Estimation of the Genome Size and Complete Chloroplast Genome in Adenophora remotiflora: Genome Structures, Comparative Genomics, and Phylogenetic Diversity
Source abstract
Abstract
Adenophora remotiflora is a wild perennial plant used as oriental medicine and ornamental flowers in East Asia. The haploid genome size of A. remotiflora was estimated at 3.9 Gb with a 2.42% heterozygosity ratio. The chloroplast genome of 174,455 base pairs (bp) shows a circular map structure, and has four conserved regions consisting of a large single-copy region of 108,423 bp, a small single-copy region of 10,444 bp, and a pair of inverted repeats (each 27,794 bp). A total of 108 unique genes were annotated, comprising 74 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. A total of 155 repeat sequences were identified, and comparative genome structures were characterized among the Adenophora species. Phylogenetic diversity showed that A. remotiflora is in a close position within the Adenophora genus, and Adenophora erecta is in the closest evolutionary position.
Source: crossref · Quality: baseline
Research context
OpenAlex topics: Genomics and Phylogenetic Studies · Plant Pathogens and Fungal Diseases · Plant and Fungal Species Descriptions
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
Affiliations
Department of Mechanical Design Engineering, Wonkwang University, 460 Iksandae-ro, Iksan 54538, Republic of Korea
Genomics Division, National Institute of Agricultural Sciences, 166 Nongsaengmyeong-ro, Jeonju 54874, Republic of Korea
Department of Information Communication Engineering, Wonkwang University, 460 Iksandae-ro, Iksan 54538, Republic of Korea
Funding
Wonkwang University
References (35)
Show source-provided references
1. Ethanol extract of Remotiflori radix induces endoplasmic reticulum stress-mediated cell death through AMPK/mTOR signaling in human prostate cancer cells10.1038/srep08394 ↗
2. Taxonomic and biogeographic implications of a phylogenetic analysis of the Campanulaceae based on three chloroplast genes10.1002/tax.583003 ↗
3. Past, present, and future of Campanula (Campanulaceae) systematics—A review
4. Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae10.1016/j.ympev.2019.02.024 ↗
5. Flavonoids as antioxidants and developmental regulators: Relative significance in plants and humans10.3390/ijms14023540 ↗
6. Species delimitation and interspecific relationships of the genus Orychophragmus (Brassicaceae) inferred from whole chloroplast genomes10.3389/fpls.2016.01826 ↗
7. Molecular evolution of chloroplast genomes in Monsteroideae (Araceae)10.1007/s00425-020-03365-7 ↗
8. Mutation rates in plastid genomes: They are lower than you might think10.1093/gbe/evv069 ↗
9. Cheon, K.S., Kim, K.A., and Yoo, K.O. (2017). The complete chloroplast genome sequences of three Adenophora species and comparative analysis with campanuloid species (Campanulaceae). PLoS ONE, 12.10.1371/journal.pone.0183652 ↗
10. The evolution of the plastid chromosome in land plants: Gene content, gene order, gene function10.1007/s11103-011-9762-4 ↗
11. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers10.1093/bioinformatics/btr011 ↗
12. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes10.1038/s41467-020-14998-3 ↗
13. GeSeq–versatile and accurate annotation of organelle genomes10.1093/nar/gkx391 ↗
14. Artemis: Sequence visualization and annotation10.1093/bioinformatics/16.10.944 ↗
15. CPGView: A package for visualizing detailed chloroplast genome structures10.1111/1755-0998.13729 ↗
16. MISA-web: A web server for microsatellite prediction10.1093/bioinformatics/btx198 ↗
17. The Vmatch large scale sequence analysis software
18. Tandem repeats finder: A program to analyze DNA sequences10.1093/nar/27.2.573 ↗
19. Mauve: Multiple alignment of conserved genomic sequence with rearrangements10.1101/gr.2289704 ↗
20. VISTA: Computational tools for comparative genomics10.1093/nar/gkh458 ↗
21. IRscope: An online program to visualize the junction sites of chloroplast genomes10.1093/bioinformatics/bty220 ↗
22. Mafft multiple sequence alignment software version 7: Improvements in performance and usability10.1093/molbev/mst010 ↗
23. MEGA11: Molecular evolutionary genetics analysis version 1110.1093/molbev/msab120 ↗
24. Methods for obtaining and analyzing whole chloroplast genome sequences10.1016/S0076-6879(05)95020-9 ↗
25. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates10.1093/molbev/mst257 ↗
26. Taheri, S., Lee Abdullah, T., Yusop, M.R., Hanafi, M.M., Sahebi, M., Azizi, P., and Shamshiri, R.R. (2018). Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules, 23.10.3390/molecules23020399 ↗
27. Imperfect and compound microsatellites in the genomes of Burkholderia pseudomallei strains10.1134/S0026893319010084 ↗
28. Nie, X., Lv, S., Zhang, Y., Du, X., Wang, L., Biradar, S.S., Tan, X., Wan, F., and Weining, S. (2012). Complete chloroplast genome sequence of a major invasive species, Crofton weed (Ageratina adenophora). PLoS ONE, 7.10.1371/journal.pone.0036869 ↗
29. Chloroplast microsatellites: New tools for studies in plant ecology and evolution10.1016/S0169-5347(00)02097-8 ↗
30. Wang, L., He, N., Li, Y., Fang, Y., and Zhang, F. (2020). Complete chloroplast genome sequence of Chinese lacquer tree (Toxicodendron vernicifluum, Anacardiaceae) and its phylogenetic significance. BioMed Res. Int., 1.10.1155/2020/9014873 ↗
31. Liu, Y., Ren, X.X., and Jeong, B.R. (2019). Supplementary Light source affects growth, metabolism, and physiology of Adenophora triphylla (thunb.) A. BioMed Res. Int., 2019.10.1155/2019/6283989 ↗
32. Kim, K.A., and Cheon, K.S. (2021). Complete chloroplast genome sequence of Adenophora racemosa (Campanulaceae): Comparative analysis with congeneric species. PLoS ONE, 16.10.1371/journal.pone.0248788 ↗
33. Daniell, H., Lin, C.S., Yu, M., and Chang, W.J. (2016). Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biol., 17.10.1186/s13059-016-1004-2 ↗
34. Lian, C., Yang, H., Lan, J., Zhang, X., Zhang, F., Yang, J., and Chen, S. (2022). Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens. PLoS ONE, 17.10.1371/journal.pone.0266546 ↗
35. The complete chloroplast genome sequence of Adenophora kayasanensis Kitam (Campanulaceae), an endemic to Korea10.1080/23802359.2021.2002212 ↗