植物学报 ›› 2016, Vol. 51 ›› Issue (5): 609-619.doi: 10.11983/CBB15141

• 研究报告 • 上一篇    下一篇

樟属植物ITS序列多态性分析

黄建峰1,2, 李朗1, 李捷1,*()   

  1. 1中国科学院西双版纳热带植物园, 植物系统发育与保护生物学实验室, 昆明 650223
    2中国科学院大学, 北京 100049
  • 收稿日期:2015-08-11 接受日期:2015-11-13 出版日期:2016-09-01 发布日期:2016-09-27
  • 通讯作者: 李捷 E-mail:jieli@xtbg.ac.cn
  • 作者简介:

    # 共同第一作者

  • 基金资助:
    国家自然科学基金(No.31370245)

Polymorphism of the Internal Transcribed Spacer of nrDNA in Cinnamomum Schaeffer (Lauraceae)

Jianfeng Huang1,2, Lang Li1, Jie Li1*   

  1. 1Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
    2University of Chinese Academy of Sciences, Beijing 100049, China
  • Received:2015-08-11 Accepted:2015-11-13 Online:2016-09-01 Published:2016-09-27
  • Contact: Li Jie E-mail:jieli@xtbg.ac.cn
  • About author:

    # Co-first authors

摘要:

对樟科樟属(Cinnamomum Schaeffer) 17个代表样本的核糖体DNA内转录间隔区(nrDNA ITS)进行克隆测序。对获得的87条不同ITS序列的长度变异、GC含量、5.8S区二级结构的稳定性、遗传距离、进化模式以及系统发育关系进行了相关分析。研究结果显示, ITS序列在樟属植物内存在明显的多态性, 87条序列中的22条序列被鉴定为假基因序列, 其余65条序列为功能基因序列; 假基因序列采用中性进化模式, 变异明显大于功能序列。ITS序列在樟属植物中出现一致性进化不完全和假基因现象也可能发生在樟科其它类群中, 这可能是导致樟科植物ITS序列直接测序方式成功率低的重要原因。

Abstract:

In this study, nuclear ribosomal DNA (nrDNA) ITS fragments of 17 Cinnamomum samples were cloned and sequenced. A total of 87 different ITS sequences were obtained. Their length polymorphism, GC content, secondary structure stability of the 5.8S region, p-distance, evolutionary pattern and phylogenetic relationships were analyzed. The ITS sequences had a high degree of polymorphism. Among the 87 ITS sequences, 22 were pseudogenes and the other 65 were functional genes. The pseudogenes showed a neutral evolutional pattern and had a higher degree of polymorphism than functional genes. The incomplete concerted evolution of the ITS region and pseudogenes within the genus Cinnamomum may have also occurred in other Lauraceae plants, which could be responsible for the low sequencing success rate of the ITS region in Lauraceae plants.

表1

材料信息"

Code Speices Voucher Locality
H1C Cinnamomum appelianum Huang J. F. & Ding X., 14043005 (HITBC) Guizhou, China
D16 C. baileyanum Crayn D., CSIRO38 (CNS) Queensland, Australia
H5A C. bodinieri Li J. et al., 2007212 (HITBC) Zhejiang, China
H53 C. crenulicupulam Huang J. F., QSBG10 (HITBC) Chiengmai, Thailand
H18 C. heyneanum Huang J. F., H-BN012 (HITBC) Yunnan, China
H21A C. chekiangense Huang J. F., H-KZ30 (HITBC) Yunnan, China
H21B C. chekiangense Ci X. Q. et al., CXQ279 (HITBC) Zhejiang, China
H26 C. liangii Ci X. Q. et al., 20100043 (HITBC) Zhejiang, China
H35B C. pauciflorum Huang J. F., H-BN005 (HITBC) Hunan, China
B17 C. rhynchophyllum Huang J. F. et al., 2013082923 (HITBC) Bogor, Indonesia
B20 C. sintoc Huang J. F. et al., 2013082920 (HITBC) Bogor, Indonesia
B24 C. sp. Huang J. F. et al., 2013082910 (HITBC) Bogor, Indonesia
H43 C. subavenium Ci X. Q. et al., CXQ303 (HITBC) Zhejiang, China
H43A C. subavenium Huang J. F. & Li L., 2013024 (HITBC) Hainan, China
H43B C. subavenium Ci X. Q. et al., CXQ257 (HITBC) Hunan, China
H50 C. tsangii Huang J. F. & Li L., H-WZS07 (HITBC) Hainan, China
H47A C. tsoi Huang J. F. & Li L., H-JFL21 (HITBC) Hainan, China
LN Laurus nobilis Huang J. F. & Ding X., LN (HITBC) Yunnan, China

表2

樟属17个样本ITS序列特征信息"

图1

ITS克隆序列相对于月桂的遗传距离 P和ψ表示ITS假基因序列。"

图2

基于Bayesian算法对ITS克隆测序样本构建的50%一致性系统进化树 大于50%的靴带支持率/大于50%的后验率标注在进化支上(bootstrap support/posterior possibility)。C: Cinnamomum; ψ: ITS假基因序列"

1 龚洵, 潘跃芝, 杨志云 (2001). 木兰科植物的杂交亲和性. 云南植物研究 23, 339-344.
2 卢孟孟, 慈秀芹, 杨国平, 李捷 (2013). 亚热带森林乔木树种 DNA条形码研究——以哀牢山自然保护区为例. 植物分类与资源学报 35, 733-741.
3 马长乐, 周浙昆 (2006). ITS假基因对栎属系统学研究的影响及其对分子系统学研究的启示. 云南植物研究 28, 127-132.
4 徐颖, 徐晶, 高继银, 张文驹 (2011). 山茶属植物ITS的多态性——一个广泛逃离一致性进化的实例. 植物学报 46, 162-169.
5 尤欢, 周阿涛, 岳亮亮, 寸东义, 丁元明 (2014). 山茶属植物ITS的扩增及其序列特征分析. 植物研究 34, 403-408.
6 周阿涛, 岳亮亮, 李旻, 刘迪秋, 丁元明 (2013). 云南山茶(Camellia reticulata) nrDNA ITS序列多态性分析. 植物科学学报 31, 1-10.
7 Álvarez I, Wendel JF (2003). Ribosomal ITS sequences and plant phylogenetic inference.Mol Phylogenet Evol 29, 417-434.
8 Bailey CD, Carr TG, Harris SA, Hughes CE (2003). Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes.Mol Phylogenet Evol 29, 435-455.
9 Buckler ES, Holtsford TP (1996). Zea systematics: ribosomal ITS evidence.Mol Biol Evol 13, 612-622.
10 Buckler ES, Ippolito A, Holtsford TP (1996). The evolution of ribosomal DNA: divergent paralogous and phylogenetic implications.Genetics 145, 821-832.
11 CBOL Plant Wording Group (2009). A DNA barcode for land plants.Proc Natl Acad Sci USA 106, 12794-12797.
12 Chanderbali AS, van der Werff H, Renner SS (2001). Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes.Ann Missouri Bot Gard 88, 104-134.
13 Chen ZY, Xiong ZJ, Pan XY, Shen SQ, Geng YP, Xu CY, Chen JK, Zhang WJ (2015). Variation of genome size and the ribosomal DNA ITS region of Alternanthera philoxeroides (Amaranthaceae) in Argentina, the USA, and China.J Syst Evol 53, 82-87.
14 Copenhaver GP, Pikaard CS (1996). Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogeniza- tion during concerted evolution.Plant J 9, 273-282.
15 Eickbush TH, Eickbush DG (2007). Finely orchestrated movements: evolution of the ribosomal RNA genes.Genetics 175, 477-485.
16 Felsenstein J (1981). Evolutionary trees from DNA sequ- ences: a maximum likelihood approach.J Mol Evol 17, 368-376.
17 Fu YX (1996). New statistical tests of neutrality for DNA samples from a population.Genetics 143, 557-570.
18 Fu YX (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection.Genetics 147, 915-925.
19 Gonzalez IL, Sylvester JE (2001). Human rDNA: evolu- tionary patterns within the genes and tandem arrays derived from multiple chromosomes.Genomics 73, 255-263.
20 Gu ZJ, Xiao H (2003). Physical mapping of the 18S-26S rDNA by fluorescent in situ hybridization (FISH) in Camellia reticulata polyploidy complex (Theaceae).Plant Sci 164, 279-285.
21 Hall TA (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser (Oxf) 41, 95-98.
22 Hillis DM, Moritz C, Porter CA, Baker RJ (1991). Evidence for biased gene conversion in concerted evolution of ribosomal DNA.Science 251, 308-310.
23 Ho KY, Hung TY (2011). Cladistic relationships within the genus Cinnamomum (Lauraceae) in Taiwan based on analysis of leaf morphology and inter-simple sequence repeat (ISSR) and internal transcribed spacer (ITS) molecular markers.Afr J Biotechnol 10, 4802-4815.
24 Huang JF, Li L, van der Werff H, Li HW, Rohwer JG, Crayn DM, Meng HH, van der Merwe M, Conran JG, Li J (2016). Origins and evolution of cinnamon and camphor: a phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae).Mol Phylogenet Evol 96, 33-44.
25 Huelsenbeck JP, Ronquist F (2001). MRBAYES: Bayesian inference of phylogenetic trees.Bioinformatics 17, 754-755.
26 Kovari A, Matyasek R, Lim KY, Skalická K, Koukalova B, Knapp S, Chase M, Leitch AR (2004). Concerted evolu- tion of 18-5.8-26S rDNA repeats in Nicotiana allotetra- ploids.Biol J Linn Soc 82, 615-625.
27 Li DZ, Gao LM, Li HT, Wang H, Ge XJ, Liu JQ, Chen ZD, Zhou SL, Chen SL, Yang JB, Fu CX, Zeng CX, Yan HF, Zhu YJ, Sun YS, Chen SY, Zhao L, Wang K, Yang T, Duan GW (2011a). Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants.Proc Natl Acad Sci USA 108, 19641-19646.
28 Li L, Li J, Rohwer JG, van der Werff H, Wang ZH, Li HW (2011b). Molecular phylogenetic analysis of the Persea group (Lauraceae) and its biogeographic implications on the evolution of tropical and subtropical amphi-Pacific disjunctions.Am J Bot 98, 1520-1536.
29 Mayol M, Rossello JA (2001). Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus.Mol Phylogenet Evol 19, 167-176.
30 Muir G, Fleming CC, Schlotterer C (2001). Tree divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L.Mol Biol Evol 18, 112-119.
31 Okada H, Tanaka R (1975). Karyological studies in some species of Lauraceae.Taxon 24, 271-280.
32 Parkin EJ, Butlin RK (2004). Within- and between-indi- vidual sequence variation among ITS1 copies in the meadow grasshopper Chorthippus parallelus indicates frequent intrachromosomal gene conversion.Mol Biol Evol 21, 1595-1601.
33 Posada D, Buckley TR (2004). Model selection and model averaging in phylogenetics: advantages of Akaike infor- mation criterion and Bayesian approaches over likelihood ratio tests.Syst Biol 53, 793-808.
34 Posada D, Crandall KA (1998). Modeltest: testing the model of DNA substitution.Bioinformatics 14, 817-818.
35 Qiu YL, Chase MW, Parks CR (1995). A chloroplast DNA phylogenetic study of the eastern Asia-eastern North America disjunct section Rytidospermum of Magnolia (Magnoliaceae).Am J Bot 82, 1582-1588.
36 Rohwer JG (2000). Toward a phylogenetic classification of the Lauraceae: evidence from matK sequences.Syst Bot 25, 60-71.
37 Rohwer JG, Rudolph B (2005). Jumping genera: the phylogenetic positions of Cassytha, Hypodaphnis, and Neocinnamomum (Lauraceae) based on different analyses of trnK intron sequences.Ann Missouri Bot Gard 92, 153-178.
38 Ronquist F, Huelsenbeck JP (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models.Bioinfor- matics 19, 1572-1574.
39 Rozas J, Rozas R (1999). DnaSP version 3, an integrated program for molecular population genetics and molecular evolution analysis.Bioinformatics 15, 174-175.
40 Swofford DL (2003). PAUP*: Phylogenetic Analysis Using Parsimony (and other methods), Version 4.0b10. Sunderland (Massachusetts), Sinauer.
41 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013). MEGA6: molecular evolutionary genetics analysis version 6.0.Mol Biol Evol 30, 2725-2729.
42 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.Nucleic Acids Res 25, 4876-4882.
43 Tripathi AM, Tyagi A, Kumar A, Singh A, Singh S, Chaudhary LB, Roy S (2013). The internal transcribed spacer (ITS) region and trnH-psbA are suitable candidate loci for DNA barcoding of tropical tree species of India.PLoS One 8, e57934.
44 Vanin EF (1985). Processed pseudogenes: characteris- tics and evolution.Ann Rev Genet 19, 253-272.
45 Wei XX, Wang XQ (2004). Recolonization and radiation in Larix (Pinaceae): evidence from nuclear ribosomal DNA paralogues.Mol Ecol 13, 3115-3123.
46 White TJ, Bruns TD, Lee SB, Taylor JW (1990). Amplifica- tion and Direct Sequencing of Ribosomal RNA Genes and the Internal Transcribed Spacer in Fungi. PCR Protocols and Applications—a Laboratory Manual. Orlando: Academic Press. pp. 315-322.
47 Xiao LQ, Möller M, Zhu H (2010). High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: incomplete concerted evolution and the origin of pseudogenes.Mol Phylogenet Evol 55, 168-177.
48 Zheng X, Cai D, Yao L, Teng Y (2008). Non-concerted ITS evolution, early origin and phylogenetic utility of ITS pseudogenes in Pyrus. Mol Phylogenet Evol 48, 892-903.
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