EST-SSR Mining and Characterization from Aquilaria malaccensis Transcriptome Shotgun Assembly

Hasyyati Shabrina; Nurul Chaerani; Dini Lestari; Andrie Ridzki Prasetyo; Fauzan Fahrussiam

doi:10.29303/jbt.v24i2.7060

EST-SSR Mining and Characterization from Aquilaria malaccensis Transcriptome Shotgun Assembly

Authors

Hasyyati Shabrina , Nurul Chaerani , Dini Lestari , Andrie Ridzki Prasetyo , Fauzan Fahrussiam

DOI:

10.29303/jbt.v24i2.7060

Published:

2024-06-29

Issue:

Vol. 24 No. 2 (2024): April - Juni

Keywords:

Agarwood synthesis related gene; aquilaria malaccensis; microsatellite; simple sequence repeat.

Articles

Downloads

pdf

How to Cite

Shabrina, H., Chaerani, N., Lestari, D., Prasetyo, A. R., & Fahrussiam, F. (2024). EST-SSR Mining and Characterization from Aquilaria malaccensis Transcriptome Shotgun Assembly. Jurnal Biologi Tropis, 24(2), 905–915. https://doi.org/10.29303/jbt.v24i2.7060

Download Citation

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

Abstract

Aquilaria malaccensis is a member of Thymelaceae family which is one of the main trees producing agarwood compounds in Indonesia and has high economic value. A. malaccensis has Appendix II conservation status due to high exploitation in the nature. One of the several efforts to maintain agarwood production while also maintaining agarwood population is efficient induction by manipulation of the pathway for agarwood formation and using individuals with higher production of agarwood compounds. Selection of superior individuals can be done using molecular markers that are linked to certain genes, including microsatellites or simple sequence repeats (SSR). This study aimed to identify SSRs in the agarwood transcriptome and characterized SSR sites that are linked to genes involved in the synthesis of agarwood compounds. The transcriptome data used was extracted from the NCBI database with accession number GHJS00000000.1. SSR mining was carried out using Krait v.1.4.0 software, then BLASTed with the protein database to analyze the linkage with the related genes. Perfect SSRs were found in 0.37% of the total sequences, and compound SSRs were 10.89%. The abundance of imperfect SSR (107,043) was greater than perfect SSR (31,262), indicating that SSR in the transcriptome had a low mutation rate and the SSR site was more conserved in A. malaccensis. The SSRs that linked to genes related to agarwood synthesis including HMGR, PAL, Mevalonate Kinase, MAPK, Delta-guaiene synthase, Farnesyl pyrophosphate synthase, and Phenylalanine ammonia-lyase. The discovery of SSRs linked to these genes can be used to create molecular markers that can be applied in agarwood producing trees selection.

References

Abdul Kadir, F.A., Azizan, K.A. and Othman, R. (2021) ‘Transcriptome of Aquilaria malaccensis containing agarwood formed naturally and induced artificially’, BMC Research Notes, 14(1), pp. 1–4. Available at: https://doi.org/10.1186/s13104-021-05532-9.

Altschul, S.F. (1990) ‘Basic local alignment search tool’, Journal of Molecular Biology, 215(3), pp. 403–410. Available at: https://doi.org/10.1016/S0022-2836(05)80360-2.

Aminan, A. W., Hamid, A. A. A., Tajuddin, S. N., & Ramli, A. N. M. (2022). Active site and structural analysis of sesquiterpene synthase towards synthesis of aromatic compounds related to agarwood formation in Aquilaria malaccensis.1–25. https://doi.org/10.21203/rs.3.rs-1810009/v1.

Ananda, G., Hile, S. E., Breski, A., Wang, Y., Kelkar, Y., Makova, K. D., & Eckert, K. A. (2014). Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes. PLoS genetics, 10(7), e1004498. https://doi.org/10.1371/journal.pgen.1004498.

Anwar, M. S., Wardati, W., & Ardian, A. (2017). Efek pemberian pupuk kascing dan urea terhadap pertumbuhan bibit gaharu (Aquilaria malaccensis Lamk.) (Doctoral dissertation, Riau University).

Aqmarina, A., Siregar, U. J., & Turjaman, M. (2018). Kandungan Kimia Gaharu dan Ekspresi Gen Sesquiterpene synthase 1 (SesTPS1) pada Aquilaria malaccensis Lamk dan Gyrinops versteegii Domke (Doctoral dissertation, Bogor Agricultural University (IPB)).

Bordoloi, S., Ravi, N., Modi, M. K., & Jayaraj, R. S. C. (2022). Genome-wide mining of simple sequence repeats and development of polymorphic SSR markers in Aquilaria malaccensis. Indian Journal of Genetics and Plant Breeding, 82(02), 236-239. https://doi.org/10.31742/IJGPB.82.2.15.

Borisova, O. F., Shchyolkina, A. K., Chernov, B. K., & Tchurikov, N. A. (1993). Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence. FEBS letters, 322(3), 304-306. https://doi.org/10.1016/0014-5793(93)81591-M.

CITES (2018) CITES Trade Database [2018]. Compiled by UNEP-WCMC for the CITES Secretariat. Available at: trade.cites.org.

Deguerry, F., Pastore, L., Wu, S., Clark, A., Chappell, J., & Schalk, M. (2006). The diverse sesquiterpene profile of patchouli, Pogostemon cablin, is correlated with a limited number of sesquiterpene synthases. Archives of biochemistry and biophysics, 454(2), 123-136. https://doi.org/10.1016/j.abb.2006.08.006.

Ding, S., Wang, S., He, K., Jiang, M., & Li, F. (2017). Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects. BMC genomics, 18, 1-10. https://doi.org/10.1186/s12864-017-4234-0.

Du, L., Zhang, C., Liu, Q., Zhang, X., & Yue, B. (2018). Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. Bioinformatics, 34(4), 681-683. https://doi.org/10.1093/bioinformatics/btx665.

Kuleung, C., Baenziger, P. S., & Dweikat, I. (2004). Transferability of SSR markers among wheat, rye, and triticale. theoretical and Applied Genetics, 108, 1147-1150. https://doi.org/10.1007/s00122-003-1532-5.

Ellis, J. R., & Burke, J. M. (2007). EST-SSRs as a resource for population genetic analyses. Heredity, 99(2), 125-132. https://doi.org/10.1038/sj.hdy.6801001.

Feng, S. P., Li, W. G., Huang, H. S., Wang, J. Y., & Wu, Y. T. (2009). Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Molecular breeding, 23, 85-97. https://doi.org/10.1007/s11032-008-9216-0.

Gao, T., Ma, X., & Zhu, X. (2013). Use of the psbA-trnH region to authenticate medicinal species of Fabaceae. Biological and Pharmaceutical Bulletin, 36(12), 1975-1979. https://doi.org/10.1248/bpb.b13-00611.

Gao, X., Su, Q., Yao, B., Yang, W., Ma, W., Yang, B., & Liu, C. (2022). Development of EST-SSR markers related to polyphyllin biosynthesis reveals genetic diversity and population structure in Paris polyphylla. Diversity, 14(8), 589. https://doi.org/10.3390/d14080589.

Hidayat, H., Siburian, R. and Indah Yuliana, C. (2020) ‘Gaharu Alam, Jaringan Perdagangan, dan Gaharu Budidaya: Studi Kasus Kalimantan Timur’, Jurnal Biologi Indonesia, 16(1), pp. 99–110. Available at: https://doi.org/10.47349/jbi/16012020/99.

Hishamuddin, M.S. (2022) ‘Mining and analysis of chloroplast simple sequence repeats ( SSRs ) from eight species of Aquilaria Mining and analysis of chloroplast simple sequence repeats ( SSRs ) from eight species of’, 46(1). Available at: https://doi.org/10.3906/bot-2108-61.

Hu, J., Wang, L. and Li, J. (2011) ‘Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber’, Biologia Plantarum, 55(3), pp. 577–580. Available at: https://doi.org/10.1007/s10535-011-0129-0.

Islam, R. and Banu, S. (2021) ‘Transcript profiling leads to biomarker identification for agarwood resin ‑ loaded Aquilaria malaccensis’, Trees [Preprint], (0123456789). Available at: https://doi.org/10.1007/s00468-021-02180-1.

Kamaruddin, K., Titawael, R. and Gawariah, G. (2022) ‘Contribution of Gaharu (Aquilaria sp) to Community Income in Fatmite Village, Namrole District, South Buru Regency’, Jurnal Agrohut, 12(1), pp. 23–30.

Kotwal, S. et al. (2016) ‘De novo transcriptome analysis of medicinally important plantago ovata using RNA-seq’, PLoS ONE, 11(3). Available at: https://doi.org/10.1371/journal.pone.0150273.

Kumeta, Y. and Ito, M. (2011) ‘Genomic organization of d -guaiene synthase genes in Aquilaria crassna and its possible use for the identification of Aquilaria species’, pp. 508–513. Available at: https://doi.org/10.1007/s11418-011-0529-7.

Lawson, M.J., Zhang, L. and Tech, V. (2006) ‘Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes’, 7, pp. 1–11. Available at: https://doi.org/10.1186/gb-2006-7-2-r14.

Li, Z., Yun, L., Gao, Z., Wang, T., Ren, X., & Zhao, Y. (2022). EST-SSR primer development and genetic structure analysis of Psathyrostachys juncea Nevski. Frontiers in plant science, 13, 837787. https://doi.org/10.3389/fpls.2022.837787.

Liao, B., Lee, S. Y., Meng, K., Yin, Q., Huang, C., Fan, Q., ... & Chen, S. (2019). Characterization and novel Est-SSR marker development of an important Chinese medicinal plant, Morinda officinalis How (Rubiaceae). Biotechnology & Biotechnological Equipment, 33(1), 1311-1318. https://doi.org/10.1080/13102818.2019.1664322.

Liu, Y. Y., Wei, J. H., Gao, Z. H., Zhang, Z., & Lyu, J. C. (2017). A review of quality assessment and grading for agarwood. Chinese Herbal Medicines, 9(1), 22-30. https://doi.org/10.1016/S1674-6384(17)60072-8.

López-Sampson, A. and Page, T. (2018) ‘History of Use and Trade of Agarwood’, Economic Botany, 72(1), pp. 107–129. Available at: https://doi.org/10.1007/s12231-018-9408-4.

Luo, L., Yang, Y., Zhao, H., Leng, P., Hu, Z., Wu, J., & Zhang, K. (2021). Development of EST-SSR markers and association analysis of floral scent in tree peony. Scientia Horticulturae, 289, 110409. https://doi.org/https://doi.org/10.1016/j.scienta.2021.110409.

Lv, F., Yang, Y., Sun, P., Zhang, Y., Liu, P., Fan, X., ... & Wei, J. (2022). Comparative transcriptome analysis reveals different defence responses during the early stage of wounding stress in chi-nan germplasm and ordinary Aquilaria sinensis. BMC Plant Biology, 22(1), 464. https://doi.org/10.1186/s12870-022-03821-4.

Qu, J. and Liu, J. (2013) ‘A genome-wide analysis of simple sequence repeats in maize and the development of polymorphism markers from next-generation sequence data’, BMC Research Notes, 6(1), pp. 1–10. Available at: https://doi.org/10.1186/1756-0500-6-403.

R Core Team (2021) ‘R: A language and environment for statistical computing.’, R Foundation for Statistical Computing [Preprint]. Available at: https://www.r-project.org/.

Ranade, S. S., Lin, Y. C., Zuccolo, A., Van de Peer, Y., & García-Gil, M. D. R. (2014). Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC Plant Biology, 14, 1-10.

Rossetto, M. (2001) ‘Sourcing of SSR markers from related plant species.’, in J.C. Henry (ed.) Plant genotyping: the DNA fingerprinting of plants. Oxford: CABI Publishing, pp. 211–224. Available at: https://doi.org/10.1079/9780851995151.0211.

Shen, S., Chai, X., Zhou, Q., Luo, D., Wang, Y., & Liu, Z. (2019). Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia). PeerJ, 7, e6542. https://doi.org/10.7717/peerj.6542.

Shivanand, P., Arbie, N.F. and Krishnamoorthy, S. (2022) ‘Agarwood — The Fragrant Molecules of a Wounded Tree’, pp. 1–23.

Singh, S., Gupta, S., Mani, A., & Chaturvedi, A. (2012). Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus. Bioinformation, 8(3), 114.

Srivastava, D., Ahmad, M. M., Shamim, M., Maurya, R., Srivastava, N., Pandey, P., ... & Siddiqui, M. H. (2019). Modulation of Gene Expression by Microsatellites in Microbes. In New and Future Developments in Microbial Biotechnology and Bioengineering (pp. 209-218). Elsevier. https://doi.org/10.1016/B978-0-444-63503-7.00012-7.

Thiel, T., Michalek, W., Varshney, R., & Graner, A. (2003). Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and applied genetics, 106, 411-422. https://doi.org/10.1007/s00122-002-1031-0.

Vranová, E., Coman, D. and Gruissem, W. (2013) ‘Network analysis of the MVA and MEP pathways for isoprenoid synthesis’, Annual Review of Plant Biology, 64(March 2013), pp. 665–700. Available at: https://doi.org/10.1146/annurev-arplant-050312-120116.

Wang, H. Y., Wei, Y. M., Yan, Z. H., & Zheng, Y. L. (2007). EST-SSR DNA polymorphism in durum wheat (Triticum durum L.) collections. Journal of Applied Genetics, 48, 35-42.

Xu, J., Du, R., Wang, Y., & Chen, J. (2023). Wound-Induced Temporal Reprogramming of Gene Expression during Agarwood Formation in Aquilaria sinensis. Plants, 12(16), 2901.

Xu, Y., Zhang, Z., Wang, M., Wei, J., Chen, H., Gao, Z., ... & Li, W. (2013). Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis. BMC genomics, 14, 1-16. https://doi.org/10.1186/1471-2164-14-227.

Zhang, J., Kuo, C.C.J. and Chen, L. (2011) ‘GC content around splice sites affects splicing through pre-mRNA secondary structures’, BMC Genomics, 12. Available at: https://doi.org/10.1186/1471-2164-12-90

License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Jurnal Biologi Tropis is licensed under a Creative Commons Attribution 4.0 International License.

The copyright of the received article shall be assigned to the author as the owner of the paper. The intended copyright includes the right to publish the article in various forms (including reprints). The journal maintains the publishing rights to the published articles.

Authors are permitted to disseminate published articles by sharing the link/DOI of the article at the journal. Authors are allowed to use their articles for any legal purposes deemed necessary without written permission from the journal with an acknowledgment of initial publication to this journal.

EST-SSR Mining and Characterization from Aquilaria malaccensis Transcriptome Shotgun Assembly

Authors

DOI:

Published:

Issue:

Keywords:

Articles

Downloads

How to Cite

Downloads

Metrics

Abstract

References

License

Most read articles by the same author(s)

Similar Articles

Menu

Manuscript Template

visitor

Keywords

Mitra Kerja sama

Open Access Journals

Contact Us

Information

Share & Follow