The complete chloroplast genome of Durio zibethinus L. cultivar Ri6 (Helicteroideae, Malvaceae)

Abstract

Durian, a member of the Malvaceae family, is famous for its delicious fruits, which have strong scents and are rich in nutrients. In this study, we sequenced and characterized the complete chloroplast genome of Durio zibethinus L. 1774 cultivar Ri6, a popular durian cultivar in Vietnam, using the Illumina Hiseq platform. The results showed a circular chloroplast genome composed of a large single copy of 96,115 bp, a small single copy of 20,819 bp, and two inverted repeat regions of 24,185 bp. This genome consisted of 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The overall GC content of this genome was 35.7%. Phylogenetic analysis inferred from 78 protein-coding regions revealed monophyly of Durio species and a close relationship between D. zibethinus cultivar Ri6 and cultivar Mongthong. This study provides essential information for further studies examining genetic population, breedings, and species identification among Durio taxa and cultivars.

Keywords: Durian; Malvaceae; king fruit; phylogeny; plastome.

Figure 1.

The photo of Durio zibethinus cultivar Ri6. A. The whole plant. B. The adaxial surface of leaves. C. The abaxial surface of leaves. D. The young fruits. E. The fruits cut in half. Note: the tree branch type is intermediate. The leaf is oblong; the upper surface is dark green, and the lower surface is beige or brown. The fruit is green and oval with five carpels.The photo was self-taken by the first authors (Nguyen Pham Anh Thi) at Cho Lach, Ben Tre province, Vietnam.

Figure 2.

Map of the D. zibethinus cultivar Ri6 chloroplast genome. The arrows showed the direction of transcription including genes inside the circle that are transcribed clockwise, and those outside the circle are counterclockwise transcribed otherwise. The inner circle correspond to locations of LSC (large single copy), SSC (small single copy), and IRA/IRB (inverted repeat) regions. Different functional groups are signed according to the colored legend.

Figure 3.

Phylogenetic tree of D. zibethinus cultivar Ri6 and related species inferred from 78 protein-coding regions of chloroplast genomes using maximum likelihood and Bayesian inference methods. A. The Bayesian infererence method based phylogenetic tree. B. The cladogram of phylogenetic tree with the bootstrap values < 100 and posterior probabilitiy values < 1. Note: the best substitution model was TVM + I + G (Akaike information criteria). The numbers indicate the bootstrap values and posterior probabilities. The scale bar means the expected number of nucleotide substitutions per site. The chloroplast genome of dipterocarpus littoralis and Muntingia calabura was used as an outgroup. BOM: Bombacoideae; BRO: Brownlowioideae; BYT: Byttnerioideae; DOM: Dombeyoideae; GRE: Grewioideae; HEL: Helicteroideae; MAL: Malvoideae; STE: Sterculioideae; TIL: Tilioideae; DIP: Dipterocarpaceae; MUN: Muntingiaceae. The following sequences were used: Colona floribunda NC_054164 (Wang et al. 2021); Gossypium nelsonii NC_033399 (Chen et al. 2017); Durio zibethinus NC_036829 (Cheon et al. 2017); Durio zibethinus Ri6 OR731187 (this study); Abelmoschus sagittifolius NC_053354 (Li et al. 2020); Pachira macrocarpa NC_057439 (Xu et al. 2020); Theobroma cacao NC_014676 (Abdullah et al. 2020); Grewia biloba NC_058214 (Xu et al. 2021); Melochia corchorifolia NC_081971 (No reference); Theobroma grandiflorum NC_054233 (Niu et al. 2019); Abutilon megapotamicum NC_077649 (No reference); Reevesia lofouensis NC_063748 (No reference); Brachychiton acerifolius NC_071829 (No reference); Urena procumbenes NC_054171 (Wang et al. 2021); Craigia yunnanensis NC_045284 (Wariss et al. 2019); Bombax ceiba NC_037494 (Gao et al. 2018); Grewia chungii NC_054166 (Wang et al. 2021); Ochroma pyramidale OR567246 (No reference); Bombax buonopozense NC_054162 (Wang et al. 2021); Corchorus capsularis NC_044467 (Fang et al. 2021); Pterospermum truncatolobatum NC_054168 (Wang et al. 2021); Microcos paniculata NC_073501 (No reference); Colona auriculata NC_073500 (No reference); Pterospermum kingtungense NC_042885 (Wang et al. 2018b); Triumfetta japonica NC_073499 (No reference); Hibiscus cannabinus NC_045873 (Chen et al. 2020); Hermannia pinnata NC_073496 (No reference); Durio oxleyanus NC_064728 (Wong et al. 2022); Talipariti tiliaceum NC_053627 (Qiu et al. 2021); Durio zibethinus Mongthong MT321069 (Shearman et al. 2020); Durio dulcis NC_073110 (No reference); Tilia mongolica NC_057237 (Zheng et al. 2021); Pterospermum mengluense NC_057978 (Guan-Song et al. 2021); Excentrodendron hsienmu NC_054163 (Wang et al. 2021); Firmiana pulcherrima NC_036395 (Wang et al. 2018a); Sterculia nobilis NC_063575 (No reference); Ceiba speciosa NC_057077 (Huang et al. 2019); Reevesia pubescens NC_063749 (No reference); Tilia cordata NC_065062 (Yan et al. 2022); Corchorus olitorius NC_044468 (Fang et al. 2021); Thespesia lampas NC_070217 (No reference); Rulingia hermanniifolia NC_073498 (No reference); Dipterocarpus littoralis NC_081465 (No reference); Diplodiscus trichospermus NC_065808 (Wu et al. 2023); Kleinhovia hospita NC_073497 (No reference); Muntingia calabura NC_056948 (No reference).