Chin Bull Bot ›› 2016, Vol. 51 ›› Issue (5): 609-619.doi: 10.11983/CBB15141

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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:2016-09-27 Published:2016-09-01
  • Contact: Li Jie E-mail:jieli@xtbg.ac.cn
  • About author:

    # Co-first authors

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.

Table 1

Details of materials"

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

Table 2

Characteristic information of ITS regions of 17 Cinnamomum samples"

Figure 1

Distribution of p-distance from ITS clone sequences to Laurus nobilis P and ψ indicate ITS pseudogene sequences."

Figure 2

Fifty percent majority rule consensus tree from Bayesian analysis of ITS clone sequence dataset Bootstrap support values (≥ 50%)/Bayesian posterior possibilities (≥ 50%) are shown above the branches. C: Cinnamomum; ψ: ITS pseudogene sequences"

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