Infrageneric Phylogeny of the Genus Viola (Violaceae) Based on trnLtrnF, psbAtrnH, rpL16, ITS Sequences, Cytological and Morphological Data

doi:10.3724/SP.J.1143.2010.10122

Abstract

Abstract:

The sequences of chloroplast trnLtrnF (20 species), psbAtrnH(17 species), rpL16 (17 species) and ITS(one species) regions of the genus Viola were analyzed for phylogenetic relationships in the genus with the maximum parsimony (MP) and Bayesian inference (BI) analyses. Hybanthus enneaspermus, Scyphellandra pierrei and Rinorea bengalensis were used as outgroups. Additional sequences corresponding to the same DNA regions for the other taxa in Viola were downloaded from GenBank. The phylogenetic tree indicated that subgenViola is not monophyletic. Moreover, some intrageneric relationships in Viola were clarified. Combining sequences with morphological characters and chromosome number, the inference of morphological evolution in Viola was put forward. It was inferred that: 1) erect stems might well be more primitive than stolons and rosettes; 2) long fimbriate margin in stipules and stipules with 1/2-3/4 adnate part might represent distinctive evolutionary trends of sectTrigonocarpae and of sectAdnatae respectively; 3) species with stigmatic beaks might have been derived from ancestors without beaks; simple structure stigmas transformed into complex structure stigmas, and then transformed back to simple stucture patterns.

Key words: Viola, ITS, trnL-trnF, psbA-trnH, rpL16, Phylogeny

摘要：

以鼠鞭草(Hybanthus enneaspermus)、鳞隔堇(Scyphellandra pierrei)、雷诺木(Rinorea bengalensis)作为外类群，对堇菜属(Viola)20个类群的trnLtrnF序列，17个类群的psbAtrnH、rpL16序列以及1个类群的nrDNA ITS序列进行了测定，并从GenBank下载相应的序列，运用最大简约法以及贝叶斯推论法进行系统分析，构建系统发育树。结果表明：堇菜亚属(subgen.Viola)不是一个单系类群，并明确了堇菜属部分组间类群的亲缘关系。本文还结合形态与细胞学证据对堇菜属进行性状演化的推测。结果表明：1）直立茎较匍匐茎、莲座状茎（叶基生）原始；2）托叶边缘长流苏状与托叶1/2~3/4合生分别是鸟嘴柱头堇菜组（sect.Trigonocarpae）和合生托叶组（sect.Adnatae）演化路线的重要性状标志；3）花柱样式从柱头无喙演化至柱头有喙，并由柱头简单演化至柱头复杂，再趋向于柱头简化。

关键词: 堇菜属, ITS, trnL-trnF, psbA-trnH, rpL16, 系统发育

CLC Number:

Q949
Q943

LIANG Guan-Xin-, , XING Fu-Wu. Infrageneric Phylogeny of the Genus Viola (Violaceae) Based on trnLtrnF, psbAtrnH, rpL16, ITS Sequences, Cytological and Morphological Data[J]. Plant Diversity, 2010, 32(6): 477-488.

梁冠欣1,2, , 邢福武1. 堇菜属组间的系统发育与亲缘关系：基于trnL-trnF、psbAtrnH、rpL16、ITS序列，细胞学以及形态学证据[J]. Plant Diversity, 2010, 32(6): 477-488.

References

王庆瑞, 1991. 中国植物志, 第51卷 \[M\]. 北京: 科学出版社
吴征镒, 路安民, 汤彦承等, 2003. 中国被子植物科属综论 \[M\]. 北京: 科学出版社
Altekar G, Dwarkadas S, Huelsenbeck JP et al, 2004. Parrallel Metropolis coupled Markov chain Monte Karlo for Bayesian phylogenetic inference \[J\]. Bioinformatics, 20 (3) : 407—415
Ballard HE, 1996. Phylogenetic relationship and infrageneric groups in Viola (Violaceae) based on morphology, chromosome numbers, natural hybridization and Internal Transcribed Spacer (ITS) sequences \[D\] (ph. D. Dissertation). Madison: University of WisconsinMadison
Beattie AJ, 1974. Floral evolution in Viola \[J\]. Annals of the Missouri Botanical Garden, 61: 781—793
Becker W, 1916. Violae Asiaticae et AustralensisⅠ\[J\]. Beiheft zum Botanisches Cenetralblblatt, 34 (2): 208—396
Becker W, 1925. Viola \[A\]. In: Engler and Prantl. Die Natürlichen Pflanzenfamilien \[M\]. Leipzig: Verlag von Wilhelm Engelmanna , 21: 363—376
Becker W, 1929. Violae Asiaticae Novae \[J\]. Bulletin of Miscellaneous Information, Kew, 6: 200—203
Belaeva VA, Siplivinsky VN, 1975. Chromosome numbers and taxonomy of some species of Baikal flora \[J\]. Botanicheskii Zhurnal, 60: 864—872
Clausen J, 1927. Chromosome number and the relationship of species in the genus Viola \[J\]. Annals of Botany, 41: 677—714
Clausen J, 1929. Chromosome number and relationship of some north American species of Viola \[J\]. Annals of Botany, 43: 741—764
Clausen J, 1931. Cytogenetic and taxonomic investigation in Melanium violets \[J\]. Hereditas, 15: 219—304
Clausen J, 1951. Stages in the Evolution of Plants Species \[M\]. New York: Cornell University Press
Clausen J, 1964. Cytotaxonomy and distributional ecology of western North American violets \[J\]. Madroo, 17: 173—204
Chen YS, Yang QE, Ohba H et al, 2007. Viola Linnaeus \[A\]. In: Wu ZY, Raven PH eds. Flora of China \[M\]. Beijing: Science Press; St. Louis: Missouri Botanical Garden Press, 13: 74—111
Chen YS (陈又生) , 2006. Toxonomic revision of Viola L. (Violaceae) in China \[D\] (ph. D. Dissertation) . Beijing: Institue of Botany, Chinese Academy of Sciences
Doyle JJ, Doyle JL, 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue \[J\]. Phytochemical Bulletin, 19: 11—15
Donoghue MJ, Sanderson MJ, 1992. The suitability of molecular and morphological evidence in reconstructing plant phylogeny \[A\]. In: Soltis PS, Soltis DE, Doyle JJ eds. Molecular Plant Systematics \[M\]. New York: Champman and Hall, 340—368
Ge CJ (葛传吉) , Li YK (李岩坤) , Zhou Y (周月) et al, 1987. Observations on the chromosome numbers of medicinal plants of Shandong Province \[J\]. Acta Botanica Yunnanica (云南植物研究), 9 (3) : 333—338
Gingins FC, 1824. Violarieae \[A\]. In: de Candolle AP ed. Prodromus Systematis Naturalis Regni Vegetabilis \[M\]. Paris: Treuttel and Würtz, 1: 291—306
Gong Q (龚琴), 2008. Molecular systematics of the genus Viola in China \[D\] (MS Dissertation).Guangzhou: South China Botanical Garden, Chinese Academy of Sciences
Hamilton MB, 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation \[J\]. Molecular Ecology, 8: 521—523
Hsu CC, 1968. Preliminary chromosome studies on the vascular plants of Taiwan (Ⅱ) \[J\]. Taiwania, 14: 11—27
Huang RF (黄荣福) , Shen SD (沈颂东) , Lu XF (卢学峰) , 1996. Studies of the chromosome numbers and polyploidy for some plant in the northeast QinghaiXizang plateau \[J\]. Acta Botanica BorealiOccidentalia Sinica (西北植物学报), 16: 310—318
Huelsenbeck JP, Ronquist F, Nielsen R et al, 2001. Bayesian inference of phylogeny and its impact on evolutionary biology \[J\]. Science, 294: 2310—2314
Ji YH, Fritsch PW, Li H et al, 2006. Phylogeny and classification of Paris (Melanthiaceae) inferred from DNA sequence data \[J\]. Annals of Botany, 98: 245—256
Jordan WC, Courtney MW, Neigel JE, 1996. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in notrh American duckweeds (Lemnaceae) \[J\]. American Journal of Botany , 83 (4) : 430—439
Kelchner SA, Clark LG, 1997. Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae) \[J\]. Molecular Phylogenetics and Evolution, 8: 385—397
Kim KS, Sun BY, Whang SS et al, 1991. Biosystematic study on the genus Viola in KoreaComparative study of the Viola albida complex \[J\]. Korean Journal of Botany, 34 (3): 229—238
Lee YN, 1967. Chromosome numbers of flowering plants in Korea \[J\]. Journal of Korean Research Institute Ewha Women′s University, 11: 455—478
Li LF (李连方) , Yin ZT (尹祖棠), 1997. A primary chemotaxonomy of the genus Viola from NorthChina \[J\]. Journal of China Agricultural University(中国农业大学学报) , 2 (1) : 74—82
Linnaeus C, 1753. Species Plantarum \[M\]. Stockholm, 2: 933—937
Maddison WP, Maddison DR, 2008. Mesquite: A Modular System for Evolutionary Analysis \[DB/OL\]. Version 25, http://mesquiteprojectorg
Marcussen T, 2003. Evolution, phylogeography, and taxonomy within the Viola alba complex (Violaceae) \[J\]. Plant Systematics and Evolution, 237: 51—74
Nishikawa T, 1985. Chromosome counts of flowering plants of Hokkaido (9) \[J\]. Journal of Hokkaido University of Education(Section 2B), 36: 25—40
Posada D, Crandall KA, 1998. Modeltest: testing the model of DNA substitution \[J\]. Bioinformatics, 14: 817—818
Posada D, Buckley TR, 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests \[J\]. Systematic Biology , 53: 793—808
Rambaut A, 2002. SeAl sequence alignment editor, v 20 a 11 \[DB/OL\]. Oxford: University of Oxford, http://evolvezoooxacuk/
Raunkiaer C, 1934. The Life Forms of Plants and Statistical Plant Geography \[M\]. Oxford: Oxford University Press
Roalson EH, Friar EA, 2004. Phylogenetic relationships and biogeographic patterns in North American members of Carex section Acrocystis (Cyperaceae) using nrDNA ITS and ETS sequence data \[J\]. Plant Systematics and Evolution, 243: 175—187
Ronquist F, Huelsenbeck JP, 2003. MrBayes3: Bayesian phylogenetic inference under mixed models \[J\]. Biometrics, 19: 1572—1574
Shaw J, Lickey EB, Beck JT et al, 2005. The tortoise and the hare Ⅱ: relative utility of 21 noncoding chloroplast DNA sqences for phylogenetic analysis \[J\]. American Journal of Botany, 92: 142—166
Sokolovskaya AP, Probatova NS, 1986. Chromosome numbers in some repredentatives of the Asteraceae, Iridaceae, Poaceae, Primulaceae, Violaceae families from the Far East of USSR \[J\]. Botanicheskii Zhurnal , 71 (10): 1423—1425
Starodubtsev VN, 1985. Chromosome numbers in the representatives of some families from the Soviet Far East \[J\]. Botanicheskii Zhurnal, 70 (2) : 275—277
Stepanov NV, Muratova EN, 1995. Chromosome numbers of some taxa of higher plants of Krasnoyarsk territory \[J\]. Botanichekii Zhurnal, 80 (6): 114—116
Sun K (孙坤) , Wang QR (王庆瑞) , 1991. Notes on the Chinese Violaceae (Ⅱ)——cytological studies on some violets of China \[J\]. Bulletin of Botanical Research (植物研究), 11 (1): 69—72
Sun K (孙坤) , Wang QR (王庆瑞) , 1996. Cytological studies on 6 species of Viola from northwest China \[J\]. Chinese Bulletin of Botany (植物学通报) , 13 (1): 46—47
Sun K (孙坤) , Wang QR (王庆瑞) , Wang Y (王漪) , 1997. Numerical taxonomic study of Viola in China \[J\]. Jouranl of Northweat Normal University (Natural Science) (西北师范大学学报, 自然科学版) , 33 (3) : 69—73
Swofford DL, 2002. PAUP* 40: phylogenetic analysis using parsimony (* and other methods), Beta version 40 b 10 \[CP\]. Sunderland: Sinauer Associates
Taberlet P, Gielly L, Pautou G et al, 1991. Universal primers for amplification of three noncoding regions of chloroplast DNA \[J\]. Plant Molecular Biology , 17: 1105—1109
Thompson JD, Gibson TJ, Plewniak F et al, 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools \[J\]. Nucleic Acids Research, 25: 4876—4882
Wang JC (王震哲) , 1989. A Taxonomic study of Viola L. (Violaceae) of Taiwan \[D\]. Taipei: ph. D thesis of Taiwan University
White TJ, Brums TD, Lee SB et al, 1990. Amplification and direct sequenceing of ribosomal RNA genes and the internal transcribed spacer in fungi \[A\]. In: Innis MA, Gelfand GH, Sninsky JJ et al eds. PCRProtocols and ApplicationsA Laboratory Manual \[M\]. San Diego: Academic Press, 315—322
Yoo KO, Jang SK, Lee WT, 2005. Phylogeny of Korean Viola based on ITS sequences \[J\]. Korean Journal of Plant Taxonomy, 35: 7—23
Yuzepchuk SV, Klokov MV, 1949. Violaceae \[A\]. In: Shishkim BK ed. Flora of the USSR \[M\]. Jerusalem : Keter Publishing House, 262—360
Zhou JS (周劲松) , 2008 . Systematics of the genus Viola L. (Violaceae) in China \[D\] (ph. D. Dissertation). Guangzhou: South China Botanical Garden, Chinese Academy of Sciences
Zimmer EA, Roalson EH, Skog LE et al, 2002. Phylogenetic relationships in the Gesnerioideae (Gesneriaceae) based on nrDNA ITS and cpDNA trnLF and trnET spacer region sequences \[J\]. American Journal of Botany, 89: 296—311云南植物研究 2010，32(6)： 489～494Acta Botanica Yunnanica DOI: 103724/SPJ1143201010128

[1]	Ibrokhimjon Ergashov, Ziyoviddin Yusupov, Alireza Dolatyari, Mina Khorasani, İsmail Eker, Nazgul Turdumatova, Georgy Lazkov, Farruhbek Rasulov, Hang Sun, Tao Deng, Komiljon Tojibaev. New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences [J]. Plant Diversity, 2025, 47(04): 561-575.
[2]	Zhi-Chao Li, Chao-Qun Xu, Wei Zhao, Shuai Nie, Yu-Tao Bao, Hui Liu, Zhen Xing, Jian-Feng Mao, Xiao-Ru Wang. Ecophysiological transition mediated by hybridization in a hybrid pine species complex [J]. Plant Diversity, 2025, 47(04): 604-619.
[3]	Lang Li (李朗), Bing Liu (刘冰), Yu Song (宋钰), Hong-Hu Meng (孟宏虎), Xiu-Qin Ci (慈秀芹), John G. Conran, Rogier P.J. de Kok, Pedro Luís Rodrigues de Moraes, Jun-Wei Ye (叶俊伟), Yun-Hong Tan (谭运洪), Zhi-Fang Liu (刘志芳), Marlien van der Merwe, Henk van der Werff, Yong Yang (杨永), Jens G. Rohwer, Jie Li (李捷). Global advances in phylogeny, taxonomy and biogeography of Lauraceae [J]. Plant Diversity, 2025, 47(03): 341-364.
[4]	Yu-Mei Yan, Ze-Xin Fan, Pei-Li Fu, Zhi-Yong Zhang. Drought tolerance traits explain differential stem growth rates of evergreen and deciduous trees in a tropical karst forest [J]. Plant Diversity, 2025, 47(03): 454-465.
[5]	Xue Wang, Xinrui Liu, Shuang Chen, Jiang Zhu, Yanqi Yuan, Rong Zhu, Kaixi Chen, Xue Yang, Xiaochun Wang, Weiyi Mo, Ruili Wang, Shuoxin Zhang. Elevational variation in anatomical traits of the first-order roots and their adaptation mechanisms [J]. Plant Diversity, 2025, 47(02): 291-299.
[6]	Wei Gu, Ting Zhang, Shui-Yin Liu, Qin Tian, Chen-Xuan Yang, Qing Lu, Xiao-Gang Fu, Heather R. Kates, Gregory W. Stull, Pamela S. Soltis, Douglas E. Soltis, Ryan A. Folk, Robert P. Guralnick, De-Zhu Li, Ting-Shuang Yi. Phylogenomics, reticulation, and biogeographical history of Elaeagnaceae [J]. Plant Diversity, 2024, 46(06): 683-697.
[7]	Wenjie Guo, Lu Gong, Yan Luo, Qian Guo. Does season regulate heterochronous leaf growth? Mechanisms of petiole-lamina trade-offs in broad-leaved woody plants of the Tianshan Mountains [J]. Plant Diversity, 2024, 46(06): 755-765.
[8]	Tana Wuyun, Lu Zhang, Tiina Tosens, Bin Liu, Kristiina Mark, José ángel Morales-Sánchez, Jesamine Jöneva Rikisahedew, Vivian Kuusk, ülo Niinemets. Extremely thin but very robust: Surprising cryptogam trait combinations at the end of the leaf economics spectrum [J]. Plant Diversity, 2024, 46(05): 621-629.
[9]	Jun-Yi Zhang, Yue-Hong Cheng, Min Liao, Yu Feng, Sen-Long Jin, Ting-Mei He, Hai He, Bo Xu. A new infrageneric classification of Gastrochilus (Orchidaceae: Epidendroideae) based on molecular and morphological data [J]. Plant Diversity, 2024, 46(04): 435-447.
[10]	Fangbing Li, Hong Qian, Jordi Sardans, Dzhamal Y. Amishev, Zixuan Wang, Changyue Zhang, Tonggui Wu, Xiaoniu Xu, Xiao Tao, Xingzhao Huang. Evolutionary history shapes variation of wood density of tree species across the world [J]. Plant Diversity, 2024, 46(03): 283-293.
[11]	Jingya Zhang, Cui Xiao, Xiaoyu Duan, Xin Gao, Hao Zeng, Rong'an Dong, Gang Feng, Keping Ma. Species' geographical range, environmental range and traits lead to specimen collection preference of dominant plant species of grasslands in Northern China [J]. Plant Diversity, 2024, 46(03): 353-361.
[12]	Rong Ma, Qi Xu, Yongqian Gao, Deli Peng, Hang Sun, Bo Song. Patterns and drivers of plant sexual systems in the dry-hot valley region of southwestern China [J]. Plant Diversity, 2024, 46(02): 158-168.
[13]	Ju Li, Shu-Bin Zhang, Yang-Ping Li. Photosynthetic response dynamics in the invasive species Tithonia diversifolia and two co-occurring native shrub species under fluctuating light conditions [J]. Plant Diversity, 2024, 46(02): 265-273.
[14]	Xin-Mao Zhou, Li-Bing Zhang. Phylogeny, character evolution, and classification of Selaginellaceae(lycophytes) [J]. Plant Diversity, 2023, 45(06): 630-684.
[15]	Ming-Yue Jin, Daniel J. Johnson, Guang-Ze Jin, Qing-Xi Guo, Zhi-Li Liu. Soil water content and nitrogen differentially correlate with multidimensional leaf traits of two temperate broadleaf species [J]. Plant Diversity, 2023, 45(06): 694-701.