cpSSR.ssr.primer.xls

To investigate the chloroplast microsatellite and codon preference in Thalictrum baicalense 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 Thalictrum baicalense 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 Thalictrum baicalense 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>1 (34) and ΔRSCU ≥ 0.08 (22) were identified as the optimal codons for the Thalictrum baicalense 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 Thalictrum baicalense Turcz. ex Ledeb. is influenced by various factors such as selection pressure and mutational pressure.

为探讨瓣蕊唐松草（Thalictrum baicalense Turcz. ex Ledeb.）的叶绿体微卫星特征与密码子使用偏好性，本研究采用MISA v1.0与Primer3软件，对其叶绿体基因组微卫星进行分析并完成引物设计；同时采用CodonW 1.4.2与CUSP在线软件，分析其密码子使用偏好性及其成因。结果显示，本研究在瓣蕊唐松草的叶绿体基因组中共鉴定出228个简单序列重复（Simple Sequence Repeat, SSR）位点。其中多数位点分布于大单拷贝区（占比63.20%），共包含4种重复类型，单核苷酸重复占比最高（57.32%），四核苷酸重复占比最低（3.77%）。SSR的长度分布于8~31 bp之间，其中9个SSR长度超过20 bp（占比3.95%），具备多态性潜力。通过分析瓣蕊唐松草叶绿体基因组的密码子相对使用度与第三位碱基GC含量（GC3，平均占比29.93%），结果显示其密码子偏好以A、U结尾。有效密码子数（ENC）分布范围为35.66~55.55，平均值为46.85，表明其密码子使用偏好性较弱。本研究共鉴定出15个最优密码子（GCA、GCU、AGA、CGU、UGU、GGU、AUU、UUA、UUG、UUC、CCU、AGU、ACC、ACU、GUA），这些密码子同时满足相对同义密码子使用度（Relative Synonymous Codon Usage, RSCU）>1（共34个）与ΔRSCU≥0.08（共22个）的筛选条件。此外，中性绘图分析、有效密码子数绘图分析与PR2-绘图分析结果均表明，瓣蕊唐松草叶绿体基因组的密码子使用偏好性受选择压与突变压等多种因素共同影响。