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

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

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