Plant Diversity ›› 2013, Vol. 35 ›› Issue (2): 158-164.DOI: 10.7677/ynzwyj201312070

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Comparative Analyses of Indels Based on the Whole Chloroplast Genome of Cuscuta reflexa between European and Asian Populations

 WANG  Chao-Bo-1、2, GONG  Xun-1   

  1. 1 Key Laboratory of Economic Plant and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences,
    Kunming 650201, China; 2 University of Chinese Academy of Sciences, Beijing 100049, China
  • Received:2012-05-07 Online:2013-03-25 Published:2012-06-15
  • Supported by:

    The Joint Funds of the National Natural Science Foundation of China and Yunnan Provincial Government (U1136602)


We determined the complete nucleotide sequence of the chloroplast genome of Asian Cuscuta reflexa which is a world distributed dodder using shotgun method at Illumina’s Genome Analyzer, and then compared it with the corresponding published sequence of the same species that distributed in Europe. The chloroplast genome length was 120972bp, which was 549bp shorter than the European one, with a large single copy (LSC) region of 79499bp, a small single copy (SSC) region of 8369bp and two inverted repeats (IR) of 16552bp each. The overall GC content was 38.3%, which is slightly higher than European C.reflexa. The chloroplast genome of C.reflexa from both area encoded identical functional genes in the same order. On the other hand, detailed analyses revealed 251 insertions and 210 deletions. The length of indels substitution sum to 7649bp and the largest insertion and deletion reached 426bp and 435bp respectively. Meanwhile, 3720bp base substitution events were found in the entire chloroplast genome of Asian C.reflaxa. Majority of the indels observed were singlebase but four large length mutations longer than 200bp were also detected, including two deletions in ycf2 region, one insertion in trnFpsbE and another insertion in matKtrnQ. Most indels located in the intergenic regions of the LSC region while rare in the IR region. This research initially compared the whole chloroplast genome of same heterotrophic plants distributed in different continents.

Key words: Cuscuta reflexa, Chloroplast genome, Indels, Comparative analysis

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