The complete plastome sequence of Durian, Durio zibethinus L. (Malvaceae)

Abstract

The complete plastome sequence of Durio zibethinus L. (Malvaceae) is determined in this study (NCBI acc. no. MG138151). D. zibethinus is an important fruit crop in Southeastern Asia and known as the 'king of fruit'. Our D. zibethinus plastome is the first reported sequences from the subfamily Helicteroideae of Malvaceae. The plastome sequence of D. zibethinus is 163,974 bp in length and it is composed of a pair of 23,679 bp inverted repeat regions separated by large and small single-copy regions of 95,704 bp and 20,912 bp, respectively. The gene order and structure of the D. zibethinus are similar to those of the typical plastome of land plants. The plastome encodes 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fifteen genes contain single intron and two genes have two introns. A total of 144 simple sequence repeats (SSR) were identified in the genome. Phylogenetic analysis show that D. zibethinus (Helicteroideae) is sister group of Tilia (Tilioideae) clade with 100% bootstrap support.

Assembly of the durian chloroplast genome using long PacBio reads

“…2 ). The unsupported junction occurs at the point of the IR that Cheon et al 2 reported, which is consistent with the lack of an IR in our assembly. The chloroplast genome tends to have relatively low diversity within a species 4 , 14 , 15 , so we do not expect that both assemblies would be correct, especially since they are from the same variety.…”

“…4 ). The results show durian sharing ancestry with Tilia species and Theobroma cacao , consistent with analyses performed using the whole genome assembly 1 and the chloroplast genome 2 . All of the closest species to durian are reported to contain an IR, so the loss of the IR must have occurred after durian split from these species.…”

“…1 ). This was unexpected since the published durian chloroplast genome (MG138151.1), also from a Thai Monthong variety, was 163,974 bp and included an IR 2 . The junction of the IR in the published chloroplast is a 169 bp small inverted repeat in our assembly.…”

“…A high-quality draft assembly of the durian genome was published in 2017 using PacBio reads and Chicago Hi-C, where approximately 95% of the ~ 738 Mb genome was covered by 30 scaffolds 1 . The durian chloroplast genome was assembled from Illumina sequence data into a 164 kb cyclic sequence 2 . Chloroplast sequences often, but not always, have a quadripartite structure consisting of a large single copy sequence and a short single copy sequence separated by a pair of large inverted repeats (IR) that range in size between 10 and 30 kb depending on the species 3 .…”

“…Chloroplast sequences often, but not always, have a quadripartite structure consisting of a large single copy sequence and a short single copy sequence separated by a pair of large inverted repeats (IR) that range in size between 10 and 30 kb depending on the species 3 . The durian chloroplast was reported to have a large single copy sequence that was 95.7 kb and a short single copy sequence of 20.9 kb with a 23.6 kb inverted repeat 2 .…”