Abstract:
Objective To analyze the structural characteristics of Anabasis aphylla chloroplast genome, clarify the taxonomic status of Anabasis in Chenopodiaceae for further exploring its codon preference and determining the optimal codon. Method Total genomic DNA was extracted from fresh assimilation twigs of A. aphylla based on CTAB method. Sequencing was performed using the Illumina HiSeq 2000 high-throughput sequencing platform. The chloroplast genome sequence was assembled and annotated by GetOrganelle and Plann. Simple sequence repeat (SSR) in chloroplast genome was analyzed by MISA. Multiple sequence alignment and ML phylogenetic tree construction were analyzed using MAFFT v.7.450 and IQ-TREE v.2.1.1 software. The nucleotide polymorphism values were calculated using DnaSP 6.0 software. The codon preference was studied by CUSP and Codon W 1.4.2. software. Result The full-length chloroplast genome of A. aphylla was 154 084 bp, including a large single copy region (LSC, 85 124 bp), a small single copy region (SSC, 18 934 bp), and a pair of inverted repeat regions (IRa and IRb, 25 013 bp). A total of 132 genes were annotated, including 83 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 4 pseudogenes. The number of SSRs located in the intergenic region was the largest (70.4%), and the number of single-base (A/T) repeat type SSRs was the largest. The optimal model of phylogenetic tree was TVM + F + R3, and Chenopodiaceae was divided into four clustering groups. Among them, A. aphylla showed the closest relationship with Haloxylon and Salsola. TrnS-trnG(exon1)、ndhF-rpl32、rpl32-trnL、rps16(exon1)-trnQ and ycf1 were high nucleotide polymorphism regions. A total of 20 optimal codons (UUU, UAU, UGU, CAU, UCU, UCA, UUA, CUU, CCU, AGA, GAA, ACU, ACA, AAU, GAU, AAA, GUU, GCU, GGU, CAA) were determined, all ending with A/U. The codon usage preference was mainly affected by natural selection, and the influence of mutation and other influencing factors was weak. Conclusion The chloroplast genome structure of A. aphylla is conservative, showing typical quadripartite structure. In the phylogeny of Chenopodiaceae, A. aphylla has the closest relationship with Haloxylon and Salsola. The identified hypervariable regions and SSR loci can be used for molecular identification of intergeneric species in Chenopodiaceae. The codon of the chloroplast genome of A.aphylla prefer endings with A/U, and the 20 optimal codons determined are useful for the optimization of its exogenous codons. The results can provide a reference for molecular marker development, phylogeny and chloroplast gene engineering of A. aphylla.