Abstract
Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we have reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandifloras, and S. validus) and carried out a comprehensive comparative analysis. All four Selenicereus plastomes have a typical quartile structure. The plastome size ranged from 133,146 to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the inverted repeat regions had undergone a dramatic expansion and formed a previously unreported small single copy/inverted repeat border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Our study enriches the plastome in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships.
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Data availability
The raw sequencing data generated in this study and the four plastome sequences were deposited in NCBI (https://www.ncbi.nlm.nih.gov/)with accession number: SAMN18357737, SAMN18357760, SAMN18357760, SAMN18357760, MW553055, MW553068, MW553069 and MW553070. All the samples are deposited at the Herbarium of Southwest University, Chongqing, China. All other data and material generated in this manuscript are available from the corresponding author upon reasonable request.
Abbreviations
- SSR:
-
Simple sequence repeat
- IRs:
-
Inverted repeats
- LSC:
-
Large single-copy
- SSC:
-
Small single-copy
- ML:
-
Maximum-likelihood
- BI:
-
Bayesian inference
- DnaSP:
-
DNA Sequence Polymorphism
- CTAB:
-
Cetyl trimethylammonium bromide
- NCBI:
-
National Center for Biotechnology Information
- Pi:
-
Nucleotide diversity/polymorphism
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Acknowledgements
The authors are grateful to the technical support provided by Novogene. This work was supported by the National Natural Science Foundation of China [31772260] and Chongqing Study Abroad Innovation Project [cx2019052]. The funders were not involved in the study design, data collection, and analysis, decision to publish, or manuscript preparation.
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JY conceived the study and designed experiments; FH collected the samples and extracted DNA for sequencing by using the Illumina platform; YCX assembled and annotated the plastid genomes; SYZ and JLL carried out the comparative chloroplast analysis; QLQ drafted the manuscript. All authors have read and approved the final manuscript.
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The four collected Selenicereus species are widely cultivated in China as ornamental or edible fruits. Experimental researches do not include the genetic transformation, preserving the genetic background of the species used, and any other processes requiring ethics approval.
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Table S1. Summary of the assembly information of the 4 Selenicereus species. Table S2. List of plastomes used for phylogenetic analysis. Table S3. Statistics on simple sequence repeats (SSRs) in the 4 plastomes. Table S4. Repeats (>= 30bp) identified in the four Selenicereus species. Table S5. Percentages of variable sites in 67 orthologous genes among the 4 Selenicereus species. Table S6. Summary of sequencing data quality. (PDF 390 kb)
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Qin, Q., Li, J., Zeng, S. et al. The complete plastomes of red fleshed pitaya (Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, inverted repeat expansions and phylogenomic implications. Physiol Mol Biol Plants 28, 123–137 (2022). https://doi.org/10.1007/s12298-021-01121-z
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DOI: https://doi.org/10.1007/s12298-021-01121-z