DOI: · Available from: Aaron Liston. Aug 24, 2015. Click to see the full-text of:. Article: Detecting Nucleotide Additivity from Direct Sequences is a SNAP: An Example from Sidalcea (Malvaceae). Original Paper. Abstract: Superimposed nucleotide additivity patterns (SNAPs). were detected from direct sequences of the nuclear ribosomal.
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DNA internal transcribed spacers in a complex ofperennial Sidal-. cea species (Malvaceae) from the Pacific Northwest of the Unit-. ed States. Although only 2. 8% sequence variation exists among.
the eight ITS accessions, parsimony analysis identified two dis-. tinct lineages within this complex consistent with known ploidy. levels. Six SNAPs were identified in a knowntetraploid S. virgata. suggesting allopolyploid origins from diploid S. virgata and one.
of twohexaploid Sidalcea species. A dosage effectdetected at all. six SNAP sites is consistent with the unequal sized parental gen-. omes of allopolyploid S.
virgata. Key words: Sidalcea, nucleotide additivity,allopolyploid hybridi-. zation, ITS, sequence polymorphism. Nuclear ribosomal DNA (nrDNA) has been shown to display. additive patterns following allopolyploid hybridization in. gymnosperms (Quijada et al. ,1997[23]) and angiosperms (Soltis.
and Soltis,1991[29]; Brochmann et al. 1992[4]; Kim and Jansen. 1994[16]; Sang et al. ,1995[26]; O’Kane et al. ,1996[22]; Waters and. Schaal, 1996[31]; Campbell et al. 1997[6]).
Detection of internal. transcribed spacer (ITS) sequence polymorphisms have been. reported from a comparison of direct sequences (Sang et al.
1995[26]) and combinations of direct sequences and clone se-. quences (O’Kane et al.
1996[22]; Campbell et al. 1997[6]; Wid-. mer and Baltisberger, 1999[34]). Persistent ITS polymorphisms. can be attributed to one or a combination of factors that slow. concerted evolution including increased mutation rates, inter-. specific hybridization, decreased meiotic behavior (i.
par-. thenogenic and vegetative reproduction) and location of loci. on nonhomologous chromosomes (Dover, 1988[7]; Arnheim.
1983[1]; Baldwin et al. 1995[2]; Campbell et al. 1997[6]). Al-. though bidirectional concerted evolution of nrDNA repeats.
has been documented in allopolyploid Gossypium gossipioides. (Wendel et al. 1995[33]), nucleotide additivity patterns are. predicted following recent hybridization events combining. unique nrDNA types into a hybrid genome (Baldwin et al.
1995[2]; Sang et al. ,1995[26]; Campbell et al. ,1997[6]). The genus Sidalcea A.
Gray (Malvaceae) is comprised of ap-. proximately 20 annual and perennial herbaceous plant species. restricted to western North America (Roush, 1931[25]). Species. delineation among the perennial taxa is difficult and various. taxonomic treatments have been proposed (Roush, 1931[25];. Hitchcock, 1957[13]; Hitchcock and Cronquist, 1969[15]; Hitch-.
cock, 1973[14]; Hill, 1993[12]). Roush (1931[25]) monographed. the genus and concluded that the apparent morphological.
continuum among the perennial species was not influenced. by hybridization. A critical evaluation of the perennial species. of Sidalceawas then conductedusing taxonomic, cytologic and. biosystematic approaches (Hitchcock, 1957[13]; Kruckeberg. 1957[17]).
Hitchcock and Kruckeberg recognized that the over-. lapping distributions, intermediate morphologies and genetic. compatibility between many of the species could lead to nat-. ural hybridization. The contrasting hypotheses of Roush.
(1931[25]) and Hitchcock (1957[13]) and Kruckeberg (1957[17]). have not been rigorously tested.
A complexof five perennial Sidalcea species endemic to the Pa-. cific Northwest of the United States (Fig. 1) remains poorly de-. fined by morphological characters. The taxa are characterized.
by genetic compatibility (Kruckeberg, 1957[17]; Gisler, unpub-. lished data), partial sympatry and slight ecological differences. Sidalcea campestris Hitchc.
and S. nelsoniana Piper are restrict-. ed to Oregon’s Willamette Valley and adjacent Washington. (Fig. 1).
The distributions of S. cusickii Piper and S. virgata Ho-. wellextendtosouthwesternOregonfromLane Co. andYamhill. Co. respectively (Fig.
1). Sidalcea hirtipes Hitchc. is restrictedto. the west side of the Coast Range from Lincoln Co. Oregon to. southwestern Washington (Fig. 1).
The base chromosome. number for the genus is 10. This complex includes diploids. (2n=2×=20; S. nelsoniana, S.
cusickii and S. virgata), tetra-. ploids (2n=4×=40; S. virgata), and hexaploids (2 n=6×=60;.
S. hirtipes and S. campestris) (Kruckeberg,1957[17]; Halse et al.
1989[9]). Although most Pacfic Northwestern Sidalcea species. examined have a single ploidy level, diploid and tetraploid S.
virgata have been identified (Kruckeberg,1957[17]). To determine phylogenetic affinities within this Pacific North-. western Sidalcea complex, the ITS region was sequenced for. five species. In testing for hybridization among the lineages. an examination of variable sites for patterns of nucleotide ad-. ditivity was conducted.
The potential for direct sequencing to. detect dosage effects in hybrids from parents with unequal.
sized genomes was investigated. The phylogenetic and hybri-. dization results are interpreted in light of cytological, morpho-. logical and biogeographic data. Materials and Methods. Eight accessions representing five species of Sidalcea were ex-. amined for ITS sequence variation (Fig.
1, Table 1). Two acces-. sions (Table 1) are chromosome number vouchers from the. study of Kruckeberg (1957[17]). Ploidy levels for all other acces-.
sions were inferred based on published counts for the species. (Kruckeberg,1957[17]; Halse et al. ,1989[9]).
Voucherswill be de-. posited at OSC. Genomic DNA was extracted from 0. 2–0. 5g of. leaf tissue following the protocol of the DNeasy Plant Mini Kit. (Qiagen, Chatsworth, CA).
Genomic DNAs were electropho-. resed on 1. 2% TBE agarose gels stained with ethidium bromide. and quantified using mass ladder (New England Biolabs, Bev-. erly, MA). Approximately 25 ng of genomic DNA was added to. 50µl aliquots of a PCR master mix consisting of 36µl ddH2O.
4µl 10× Tfl polymerase buffer (1. 0M Tris-HCl, 0. 4M ammo-. nium sulfate), 2. 5 µl MgCl2(25 mM), 2.
5 µl dNTPs, 1µl 10×. BSA, 1µl DMSO, 50pmol of each primer ITS 5* (Liston et al. 1996[18]) and ITS 26S-25R (Liston et al. 1996[18]), and 1 unit Tfl.
polymerase (Epicentre Technologies, Madison, WI). Reaction. mixtures were covered with 2 drops mineral oil and cycled on. a PTC-100 Programmable Thermal Cycler (MJ Research, Wal-. tertown, MA) beginning at 92?C (2min), followed by 35 cycles. of 94?C (60sec), 55?C (45sec), and 72?C (45 sec). After a final.
extension at 72?C (5min), reactions were held at 4?C. PCR pro-. ducts were electrophoresed on 1. 2% TBE agarose and gel puri-. fied following the protocol for QIAquick Gel Purification (Qia-. gen, Chatsworth, CA). Purificates were quantified and com-.
pared with both size and mass ladders on a 1. 2% TBE agarose. gel prior to sequencing. Approximately 30ng purified PCR products were fluorescently. cycle sequenced using the PCR primers following the BigDye. Terminator protocol (PE, Applied Biosystems, Inc.
Foster City. CA) and separated on the ABI Prism 377 (PE, Applied Biosys-. tems) using a 5% polyacrylamide denaturing gel. Five acces-. butions. Approximate distribution limits of. five perennial Sidalcea species in western.
Oregon and Washington estimated from. herbarium specimens and field observations.
(A) S. nelsoniana (···) and S. cusickii (––); (B).
S. hirtipes (···) and S. campestris (––); (C) S.
virgata (––). Accession localities are approxi-. mated with arrows. CR = Coast Range; WV =. Willamette Valley; PT = Putative Tetraploid.
Pacific Northwestern Sidalcea distri-. Vouchers are deposited at OSC. Two accessions of known ploidy level (*) came from chromosome number vouchers. Ploidy levels of other sam-. ples (**) are inferred from chromosome counts for the species. Accession data.
Localities, voucher information, ploidy levels and Genbank Accession numbers for the samples used in this study. Sample NameLocalityVoucher Ploidy LevelAccession Numbers.