Molecular phylogenetics of Malesian Diospyros (Ebenaceae) based trnL-F spacer sequences

Abstract

Abstract. Wanda IF, Djuita NR, Chikmawati T. 2021. Molecular phylogenetics of Malesian Diospyros (Ebenaceae) based trnL-F spacer sequences. Biodiversitas 22: 4106-4114. Diospyros is a genus composed of potential species as an economic commodity with high diversity. However, there is limited information on the phylogenetic relationship of this genus in the Malesian region. This study aimed to provide information on the species diversity through a DNA barcoding approach and revealing the phylogenetic information of Diospyros spp. in the Malesian region. This study used 20 Diospyros accessions from Bogor Botanical Garden collections, 40 Diospyros accessions, and four outgroup accessions obtained from the NCBI database. The DNA barcoding primer utilized comes from plastids, trnL-F intergenic spacer. The phylogenetic trees were constructed using the Maximum-Parsimony method. A total of 20 accessions of Diospyros were validated with sequence data on the genebank. The result showed that all accessions had relationships with 44 other Diospyros species globally. Here, we reported 10 new trnL-F intergenic spacer sequences of Malesian Diospyros species. A phylogenetic tree grouped 64 monophyletic Diospyros species into seven clades. The phylogenetic results supports the biogeographic hypothesis: the Malesian region, the Malesian-Caledonian Region, and Cosmopolite species in almost all bioregions.

Short Communication: Assessment of cogongrass (Imperata cylindrica (L.) P.Beauv.) genetic variation in Java, Indonesia using atpB-rbcL and trnL-F intergenic spacer

“…Meanwhile, the amplicons produced by trnL-F primers were also somewhat longer than the counterparts obtained in Diospyros spp. (Ebenaceae), showing 367 bp long trnL-F IGS sequences (Wanda et al 2021). After manual editing, the putative trnL-F IGS had 372 bp length, which was still longer than the sequences found in Diospyros spp.…”

Phenotypic and Estimated Genetic Variability in Endemic Diospyros celebica Bakh. and Widely-spread D. blancoi A.Dc. Cultivated at Purwodadi Botanic Garden, Indonesia

“…Diospyros (family: Ebenaceae) is an ecologically and economically important group of flowering plants, covering many species of ebonies and persimmons. Its members comprise more than 500 species worldwide, with most species found across the Indo-Pacific region (Wallnöfer 2001;Wanda et al 2021). Plant species belonging to this genus are mostly dioecious with separated male and female plants.…”

“…Due to their economic and ecological importance, Diospyros conservation through botanic gardens is crucial to facilitate intensive studies on their biology and prospective sustainable uses. Such studies on Diospyros have been continuously carried out at the Indonesian Botanic Gardens to support the conservation of this genus (Rindyastuti 2021;Rindyastuti et al 2021;Wanda et al 2021).…”

Genetic variation and phylogenetic position of Taxus sumatrana (Miq.) de Laub. (Taxaceae) in Sumatra, Indonesia based on trnL-trnF region

“…The trnL-trnF gene is widely used since the 1990s (D'yachenko et al 2015;Hartvig et al 2015;Koohdar and Sheidai 2022;Kipkiror et al 2023), and has shown successful application in plant molecular systematics in flowering plants (Chen et al 2013), such as Mangifera spp. (Fitmawati et al 2017), Laurus nobilis , Taxus (Liu et al 2011(Liu et al , 2018, Diospyros (Wanda et al 2021), and Ziziphora (Dündar and Tümen 2023). It also can be used to distinguish plant species, such as Pteridaceae (Chen et al 2013), Syzygium sp.…”