Subjects: Biology >> Botany >> Applied botany submitted time 2021-12-19 Cooperative journals: 《广西植物》
Abstract： The purpose of this study was to clone the RT genes of Ty1-copia-like retrotransposons, and to provide sequences basis for isolating the full-length sequences of Ty1-copia-like retrotransposons and studying their function in genus Arachis. Degenerate primers were designed according to the conserved region of RT genes, the genomic DNA of wild peanut species “Arachis duranensis” with AA genome was amplified by PCR using the degenerated primers. The amplified targeted bands were recovered, cloned and sequenced, and then sequences were analyzed through bioinformatics strategy. The results were as follows: (1) The amplified targeted bands were all about 260 bp in size. Forty-one and twenty-seven RT genes sequences were cloned from the two wild peanut species respectively. The length of sixty-eight sequences varied from 256 bp to 270 bp. The proportion of AT, AT/GC and the similarity between nucleotide sequences ranged from 55.86% to 68.42%, 1.27% to 2.17%, and 49.8% to 99.2% respectively, showing a higher heterogeneity. (2) The sixty-eight sequences were divided into six families, family I and family IV were the main components. (3) Nineteen of sixty-eight sequences had nonsense mutations, and Arachis duranensis (PI219823) had a higher nonsense mutations rate than Arachis duranensis (PI262133). (4) The similarity between amino acid sequences ranged from 4.7% to 100%, showing high heterogeneity. (5) The tertiary structures of proteins representing sequences in each family were basically similar in overall configuration, but there were great differences in the number of helix structures, folding structures, turns and hydrogen bonds. (6) The conserved motifs among sequences were generally consistent, but there were also some variations, showing a certain degree of heterogeneity. The phylogenetic tree divided sixty-eight sequences into ten classes. Most of sequences are clustered in A and B classes. (7) Some of RT genes sequences from two wild peanut species with AA genome were closely related to RT genes sequences from other plant species, which indicated that there might be transposon horizontal transmission between them. This study laid a foundation for the development and application of new molecular markers based on Ty1-copia-like retrotransposons in genus Arachis.
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