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The chloroplasts genomic analyses of Caragana arborescens and Caragana opulens
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  • LiE Liu,
  • wu zhou,
  • HongYan Li,
  • JiaXin Li,
  • XinJuan Li,
  • na hu,
  • Honglun Wang
LiE Liu
Qinghai University
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wu zhou
Qinghai University

Corresponding Author:[email protected]

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HongYan Li
Qinghai University State Key Laboratory of Plateau Ecology and Agriculture
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JiaXin Li
Qinghai University
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XinJuan Li
Qinghai University
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na hu
Northwest Institute of Plateau Biology Chinese Academy of Sciences
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Honglun Wang
Northwest Institute of Plateau Biology Chinese Academy of Sciences
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Abstract

Numerous species within the genus Caragana have high ecological and medicinal value. In this genus, however, species identification based on morphological characteristics is quite complicated; this issue can be resolved by analyzing the complete plastid genomes. We obtained the chloroplast genomes of two species using lllumina sequencing technology: Caragana arborescens and Caragana opulens, with lengths of 129,473 bp and 132,815 bp, respectively. The absence of inverted repeat sequences in the two species allowed them to be ascribed to the inverted repeat-lacking clade (IRLC). They comprise a total of 111 distinct genes (4 rRNA, 31 tRNA, and 76 protein-coding genes). In addition, 16 genes containing introns were identified in two genomes, the majority of which contained a single intron. C. arborescens and C. opulens were found to contain 129 and 229 repeats, as well as 277 and 265 simple repeats, respectively. The codon usage bias analysis revealed that the two Caragana species exhibit similar codon usage patterns. rpoC2-rps2, accD-cemA, rps18-clpP, rpoA-rpl36, and rpl2-rpl23 were identified as the five regions most likely to be mutated based on analysis of nucleotide diversity (Pi). Analysis of sequence divergence revealed that certain intergenic regions (matK-rbcL, psbM-petN, atpA-psbI, petA-psbL, psbE-petL, and rps7-rps12) are highly variable. Phylogenetic analysis showed that C. arborescens and C. opulens were related and clustered together as the other four Caragana species. And the genus Astragalus and Caragana were relatively closely related. These results provide a foundation for future phylogenetic research and the development of molecular markers for Caragana plants.