A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensis
Article Sidebar
Issue
Vol. 30 No. 3 (2024)
Accepted
29 October 2024
Published
1 December 2024
Keywords:
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chloroplast, GetOrganelle, mitochondria, NOVOplasty, short-read
Abstract
Gyrinops versteegii and Aquilaria malaccensis are two important species of the Aquilarieae tribe. The main problem of this tribe is the challenge of species identification that is strongly dependent on the presence of flowers and fruit, which are not always available. The availability of whole genome information is expected to address the problems of species identification. This research aims to construct and compare the chloroplast and mitochondrial genomes of G. versteegii and A. malaccensis from short-read data using the NOVOplasty and GetOrganelle assembler. The chloroplast genome assembly revealed a full-length quadripartite circular structure with sizes of 174.814 bp (G. versteegii) and 174.821–174.822 bp (A. malaccensis), with highly conserved gene and organization. Meanwhile, the mitochondrial genome is multipartite with a size of 400.012 bp (G. versteegii) and 400.000 bp (A. malaccensis), with highly variable genes and organization due to the presence of gene cluster repeats. The LSC/IR/SCC region borders and phylogenetic analysis in chloroplasts indicate variations between the genomes of these two species. The investigation of nucleotide diversity in the chloroplast genome revealed that the trnL-rpl32 region had the highest nucleotide diversity (Pi = 0.03). This information will be useful in the future for a variety of downstream analyses.
References
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Wu, Z. Q., Liao, X. Z., Zhang, X. N., Tembrock, L. R., & Broz, A. (2022). Genomic architectural variation of plant mitochondria-A review of multichromosomal structuring. Journal of Systematics and Evolution, 60(1), 160168. https://doi.org/10.1111/jse.12655
Yu, X., Wei, P., Chen, Z., Li, X., Zhang, W., Yang, Y., Liu, C., Zhao, S., Li, X., & Liu, X. (2023). Comparative analysis of the organelle genomes of three Rhodiola species provide insights into their structural dynamics and sequence divergences. BMC Plant Biology, 23(1), 156. https://doi.org/10.1186/s12870-023-04159-1
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Bullerwell, C. E. (Ed.). (2011). Organelle genetics: Evolution of organelle genomes and gene expression. Springer Science & Business Media.
Dierckxsens, N., Mardulyn, P., & Smits, G. (2017). NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 45(4), e18. https://doi.org/10.1093/nar/gkw955
Doyle, J. J., & Doyle, J. I. (1990). Isolation of plant DNA from fresh tissue. Focus, 12(1), 13–15.
Farah, A. H., Lee, S. Y., Gao, Z., Yao, T. L., Madon, M., & Mohamed, R. (2018). Genome size, molecular phylogeny, and evolutionary history of the tribe Aquilarieae (Thymelaeaceae), the natural source of agarwood. Frontiers in Plant Science, 9, 321994. https://doi.org/10.3389/fpls.2018.00712
Fauron, C., Allen, J., Clifton, S., & Newton, K. (2004). Plant mitochondrial genomes. In H. Daniell, & C. Chase, C. (Eds.), Molecular biology and biotechnology of plant organelles: Chloroplasts and mitochondria (pp. 151–177). Springer. https://doi.org/10.1007/978-1-4020-3166-3_6
Freudenthal, J. A., Pfaff, S., Terhoeven, N., Korte, A., Ankenbrand, M. J., & Förster, F. (2020). A systematic comparison of chloroplast genome assembly tools. Genome Biology, 21, 254. https://doi.org/10.1186/s13059-020-02153-6
Hannon, G. J. (2010). FastX-toolkit. Retieved from http://hannonlab.cshl.edu/fastx_toolkit
Hartati, H., Pratama, R., Hartati, N., Siregar, U. J., Rahmawati, S., Ardiyani, M., Majiidu, M, & Siregar, I. Z. (2023). Phylogenetic study of Gyrinops versteegii (Gilg) Domke, the agarwood-producing tree from Indonesia. AIP Conference Proceedings, 2972, 060011. https://doi.org/10.1063/5.0184218
Hishamuddin, M. S., Lee, S. Y., Ng, W. L., Ramlee, S. I., Lamasudin, D. U., & Mohamed, R. (2020). Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships. Scientific Reports, 10(1), 13034. https://doi.org/10.1038/s41598-020-70030-0
Jin, J. J., Yu, W. B., Yang, J. B., Song, Y., dePamphilis, C. W., Yi, T. S., & Li, D. Z. (2020). GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology, 21, 241. https://doi.org/10.1186/s13059-020-02154-5
Krämer, C., Boehm, C.R., Liu, J. Yin-ting, M. K., Hertle, A. P., Former, J., Ruf, S., Schottler, M. A., Zoschke, R., & Bock, R. (2024). Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number. Nat. Plants. 10, 923–935. https://doi.org/10.1038/s41477-024-01709-9
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. https://doi.org/10.1093/molbev/msw054
Lee, S. Y., & Mohamed, R. (2016). The origin and domestication of Aquilaria, an important agarwood-producing genus. In R. Mohamed (Ed.), Agarwood. Science behind the fragrance (pp. 1–20). Tropical Forestry. Springer. https://doi.org/10.1007/978-981-10-0833-7_1
Lee, S. Y., Turjaman, M., & Mohamed, R. (2018). Phylogenetic relatedness of several agarwood-producing taxa (Thymelaeaceae) from Indonesia. Tropical Life Sciences Research, 29(2), 13. https://doi.org/10.21315/tlsr2018.29.2.2
Lee, S. Y., Turjaman, M., Chaveerach, A., Subasinghe, S., Fan, Q., & Liao, W. (2022). Phylogenetic relationships of Aquilaria and Gyrinops (Thymelaeaceae) revisited: Evidence from complete plastid genomes. Botanical Journal of the Linnean Society, 200(3), 344–359. https://doi.org/10.1093/botlinnean/boac014
Librado, P., & Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11), 1451–1452. https://doi.org/10.1093/bioinformatics/btp187
Liu, H., Hou, Z., Xu, L., Ma, Q., Wei, M., Tembrock, L. R., Zhang, S., & Wu, Z. (2023). Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives. Frontiers in Plant Science, 14, 1228551. https://doi.org/10.3389/fpls.2023.1228551
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal, 17(1), 10–12. https://doi.org/10.14806/ej.17.1.200
Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D., & Gurevich, A. (2018). Versatile genome assembly evaluation with QUAST-LG. Bioinformatics, 34(13), i142–i150. https://doi.org/10.1093/bioinformatics/bty266
Naziz, P. S., Das, R., & Sen, S. (2019). The scent of stress: Evidence from the unique fragrance of agarwood. Frontiers in Plant Science, 10, 840. https://doi.org/10.3389/fpls.2019.00840
Palmer, J. D. (1985). Comparative organization of chloroplast genomes. Annual Review of Genetics, 19(1), 325–354. https://doi.org/10.1146/annurev.ge.19.120185.001545
Rozewicki, J., Li, S., Amada, K. M., Standley, D. M., & Katoh, K. (2019). MAFFT-DASH: Integrated protein sequence and structural alignment. Nucleic Acids Research, 47(W1), W5–W10. https://doi.org/10.1093/nar/gkz342
Tillich, M., Lehwark, P., Pellizzer, T., Ulbricht-Jones, E. S., Fischer, A., Bock, R., & Greiner, S. (2017). GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Research, 45(W1), W6–W11. https://doi.org/10.1093/nar/gkx391
Tonti‐Filippini, J., Nevill, P. G., Dixon, K., & Small, I. (2017). What can we do with 1000 plastid genomes? The Plant Journal, 90(4), 808–818. https://doi.org/10.1111/tpj.13491
Twyford, A. D., & Ness, R. W. (2017). Strategies for complete plastid genome sequencing. Molecular Ecology Resources, 17(5), 858–868. https://doi.org/10.1111/1755-0998.12626
Wang, X., Cheng, F., Rohlsen, D., Bi, C., Wang, C., Xu, Y., Wei, S., Ye, Q., Yin, T., & Ye, N. (2018). Organellar genome assembly methods and comparative analysis of horticultural plants. Horticulture Research, 5, 3. https://doi.org/10.1038/s41438-017-0002-1
Wang, Z. F., & Cao, H. L. (2021). The complete mitochondrial genome sequence of Aquilaria sinensis. Mitochondrial DNA Part B, 6(2), 381–383. https://doi.org/10.1080/23802359.2020.1869609
Wu, Z. Q., Liao, X. Z., Zhang, X. N., Tembrock, L. R., & Broz, A. (2022). Genomic architectural variation of plant mitochondria-A review of multichromosomal structuring. Journal of Systematics and Evolution, 60(1), 160168. https://doi.org/10.1111/jse.12655
Yu, X., Wei, P., Chen, Z., Li, X., Zhang, W., Yang, Y., Liu, C., Zhao, S., Li, X., & Liu, X. (2023). Comparative analysis of the organelle genomes of three Rhodiola species provide insights into their structural dynamics and sequence divergences. BMC Plant Biology, 23(1), 156. https://doi.org/10.1186/s12870-023-04159-1
Authors
HartatiH., CartealyI. C., Supatmi S., RahmawatiS., HartatiN. S., SiregarU. J., & SiregarI. Z. (2024). A Comparative Study of the Organellar Genome of Gyrinops versteegii and Aquilaria malaccensis. Jurnal Manajemen Hutan Tropika, 30(3), 326. https://doi.org/10.7226/jtfm.30.3.326
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