The Complete Chloroplast Genome of Medinilla tapete-magicum (Melastomataceae) from Sulawesi, Indonesia

https://doi.org/10.22146/jtbb.87932

Arief Priyadi(1), Paramita Cahyaningrum Kuswandi(2), Evy Yulianti(3), Risha Amilia Pratiwi(4), Ni Putu Sri Asih(5*)

(1) Research Center for Applied Botany, Research Organization for Life Sciences and Environment; National Research and Innovation Agency (BRIN), Jl. Raya Jakarta - Bogor KM. 46 Cibinong, Bogor 16911, West Java, Indonesia.
(2) Department of Biology Education, Faculty of Mathematics and Natural Sciences, Universitas Negeri Yogyakarta, Jl. Colombo Yogyakarta No.1, Karangmalang, Depok, Sleman, Yogyakarta. Indonesia 55281
(3) Department of Biology Education, Faculty of Mathematics and Natural Sciences, Universitas Negeri Yogyakarta, Jl. Colombo Yogyakarta No.1, Karangmalang, Depok, Sleman, Yogyakarta. Indonesia 55281
(4) Research Center for Applied Botany, Research Organization for Life Sciences and Environment; National Research and Innovation Agency (BRIN), Jl. Raya Jakarta - Bogor KM. 46 Cibinong, Bogor 16911, West Java, Indonesia.
(5) Research Center for Biosystematics and Evolution; Research Organisation for Life Sciences and Environment; National Research and Innovation Agency (BRIN), Jl. Raya Jakarta - Bogor KM. 46 Cibinong, Bogor 16911, West Java, Indonesia
(*) Corresponding Author

Abstract


In this study, the genome of an endemic Sulawesi’s plant, Medinilla tapete-magicum was sequenced using Illumina NextSeq 500 and assembled the whole chloroplast genome. Results showed that the cpGenome is 155,602 bp in size with typical quadripartite structure of a large single copy (LSC) region (85,409 bp), a short single copy (SSC) region (16,629 bp), and a pair of inverted repeats (IRs) regions (26,782 bp). The cpGenome is composed of 132 genes, which consists of 87 protein coding genes, 37 tRNAs, and 8 rRNAs. The sliding window analyses showed that psbB-psbH and ndhF-rpl32 can potentially be used as markers. Microsatellite motifs of mononucleotide A and T dominated in the cpGenome. The phylogenetic trees from the concatenated 76 shared protein coding gene sequences showed the Medinilla clade was monophyletic and M. tapete-magicum is a sister species in the SE Asian clade which contain M. magnifica and M. speciosa.

 


Keywords


Annotation; Assembly; NGS; Phylogeny; Super-barcode

Full Text:

PDF


References

Andrews, S., 2010. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom.

Beier, S. et al., 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics, 33(16), pp.2583-2585. doi:10.1093/bioinformatics/btx198.

Bolger, A.M., Lohse, M. & Usadel, B., 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), pp.2114-2120. doi: 10.1093/bioinformatics/btu170.

Cámara-Leret, R. & Veldkamp, J., 2011. A remarkable new Medinilla (Melastomataceae) from Celebes (Sulawesi), Indonesia. Gardens’ Bulletin Singapore, 62(2), pp.1-9.

Chen, J. & Renner, S., 2007. Melastomataceae. Flora of china, 13, pp.360-399.

Danecek, P. et al., 2021. Twelve years of SAMtools and BCFtools. GigaScience, 10(2). doi: 10.1093/gigascience/giab008.

Darling, A.C.E. et al., 2004. Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements. Genome Research, 14(7), pp.1394-1403. doi: 10.1101/gr.2289704.

Darriba, D. et al., 2019. ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. Molecular Biology and Evolution, 37(1), pp.291-294. doi: 10.1093/molbev/msz189.

Dierckxsens, N., Mardulyn, P. & Smits, G., 2016. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 45(4), pp.e18-e18. doi: 10.1093/nar/gkw955.

Greiner, S., Lehwark, P. & Bock, R., 2019. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research, 47(W1), pp.W59-W64. doi: 10.1093/nar/gkz238.

Hoang, D.T. et al., 2018. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution, 35(2), pp.518-522. doi: 10.1093/molbev/msx281.

Kartonegoro, A. et al., 2021. Molecular phylogenetics of the Dissochaeta alliance (Melastomataceae): Redefining tribe Dissochaeteae. Taxon, 70(4), pp.793-825. doi: 10.1002/tax.12508.

Kartonegoro, A., 2022. Annotated checklist of the Medinilla (Melastomataceae) of Malesia. Rheedea, 32, pp.221-279. doi: 10.22244/rheedea.2022.32.04.02.

Kuznetsov, A. & Bollin, C.J., 2021. NCBI Genome Workbench: desktop software for comparative genomics, visualization, and GenBank data submission. In Multiple Sequence Alignment. Humana Press, Springer, pp.261-295. doi: 10.1007/978-1-0716-1036-7_16.

Langmead, B. & Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), pp.357-359. doi: 10.1038/nmeth.1923.

Li, B. et. al., 2022. Complete chloroplast genome sequences of three Aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships. BMC Genomics, 23(1), pp.218. doi: 10.1186/s12864-022-08400-3.

Liu, S. et al., 2023. CPGView: A package for visualizing detailed chloroplast genome structures. Molecular Ecology Resources, 23(3), pp.694-704. doi: 10.1111/1755-0998.13729.

Minh, B.Q. et al., 2020. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution, 37(5), pp.1530-1534. doi: 10.1093/molbev/msaa015.

Okonechnikov, K., Golosova, O. & Fursov, M., 2012. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics, 28(8), 1166. doi: 10.1093/bioinformatics/bts091.

POWO, 2023, Plants of the World Online, viewed 21 October 2023, from http://www.plantsoftheworldonline.org/.

Rambaut, A., 2009. FigTree v1. 3.1. http://tree bio ed ac uk/software/figtree/.

Ronquist, F. et al., 2012. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic Biology, 61(3), pp.539-542. doi: 10.1093/sysbio/sys029.

Rozas, J. et al., 2017. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution, 34(12), pp.3299-3302. doi: 10.1093/molbev/msx248.

Shi, L. et al., 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Research, 47(W1), pp.W65-W73. doi: 10.1093/nar/gkz345.

Tamura, K., Stecher, G. & Kumar, S., 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7), pp.3022-3027. doi: 10.1093/molbev/msab120.

Veranso-Libalah, M.C. et al., 2022. Phylogeny and systematics of the tribe Sonerileae (Melastomataceae) in Africa: a revised taxonomic classification. Journal of Systematics and Evolution, 61(4), pp.657-681. doi: 10.1111/jse.12921.

Zhou, Q. et al., 2019. Analyses of plastome sequences improve phylogenetic resolution and provide new insight into the evolutionary history of Asian Sonerileae/Dissochaeteae. Frontiers in Plant Science, 10(1477). pp.1-16. doi: 10.3389/fpls.2019.01477

Zhou, Q-J. et al., 2022. Out of chaos: phylogenomics of Asian Sonerileae. Molecular Phylogenetics and Evolution, 175, 107581. doi: 10.1016/j.ympev.2022.107581.



DOI: https://doi.org/10.22146/jtbb.87932

Article Metrics

Abstract views : 987 | views : 547

Refbacks

  • There are currently no refbacks.


Copyright (c) 2024 Journal of Tropical Biodiversity and Biotechnology

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

Editoral address:

Faculty of Biology, UGM

Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia

ISSN: 2540-9581 (online)