cpSSR.ssr.primer.xls

To investigate the chloroplast microsatellite and codon preference in <em>Thalictrum baicalense</em> Turcz. ex Ledeb., this study used MISA v1.0 and Primer3 software to analyze the chloroplast genome microsatellite and complete primer design, and CodonW 1.4.2 and CUSP online software were used to analyze the codon preference and causes. The results showed that 228 SSR loci were identified in the chloroplast genome of <em>Thalictrum baicalense</em> Turcz. ex Ledeb.. Most of these loci were found in large single copy regions (63.20%); four types were present, with the highest number of mononucleotide repeat (57.32%) and the lowest number of tetraucleotide repeat (3.77%). The SSR lengths were distributed between 8-31 bp, and nine SSR were longer than 20 bp (3.95%), showing polymorphic potential. The average content (29.93%) of the third base (GC3) of the chloroplast genome of <em>Thalictrum baicalense</em> Turcz. ex Ledeb. was analyzed in relation to the relative usage of synonymous codons, both of which indicated a codon preference for A and U endings. The effective number of codon ranged from 35.66-55.55 with a mean value of 46.85 and weak codon bias. The 15 (GCA, GCU, AGA, CGU, UGU, GGU, AUU, UUA, UUG, UUC, CCU, AGU, ACC, ACU, GUA) codons that simultaneously met the conditions of RSCU&gt;1 (34) and ΔRSCU ≥ 0.08 (22) were identified as the optimal codons for the <em>Thalictrum baicalense</em> Turcz. ex Ledeb. chloroplast genome. In addition, neutrality plot, ENC-plot and PR2-plot analyses, all indicate that the preference of chloroplast genomic codons in <em>Thalictrum baicalense</em> Turcz. ex Ledeb. is influenced by various factors such as selection pressure and mutational pressure.