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Fabaceae) Inferred from Nrdna ITS and Two Cpdnas, Matk and Rpl32-Trnl(UAG) Sequences Data

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Fabaceae) Inferred from Nrdna ITS and Two Cpdnas, Matk and Rpl32-Trnl(UAG) Sequences Data Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology Official Journal of the Societa Botanica Italiana ISSN: 1126-3504 (Print) 1724-5575 (Online) Journal homepage: http://www.tandfonline.com/loi/tplb20 Phylogeny and divergence times of the Coluteoid clade with special reference to Colutea (Fabaceae) inferred from nrDNA ITS and two cpDNAs, matK and rpl32-trnL(UAG) sequences data M. Moghaddam, S. Kazempour Osaloo, H. Hosseiny & F. Azimi To cite this article: M. Moghaddam, S. Kazempour Osaloo, H. Hosseiny & F. Azimi (2016): Phylogeny and divergence times of the Coluteoid clade with special reference to Colutea (Fabaceae) inferred from nrDNA ITS and two cpDNAs, matK and rpl32-trnL(UAG) sequences data, Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, DOI: 10.1080/11263504.2016.1244120 To link to this article: http://dx.doi.org/10.1080/11263504.2016.1244120 Published online: 19 Oct 2016. Submit your article to this journal Article views: 7 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=tplb20 Download by: [Cornell University Library] Date: 30 October 2016, At: 10:43 Plant Biosystems, 2016 http://dx.doi.org/10.1080/11263504.2016.1244120 Phylogeny and divergence times of the Coluteoid clade with special reference to Colutea (Fabaceae) inferred from nrDNA ITS and two cpDNAs, matK and rpl32-trnL(UAG) sequences data M. MOGHADDAM1, S. KAZEMPOUR OSALOO1, H. HOSSEINY1, & F. AZIMI2 1Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Iran and 2Natural Resource Research Center of Ardabil Province, Iran Abstract This study reconstructed the phylogeny of the Coluteoid clade using nrDNA ITS and plastid matK and rpl32-trnL(UAG) sequences data. The analyses resolve a well-supported Coluteoid clade, as sister to Astragalus s.str. + Oxytropis, nested within the larger, strongly supported Astragalean clade. The Coluteoid clade is now composed of 12 genera including Podlechiella, Swainsona, Carmichaelia, Clianthus, Montigena, Phyllolobium, Lessertia, Sutherlandia, Sphaerophysa, Smirnowia, Eremosparton and Colutea. Within this clade, Podlechiella is the first diverging lineage followed by successive subclades of Carmichaelia + Clianthus + Swainsona, Phyllolobium, Lessertia + Sutherlandia, Sphaerophysa + Smirnowia + Eremosparton, and Colutea. We assigned the formal tribal name to this clade and redefined the tribe Coluteae. A diagnostic key to the genera of the tribe is presented. Astragalus cysticalyx and A. sinicus have no relationship with the Coluteoid clade, instead, they are nested in Astragalus s. str. Resolution within Colutea is rather low, but several smaller subclades with low to high supports are found in the genus. None of the large sections in Colutea are monophyletic. Divergence time estimates revealed that the Coluteoid clade originated in the Early Miocene (20.4 Mya). Most of its members were diverged during the Late Miocene to Pliocene. Colutea and Podlechiella form the youngest lineages where the diversification occurred in the Pliocene- Pleistocene. Keywords: Coluteae, divergence time, nrDNA ITS, phylogeny, plastid DNA, the Coluteoid clade Introduction ciliate style (Lavin & Delgado 1990). All members of the clade except the annual Podlechiella are The Coluteoid clade is a heterogeneous group of perennial herbs, subshrubs, or shrubs/small trees. morphologically and ecologically distinct genera Based on the phylogenetic analysis of the combined and species, which distributed throughout Africa to Australasia. Currently, it contains 12 genera, nrDNA ITS and matK sequences, Wojciechowski i.e. Colutea (including Oreophysa, see Kazempour (2005) indicated that Podlechiella is the first Osaloo et al. 2006), Smirnowia, Eremosparton, diverging taxon as sister to the other representatives Sphaerophysa, Lessertia, Sutherlandia, Carmichaelia, of the clade. Carmichaelia and allies formed own Clianthus, Montigena, Swainsona, Phyllolobium and subclade, as for Lessertia and Sutherlandia. In this Podlechiella as well as the two Astragalus species, study, Phyllolobium chinense Fisch. (=A. complanatus A. sinicus L. and A. cyticalalyx Ledeb. (Wojciechowski Bunge) formed a common clade with A. sinicus, and et al. 1999; Wojciechowski 2005; Lock & Schrire Colutea, represented by C. arborescense L., was sister 2005). Colutea and its allied genera were previously to A. cysticalyx. Furthermore, in the earlier study of treated in tribe Galegeae subtribe Coluteinae Wojciechowski et al. (1999), Smirnowia and allies (Polhill 1981), while Carmichaelia and its allies (including A. cysticalyx) formed a distinct subclade formed subtribe Carmichaelinae (Heenan 1998a, within the Coluteoid clade. Kazempour Osaloo 1998b; Wagstaff et al. 1999) or carmichaelioid group et al. (2003) using molecular data (nrDNA ITS and (Lock & Schrire 2005). Phyllolobium and Podlechiella plastid ndhF) clearly indicated that A. sinicus is more have been recently segregated from Astragalus closely related to members of Astragalus s.str. than (Kazempour Osaloo et al. 2003; Zhang & Podlech to the Coluteoid clade. However, the taxonomic 2006). Most members of the clade are characterized composition of the Coluteoid clade and the exact by non-interlocking wing and keel petals and a phylogenetic status of A. cyticalyx are still unclear. Correspondence: S. Kazempour Osaloo, Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran. Email: [email protected] © 2016 Società Botanica Italiana 2 M. Moghaddam et al. After Swainsona (about 80 spp.) and Lessertia fied using the primers ITS5 m of Sang et al. (1995) (about 50 spp), Colutea is the third large genus of and ITS4 of White et al. (1990) or AB101F and the clade with about 30 species. Colutea is distribut- AB102R (Douzery et al. 1999). The matK gene was ed from Mediterranean region to China, Himalaya, amplified using the primer of trnK685F (Steele & and east–northeast Africa. In Iran, Colutea has nine Wojciechowski 2003) and matK1320R (designed in species in 3–5 sections (Browicz 1984; Pooyan et al. this study). The rpl32-trnL(UAG) region was amplified 2014). Among the species-rich genera of the Colu- using primer rpl32-F and trnL(UAG) described in Shaw teoid clade, Carmichaelia and Swainsona (Wagstaff et al. (2007). The PCR amplification was carried out et al. 1999), Phyllolobium (Kang et al. 2003; Zhang in the volume of 20 μL, containing 8.2-μL deionized et al. 2012) and Colutea (Mirzaei et al. 2015) have water, 10 ml of the 2 × Taq DNA polymerase master been subjects of phylogenetic analyses using nrDNA mix Red (Amplicon, Cat. No. 180301, 150-mMTris- H ITS data. HCl P 8.5, 40-Mm (NH4)2SO4, 3.0-Mm MgCl2, By employing penalized likelihood estimates 0.4-Mm dNTPs, 0.05 units μl−1AmpliconTaq DNA of ages and rates of nucleotide substitutions using polymerase, inert red dye and a stabilizer) 0.5 μl matK sequences, Wojciechowski (2005) provided the of each primer (10 pmol/μl), and 1 μl of template estimated mean age of 13.7 (±1.70) Mya, the middle DNA (20 ng/μl). PCR procedures for nrDNA ITS Miocene, and mean rate of 0.000894 (±0.000080) region were 2 min 30 s at 94°C for predenaturation for the Coluteoid Clade. followed by 30 cycles of 45 s at 94°C for denatura- Hitherto, no detailed phylogenetic treatment tion, 40 s at 56°C for primer annealing and 40 s at and divergence time estimates using multiple 72°C for primer extension, followed by a final primer DNA sequence data have been conducted on the extension of 7 min at 72°C. for matK region, the Coluteoid clade in general and Colutea in particular. PCR condition was 2 min 30 s at 94°C followed by In this study, the nuclear ribosomal DNA internal- 32–35 cycles of 40 s at 94°C, 40 s at 53°C, and 1 min transcribed spacer (nrDNA ITS) and two plastid 20 s at 72°C, and final extension of 7 min at 72°C fragments, matK gene and rpl32-trnL(UAG) intergenic was performed. For rpl32-trnL(UAG)region, the PCR spacer, were sequenced for phylogenetic reconstruc- condition was 5 min at 80°C followed by 28 cycles of tions and estimation of ages and rates. 50 s at 95°C, 45 s at 54°C, and 50 s at 65°C, and the The main goals of present study are: (1) to evalu- final extension of 5 min at 65°C was performed. The ate the taxonomic status of the Coluteoid clade and ensuring PCR fragments were separated by electro- to elucidate relationships within it, (2) to test the phoresis in 1% agarose gels in 1 × TAE (pH = 8) monophyly of Colutea and its major sections, (3) to buffer, stained with ethidium bromide and were assess the accurate taxonomic position of Astragalus photographed with a UV gel documentation system cysticalyx, and (4) to estimate molecular divergence (UVItec, Cambridge, UK). Purification of PCR times and ages of the Coluteoid clade and its major products was performed using NucleoSpin Extract subclades. kits (MACHERY-NAGEL April 2004/Rev.01). Each region was directly sequenced using the Big Dye Terminator Cycle Sequencing Ready Reaction Materials and methods kit with the same primers in an ABI 3730xl DNA Taxon sampling Analyzer (Applied Biosystems, USA) through Pishgam Inc. Forty-three accessions representing 29 species belonging to Coluteoid clade and 12 species of the related clade (Astragalus + Oxytropis) were included Sequence alignment in the analyses. One species of Caragana and one species of Eversmania were selected as outgroups. Each of the individual data-sets was edited using In addition to the newly generated nrDNA ITS BioEdit ver. 7.0.9.0 (Hall 1999) and aligned with (23), matK (21) and rpl32-trnL (28) sequences, web-based version of MUSCLE (Edgar 2004; (UAG) at http://www.ebi.ac.uk/Tools/msa/muscle/) and 20 nrDNA ITS, 16 matK, and 1 rpl32-trnL(UAG) sequences were retrieved from GenBank. All taxa adjusted manually. The alignment of the data-sets together with their origin, voucher information, and required for the introduction of numerous single- GenBank accession numbers are listed in Table I.
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