Codon Usage Bias Analysis of Chloroplast Genomes of Eight Huperziaceae Species
[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 GC1＞GC2＞GC3,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.GC3 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.
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