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PHYLOGENETIC EVALUATION of INFRAGENERIC GROUPS of the GENUS USNEA BASED on ITS REGIONS in Rdna I

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PHYLOGENETIC EVALUATION of INFRAGENERIC GROUPS of the GENUS USNEA BASED on ITS REGIONS in Rdna I J Hattori Bot. Lab. No. 92: 231-243 (Aug. 2002) PHYLOGENETIC EVALUATION OF INFRAGENERIC GROUPS OF THE GENUS USNEA BASED ON ITS REGIONS IN rDNA I 2 YOSHIHITO OHMURA ABSTRACT. A phylogenetic tree, inferred from the sequences ofITS regions (including ITSI, 5.8S rDNA and ITS2) of rDNA, has been constructed in order to confirm the infrageneric ranks of the genus Usnea in Japan. Twenty-one species of Usnea mainly collected from Japan were analyzed using the neighbor-joining (NJ) method. Samples were selected from various infrageneric groups of the genus. The data supports the segregation of the subgenera Dolichousnea and Eumitria from sub­ genus Usnea, and the treatment of sections Usnea and Ceratinae. Although the bootstrap values of the clades of the subgenera Dolichousnea and Eumitria and section Usnea are highly reliable, the values of the subgenus Usnea and the section Ceratinae c1ades are not enough to support the branch­ es. This suggests that the subgenus Usnea and the section Ceratinae need to be divided into several phylogenetic groups. Therefore, OTUs of more species belonging to these groups should be analyzed in order to elucidate the relationships within the groups. INTRODUCTION When Ohmura (2001) revised the infrageneric groups of the genus Usnea in Japan and Taiwan, subgenus Dolichousnea Y.Ohmura was newly segregated from the subgenus Usnea. The subgenus Dolichousnea is characterized by a pendent thallus, isotomic-di­ chotomous branching, the presence of annular-pseudocyphellae between segments, a much thicker hypothecium [(70-)100-160(- 200) ,urn], and a positive iodine reaction in its axis. Ohmura (2001) also recognized the subgenus Eumitria (Stirt.) Zahlbr. based on its fistulose axis, and sections Usnea and Ceratinae (Motyka) Y.Ohmura in the subgenus Usnea distin­ guished by differences in cortical hyphae (leptodermatous type for section Usnea and pachydermatous type for section Ceratinae). However, these distinctions differ consider­ ably from Motyka's (1936-38) proposal. Sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (rDNA) are known to have phylogenetic utility at both the infraspecific and infrageneric levels (Bruns et aI. , 1991). The purpose of this study is to test the validity of the infrageneric groupings in the genus Usnea in Japan using molecular phylogenetic analysis methods based on sequences of the ITS regions in rDNA. MATERIALS Fresh specimens of various species collected between 1996 and 1999 were selected as I Part of a dissertation for the degree of Doctor of Science submitted to the University of Tokyo. 2 Domestic Research Fellow, Japan Society for the Promotion of Science. Contact address: Biodiversity and Phylogenetic Study Section, Environmental Biology Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-shi, Ibaraki-ken, 305-8506 Japan. 232 J. Hattori Bot. Lab. No. 92 2 0 0 2 the operational taxonomic unit (OTU). DNA was extracted within two years of the collec­ tion date. Collection data are shown in Table I. All voucher specimens are located in the National Science Museum, Tokyo (TNS). METHODS DNA extraction Total DNA was extracted by CTAB methods (Murray & Thompson 1980) with small modifications. (I) Approximately 50 mg dry weight of each species was washed in flowing tap water for 24 hr. Each sample was then ground to a fine powder using liquid nitrogen in a mortar. (2) Each powdered sample was then suspended in 700,u1 of 2% CTAB extraction buffer [2% CTAB (hexadecyl trimethylammonium bromide), 100 mM Tris- HCl buffer (PH 8.0), 20 mM EDTA buffer (PH 8.0), 1.4 M NaCI] . Sample tubes were incubated for I hr at 65 °C and gently mixed at 10 min intervals. (3) 700,u1 of CIA (chloroform : isoamylalcohol = 24 : I) was then added, and the tubes were gently shaken using a microdisc rotor for 20min. (4) Each sample was centrifuged at 10,000 rpm for 20 min. at 20°e. (5) The aque­ ous phase of each sample was then transferred to a fresh tube. (6) 500,u1 of isopropanol was added to each tube, and gently mixed. (7) The samples were then recentrifuged at 15 ,000 rpm for 10 min. (8) The precipitate was rinsed with 70% ethanol, dried, and dis­ solved in 45,u1 of distilled water. (9) 5,u1 of 100 ,ug/ml RNase solution was then added to each sample, after which they were incubated for I hr at 37°e. (10) The extracted DNA was cleaned using an Ultra Clean™ Gel Spin DNA Purification Kit (MO BIO) as per the manufacturer's instruction. (11) Samples were stored at - 20°C prior to analysis (-80°C for long period storage). peR amplification PCR reactions were performed using Ready-To-Go PCR Beads (Amersham Bio­ sciences). PCR primers were ITSI-F (Gardes & Bruns 1993) as the 5' primer and modified LRI (LRI-I) (5'-GGTTGGTTTCTTTTCC-3') (LRI: Vilgalys & Hester 1990) as the 3' primer. 1.0,u1 of extracted DNA solution, 1.0,u1 each of 10 pmol/,ul primer and 22,u1 of sterile water were added to the sample tube. The program for amplification using a Perkin­ Elmer DNA thermal cycler was initial by 15 cycles for I min. 30 sec. at 95 °C, I min. 30 sec. at 57°C, and 2 min. at n oc, and 25 cycles for I min. at 95 °C, 1 min. 30 sec. at 57°C, and 2 min. at noc, followed by a final extension step of 10 min. at n°e. PCR prod­ ucts were analyzed electrophoretically using a 1.0% ethidium bromide stained agarose gel. Concentrations were determined using a molecular weight standard (A/StyI digest, NIP­ PON GENE). PCR products were prepared for sequencing with a PCR product pre-se­ quencing kit (Amersham Biosciences) as per the manufacturer's instruction. Sequencing Direct sequencing of PCR products was performed using a Thermo Sequenase fluo­ rescent-Iabeled primer cycle sequencing kit (Amersham Biosciences). Manufacturer's in­ structions were followed. Cy5-labelled primers used for the sequencing reaction were ITS5 y. OHMURA: Phylogeneric evaluation of infrageneric groups of the genus Usnea 233 (White et al. 1990) as the 5' primer and modified LRl (5'-GGTTGGTTTCTTTTCCTC­ CG-3') as the 3' primer. Samples were exposed to the following temperature profiles using a Perkin-Elmer DNA thermal cycler: one cycle of 5 min. at 95°C, 30 cycles of 30 sec. at 95°C, 30 sec. at 55°C and 1 min. 20 sec. at n oc, and one cycle of 10 min. at n°e. The products were analyzed by electrophoresis using an ALFred DNA autosequencer (Amer­ sham Biosciences) after addition of 4 Jllloading buffer. ALF data were manually corrected for ambiguous sites. Sequence alignment and phylogenetic analysis The sequences of ITS regions (including ITSl, 5.8S rDNA and ITS2) were aligned using the ClustalW (Thompson et al. 1994) alignment program. After removing gaps, alignments of 447 bp sequences were used for the phylogenetic analysis. A neighbor-join­ ing (NJ) tree (Saitou & Nei 1987) was constructed by MEGA ver. 2.1 (Kumar et al. 2001) using Kimura 2-parameter distance (Kimura 1980). Bootstrap analysis with 1000 replica­ tions was performed to estimate statistical support for each branch. RESULTS AND DISCUSSION Sequencing and alignment ITS regions in rDNA were successfully sequenced for 56 samples (22 species, includ­ ing one species for the out group) (see Tables 1 and 2). PCR products amplified by the primers (ITS I-F and LRl-l) included the following re­ gions: the 3' end of the 18S rDNA (SSU), ITSl, 5.8S rDNA, ITS2, and the 5' end of28S rDNA (LSU). Each was ca. 560 or 860 bp in length. In the latter case, an insertion of ca. 300 bp was present in the SSu. A long insertion in the SSU can be a group I intron, judging from the number of bases and their position. Further research is needed to determine the nature of this long insertion. Sequences of ITS regions obtained in this study are shown in Table 2. The ITSl sec­ tion extends from position 1 to 196; the 5.8S rDNA gene extends from position 197 to 354; and the ITS2 section lies between positions 355 and 512. Phylogenetic analysis for infrageneric groups Although the genus Neuropogon has been considered the closest related group to the genus Usnea (Krog 1976, 1982), molecular data have not been available. Therefore, Ever­ nia esorediosa (MiilI.Arg.) DuRietz was used as an out group. The genus Evernia is also thought to be closely related to the genus Usnea (Krog 1982). The phylogenetic tree based on ITS regions including 5.8S rDNA for the infrageneric analysis of the genus Usn ea is shown in Fig. I. The tree is preliminary because it still lacks some species commonly found in the study area. A monophylous relationship for the sub­ genera Usnea, Dolichousnea and Eumitria and the sections Usnea and Ceratinae in the subgenus Usnea are suggested by the tree, although some of them have a low bootstrap value. The OTUs belonging to the subgenus Dolichousnea, which was newly proposed by Ohmura (2001), and the subgenus Eumitria form monophyletic clades with high bootstrap values, 98% and 99% respectively. These results show that the segregation of the subgenera N Table I. Collection data for DNA analysis samples. w """ DDBJ/EMBUGenBank Species Locality and collection date Specimen number OTU name accession number Usnea aCiculi/era Japan, Honshu, Prov. Kai, Hirano, Yamanakako-mura, Minamitsuru-gun, on Carpinus tschonoskii, V. Ohmura 4400 Ac4400 ABOSI049 ca. ISOO malt., 8.S .1998. U baileyi Japan, Honshu, Prov. Kii, en route from Ichinobashi to Okunoin, MI. Koya, on Cryptomeriajaponica, V. Ohmura 4488A Bai4488a ABOS IOSO ca. 800m all., 1.4.1999.
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