The complete chloroplast genome sequence of tung tree (Vernicia fordii): Organization and phylogenetic relationships with other angiosperms

Abstract

Tung tree (Vernicia fordii) is an economically important tree widely cultivated for industrial oil production in China. To better understand the molecular basis of tung tree chloroplasts, we sequenced and characterized its genome using PacBio RS II sequencing platforms. The chloroplast genome was sequenced with 161,528 bp in length, composed with one pair of inverted repeats (IRs) of 26,819 bp, which were separated by one small single copy (SSC; 18,758 bp) and one large single copy (LSC; 89,132 bp). The genome contains 114 genes, coding for 81 protein, four ribosomal RNAs and 29 transfer RNAs. An expansion with integration of an additional rps19 gene in the IR regions was identified. Compared to the chloroplast genome of Jatropha curcas, a species from the same family, the tung tree chloroplast genome is distinct with 85 single nucleotide polymorphisms (SNPs) and 82 indels. Phylogenetic analysis suggests that V. fordii is a sister species with J. curcas within the Eurosids I. The nucleotide sequence provides vital molecular information for understanding the biology of this important oil tree.

Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny

“…The GC content of these sequenced genomes was consistent with a previously reported genome from this genus [37,38]. The number of repeats, including forward, tandem, and palindromic repeats, were studied in the chloroplast genomes sequenced and compared, and were found in a larger amount than in the previously reported cp genome of V. fordii (49 repeats) [32]. Among these repeats, tandem repeats were found several times more than palindromic and forward repeats, which are consistent with the Teucrium and Commiphora species [30,31], as well as S. miltiorrhiza [39], as previously reported.…”

“…SSRs (simple sequence repeats) are repeats that play an important role in genome stabilization and rearrangement of genome sequences, and these SSRs make the cp genome favorable because of its use as a molecular maker and phylogenetic analysis [40,41]. In our study 101 and 119 total SSRs were found in E. larica and E. smithii respectively, which is higher than the Euphorbiaceae family members [32]. However, it is similar to the previously reported B. sacra cp genome [42].…”

“…During evolution, some genomes are liable to gain or lose introns, and this process plays a key role in expression and gene regulation [35]. In the Euphorbia species, there are 12 genes and 6 tRNA which contain introns and were found to be similar in the previously reported V. fordii cp genome belonging to Euphorbiaceae [32]. Some of the genes in the chloroplast genome contain double introns, such as rps12, clpP, and ycf3, and in some genes like rpl2 and rpl16, the second intron is absent, which is consistent with previously reported genomes of Manihot esculenta [35] and Oresitrophe [36].…”

“…Analysis of two sequenced Euphorbia genomes revealed that, like most of the higher angiosperm genomes, they comprised the tetrahedral structure containing two pairs of inverted repeats, one large single-copy region and one small single-copy region [4,31]. There was a 186 bp difference observed between the two sequenced chloroplast genomes, and the size was also comparable with other compared Euphorbia species, as well as the Vernicia fordii chloroplast genome, which is 161,528 bp in length [32], suggesting that chloroplast genomes are conserved. The result was consistent with previously reported studies [30].…”

The complete chloroplast genome of Chinese medicine (Psoralea corylifolia Linn): Molecular Structures, barcoding analysis, and phylogenetic Analysis

“…The trnH-psbA, trnK-rbcL, trnG-psbZ, psbD-trnT-trnE, petN-trnC, trnG-trnS, trnR-trnG-trnS, ndhI-ndhG, trnL-rpl32 loci and petD, rpl16, ndhA introns were most divergent regions, which were located in the intergenic spacers (IGSs) and introns, respectively. The boundary of IR regions indicated hypervariable regions with many nucleotide changes in chloroplast genomes of closely related species[43], simultaneously, the IR border expansion/contraction was considered as an evolutionary event[36]. In this study, we compared genes on the boundaries of the junction sites of the Psoralea corylifolia with other three species of Glycine ( Glycine max, Glycine gracilis, Glycine soja ) (Fig 2).…”