Cloning and Characterisation of Reverse Transcriptase Sequences of Ty1-copia Retrotransposon in Saccharum robustum
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1.National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University;2.Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute

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the National Natural Science Foundation of China (31401440, 31571730,31771863), Technology Major Project of the Fujian Province of China (2015NZ0002-2),An Open Project of the Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources (SKLCUSA-b201606)

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    Abstract:

    In order to investigate the characteristics of S. robustum Ty1-copia retrotransposon reverse transcriptase (RT), the Ty1-copia RT sequences were isolated by PCR amplification with universal primers. Sixty Ty1-copia RT sequences were successfully isolated with a length of 233 to 266 bp. Through ClustalX software analysis, several conserved domains in the amino acid sequences were revealed, such as TAFLHG, YVDDM and SLYGLKQ, which were found at the upstream, downstream and central parts, respectively. Several frameshift mutation in the code reading box and at the termination codon mutation were found. The phylogenetic tree analysis of Ty1-copia RT sequences of S. robustum and other Gramineae species suggested eight different evolutionary lineages. 20 % of S. robustum Ty1-copia RT amino acid sequences were classified as class I (Sre / Maximus), 16.7 % were classified as Class II (Retrofit / Ale), 30 % were classified as Class III (Ale), 28.3 % were classified as Class VIII (Tork / TAR), and 5 % of the sequences were classified as Class V (Tork) / Angela). This analysis indicated that S. robustum was closely related to the Saccharum spp. hybrid and Sorghum. Based on the result of dot blot hybridization, the copy number of the S. robustum Ty1-copia RT sequence was calculated to be 6.75×103 in one genome. The FISH results showed that the S. robustum Ty1-copia RT sequences were distributed on the chromosome, which the signal of telomere region was stronger than other regions in some chromosomes. These results would provide a reference for the biodiversity study and genome research of S. robustum in the future.

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History
  • Received:May 06,2019
  • Revised:July 31,2019
  • Adopted:August 16,2019
  • Online: March 17,2020
  • Published:
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