Phylogenetic study of Gyrinops versteegii (Gilg) Domke, the agarwood-producing tree from Indonesia.

Gyrinops versteegii is one of Indonesia's most important agarwood producers, with natural distributions in the Lesser Sunda, Sulawesi, Maluku, and Papua. This endemic Indonesian species from the Tymeleaecaeae family can be developed for tree breeding in the future to support sustainable agarwood cultivation and production. The major problems of Gyrinops versteegii are a rapid decline in the population of agarwood trees in their habitat, uncertainties in species identification required for conservation purposes, a lack of genomic data needed to differentiate the species, and unresolved phylogenetic relationships between Gyrinops and other Aquilaria species. Our research aimed to conduct a phylogenetic tree analysis using long reads sequences generated with MinION Oxford Nanopore Technology. Sequence datasets were de novo assembled with Nanogalaxy and followed by annotation using GeSeq. Phylogenetic analysis was conducted to determine the relatedness of six chloroplast genomes of G. versteegii from our study and two publicly available reference chloroplast genomes from Gyrinops walla and Aquilaria sinensis. Eucalyptus grandis is used as an outgroup. All sequences were aligned using MAFFTv7 and Bioedit Sequence Alignment Editor, phylogenetic analysis was performed using the Maximum Likelihood method, and the phylogenetic tree was constructed using MEGA7 with a bootstrap value of 1000 replicates. Our results showed that all samples of G. versteegii in the clade Thymelaeaceae clustered after the outgroup of E. grandis. Based on phylogenetic/phylogenomic study using a single rbcL or matK gene, or a combination of both matK and rbcL, or chloroplast genome, we make a preliminary conclusion that Gyrinops are paraphyletic to Aquilaria. [ABSTRACT FROM AUTHOR]