظتٌباط اظت. ًتایج حاصل از آًالیسّای فیلَشًتیکی بِ رٍغ حذاکثر درظتًوایی ٍ رٍغ بیسیي با ًتایج حاصل از آًالیس

1020 Phylogenetic of Wild and Cultivated Ornithogaloideae ______

خؼَِای ٍیصگیّای ریختی هَرد هقایعِ قرار گرفت. بر اظاض ًتایجِ حاصل از هطالعِ حاضر، ّوِ شًَتیپّایِ جوعآٍری ؼذُ از ایراى، در هیاى آخریي جٌطّایِ هعرفی ؼذُ در زیرخاًَادُ Ornithogaloideae، در دٍ جٌط Loncomelos ٍ Ornithogalumطبقِبٌذی ؼذًذ؛ ایي طبقِبٌذی با ًتایج حاصل از آًالیسّای ریختی ّنراظتا هیباؼذ. پراکػٌ شًَتیپّای هختلف یک گًَِ در درخت فیلَشًتیکی در گًَِّای O. ٍ O. brachystachys, O. orthophyllum sintenisiiهؽاّذُ ؼذ؛ کِ هوکي اظت بِ علت رخ دادى دٍرگگیری، تفرق ًاقص آللّا ٍ شىّای پارالَگ ITS باؼذ. تٌَّعِ طبیعیِ هَجَد هیاىِ جوعیتّایِ هختلفِ ایي گیاُ در ایراى، ٍ رٍابطِ فیلَشًتیک هیاى گًَِّای ٍحؽی ٍ کؽت ؼذُ هیتَاًذ فرصت هْوی جْت هعرفی گیاّاى زیٌتی جذیذ بِ صٌعت گیاّاى زیٌتی ٍ یا بْبَد صفات باغباًی ارقام تجاری هَجَد باؼذ.

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