石杉科8种植物叶绿体基因组密码子偏好性分析

Codon Usage Bias Analysis of Chloroplast Genomes of Eight Huperziaceae Species

【目的】探明石杉科植物叶绿体基因组密码子的使用模式及偏好性,为石杉科植物物种鉴定、系统发育及叶绿体遗传改良奠定基础。【方法】利用CUSP、Codon W 1.4.2及EMBOSS等程序对石杉科长柄石杉、亮叶石杉、蛇足石杉、皱边石杉、长白石杉、龙骨马尾杉、马尾杉和粗糙马尾杉8种植物的叶绿体基因密码子进行中性绘图、ENC-plot及PR2-plot绘图分析。【结果】密码子GC含量在属内变异范围小,石杉属总体高于马尾杉属;密码子3个位置的GC含量呈GC_(1)>GC_(2)>GC_(3),第3位碱基以A/T为主;8个物种的叶绿体基因组密码子总体偏性较弱,马尾杉属密码子偏性强于石杉属,有9个基因的ENC在全部或部分物种中低于40,petD的ENC在龙骨马尾杉和粗糙马尾杉中低于35;GC_(3)对ENC影响较大;密码子偏好主要受自然选择和突变影响,突变因素对马尾杉属的影响大于石杉属;石杉科8个物种分别确定12个、13个、12个、15个、9个、17个、17个和16个最优密码子,石杉属5个物种和马尾杉属3个物种分别确定7个和11个最优密码子,8个物种共同的最优密码子仅4个。【结论】石杉科植物叶绿体基因组密码子使用偏好性受多种因素影响,其中,突变因素对马尾杉属的影响大于石杉属,石杉属5个物种和马尾杉属3个物种分别确定7个和11个最优密码子。

【Objective】The usage patterns and preferences of chloroplast genome codons in Huperziaceae plants were explored,which laid the basis for the species identification,phylogenetic development and chloroplast genetic improvement of Huperziaceae plants.【Method】The neutrality plot,ENC-plot,and PR2-plot analysis of chloroplast genome codons in 8 Huperziaceae plants of Huperzia serrata f.longipetiolata,H.lucidula,H.serrata,H.crispata,H.asiatica,Phlegmariurus carinatus P.phlegmaria and P.squarrosus were conducted based on CUSP,Codon W 1.4.2 and EMBOSS software.【Result】The variation range of codon GC content within the genus was very small,and the overall variation range of Huperzia was higher than that of Phlegmariurus.The GC content at the three positions of the codon followed GC_(1)>GC_(2)>GC_(3),with the third base being mainly A/T.The overall codon bias of chloroplast genomes in 8 species was relatively weak,while the codon bias of Phlegmariurus was stronger than that of Huperzia.The ENC values of 9 genes were below 40 in all or some species,and the ENC values of petD were below 35 in P.carinatus and P.squarrosus.GC_(3)affected ENC greatly.Codon bias was mainly influenced by natural selection and mutation,with mutation factors having a greater impact on Phlegmariurus than on Huperzia.8 species of Huperziaceae identified respectively 12,13,12,15,9,17,17 and 16 optimal codons,while 5 species of Huperzia and 3 species of Phlegmariurus identified 7 and 11 optimal codons,respectively.The 8 species shared only 4 optimal codons.【Conclusion】The codon usage bias in the chloroplast genome of Huperziaceae plants is influenced by various factors,among which mutation factors have a greater impact on Phlegmariurus than on Huperzia.7 and 11 optimal codons are determined for 5 Huperzia species and 3 Phlegmariurus species,respectively.