Abstract
Arabis paniculata Franch (Brassicaceae) has been widely used for the phytoremediation of heavy mental, owing to its hyper tolerance of extreme Pb, Zn, and Cd concentrations. However, studies on its genome or plastid genome are scarce. In the present study, we obtained the complete chloroplast (cp) genome of A. paniculata via de novo assembly through the integration of Illumina reads and PacBio subreads. The cp genome presents a typical quadripartite cycle with a length of 153,541 bp, and contains 111 unigenes, with 79 protein-coding genes, 28 tRNAs and 4 rRNAs. Codon usage analysis showed that the codons for leucine were the most frequent codons and preferentially ended with A/U. Synonymous (Ks) and non-synonymous (Ka) substitution rate analysis indicated that the unigenes, ndhF and rpoC2, related to “NADH-dehydrogenase” and “RNA polymerase” respectively, underwent the lowest purifying selection pressure. Phylogenetic analysis demonstrated that Arabis flagellosa and A. hirsuta are more similar to each other than to A. paniculata, and Arabis is the closest relative of Draba among all Brassicaceae genera. These findings provide valuable information for the optimal exploitation of this model species as a heavy-metal hyperaccumulator.
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Abbreviations
- Cp:
-
Chloroplast
- IR:
-
Inverted repeat
- LSC:
-
Large single copy
- SSC:
-
Small single copy
- rRNA:
-
Ribosomal RNA
- tRNA:
-
Transfer RNA
- NJ:
-
Neighbor-joining
- SSR:
-
Simple sequence repeat
- RSCU:
-
The relative synonymous codon usage
- ML:
-
Maximum likelihood
- BI:
-
Bayesian inference
- Ka:
-
Non-synonymous
- Ks:
-
Synonymous
- Pb:
-
Lead
- Zn:
-
Zinc
- Cd:
-
Cadmium
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This work was supported by the by the Guizhou Provincial Science and Technology Foundation under Grant ([2020]1Y102).
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B.Z.: Writing—original draft; X.L. and C.G.: Data curation and Formal analysis; C.D.: Resources; S.Z. and Q.X.: Software; Q.W.: Validation; X.H. and X.D.: Writing—review & editing; B.Z.: Project administration and Funding acquisition. All authors read and approved the final manuscript.
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12298_2022_1151_MOESM1_ESM.tif
Figure S1. The ka/ks ratios of 71 protein-coding genes of the A. paniculata cp genome versus five closed related species. The X and Y axis represents the ka/ks ratios and 71 protein-coding genes, respectively. The different color boxes represent different comparisons at the top right corner
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Wang, H., Gan, C., Luo, X. et al. Complete chloroplast genome features of the model heavy metal hyperaccumulator Arabis paniculata Franch and its phylogenetic relationships with other Brassicaceae species. Physiol Mol Biol Plants 28, 775–789 (2022). https://doi.org/10.1007/s12298-022-01151-1
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DOI: https://doi.org/10.1007/s12298-022-01151-1