科研之友
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摘要
【Objective】Lindera setchuenensis has important medicinal value. Researches of chloroplast genome possess essential theoretical and practical significance for species identification, analysis of genetic diversity and resource protection of the genus Lindera.【Method】The complete chloroplast genome of L. setchuenensis was sequenced based on Illumina HiSeq 2000 platform, and was assembled through de novo. The genome structure, gene composition, repeats and phylogeny were analyzed.【Result】The chloroplast genome of L. setchuenensis exhibited a typical quadripartite structure. A total of 125 functional genes were detected, including 81 protein coding genes, 36 tRNA genes, and eight rRNA genes. Frequency of guanine and cytosine bases(GC3s) of the genome encoding genes was 27.96%, 20 codons were ended with A/U(T) among 21 optimal codons. Among the 27 pairs of long repeats, forward repeats and palindromic repeats accounted for 44% and 41% respectively, and the length of 30 bp and 33 bp accounted for 44% and 30% respectively. Among the 181 SSRs, 68% were A/T repeats and 55% were located in the intergenic regions. Comparing the chloroplast genomes of the genus Lindera, it was indicated that six hyper-variable loci, petA-psbJ, trnH-psbA, petK-psbI, ccsA-ndhD, rpl32-trnL, and ycf1, could potentially be used as DNA barcodes candidates for species identification. Phylogenetic analysis revealed that the genus Lindera was divided into five clades. L. setchuenensis presented the closest relationship with L. megaphylla.【Conclusion】The structure of chloroplast genome of L. setchuenensis is conservative and prefers codons ending with A or U(T). The hyper-variable regions and SSR loci can be used as DNA barcoding for species identification. The results provide a basis for the development of molecular markers, phylogeny and breeding of elite varieties of Lindera plants.
