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.为探究瓣蕊唐松草（Thalictrum baicalense Turcz. ex Ledeb.）的叶绿体微卫星与密码子偏好性，本研究借助MISA v1.0与Primer3软件对其叶绿体基因组开展微卫星分析并完成引物设计，同时采用CodonW 1.4.2及CUSP在线软件解析密码子偏好性及其成因。研究结果显示，在瓣蕊唐松草叶绿体基因组中共鉴定得到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%）；共涵盖4种重复类型，单核苷酸重复数量最多（占比57.32%），四核苷酸重复数量最少（占比3.77%）。SSR序列长度分布于8~31 bp区间内，其中9个SSR序列长度超过20 bp（占比3.95%），具备多态性潜力。对瓣蕊唐松草叶绿体基因组密码子第三位碱基的GC含量（GC3，平均为29.93%）与相对同义密码子使用度（Relative Synonymous Codon Usage, RSCU）进行关联分析，二者均表明该基因组偏好使用以A、U结尾的密码子。有效密码子数（Effective Number of Codon, ENC）的分布范围为35.66~55.55，平均值为46.85，显示其密码子偏好性较弱。本研究共筛选出15个同时满足RSCU>1（共34个）且ΔRSCU≥0.08（共22个）条件的密码子，具体为GCA、GCU、AGA、CGU、UGU、GGU、AUU、UUA、UUG、UUC、CCU、AGU、ACC、ACU、GUA，上述密码子即为瓣蕊唐松草叶绿体基因组的最优密码子。此外，中性绘图分析、ENC-绘图分析以及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偏好性受到选择压力、突变压力等多种因素的共同影响。