Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis.

Xia Liu,Yuan Li,Hongyuan Yang,Boyang Zhou

doi:10.3390/molecules23040857

Xia Liu, Yuan Li + Show 2 more

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https://doi.org/10.3390/molecules23040857

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Abstract

The complete chloroplast (cp) genome of Talinum paniculatum (Caryophyllale), a source of pharmaceutical efficacy similar to ginseng, and a widely distributed and planted edible vegetable, were sequenced and analyzed. The cp genome size of T. paniculatum is 156,929 bp, with a pair of inverted repeats (IRs) of 25,751 bp separated by a large single copy (LSC) region of 86,898 bp and a small single copy (SSC) region of 18,529 bp. The genome contains 83 protein-coding genes, 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes and four pseudogenes. Fifty one (51) repeat units and ninety two (92) simple sequence repeats (SSRs) were found in the genome. The pseudogene rpl23 (Ribosomal protein L23) was insert AATT than other Caryophyllale species by sequence alignment, which located in IRs region. The gene of trnK-UUU (tRNA-Lys) and rpl16 (Ribosomal protein L16) have larger introns in T. paniculatum, and the existence of matK (maturase K) genes, which usually located in the introns of trnK-UUU, rich sequence divergence in Caryophyllale. Complete cp genome comparison with other eight Caryophyllales species indicated that the differences between T. paniculatum and P. oleracea were very slight, and the most highly divergent regions occurred in intergenic spacers. Comparisons of IR boundaries among nine Caryophyllales species showed that T. paniculatum have larger IRs region and the contraction is relatively slight. The phylogenetic analysis among 35 Caryophyllales species and two outgroup species revealed that T. paniculatum and P. oleracea do not belong to the same family. All these results give good opportunities for future identification, barcoding of Talinum species, understanding the evolutionary mode of Caryophyllale cp genome and molecular breeding of T. paniculatum with high pharmaceutical efficacy.

Highlights

Chloroplasts are the metabolic centers of our world due to the crucial role of converting sunlight into energy and releasing oxygen
The chloroplast genome of T. paniculatum, a typical quadripartite structure, is 156,929 bp in size, including a large single copy (LSC) region of 86,898 bp ranging from trnH-GUG to rps19 (Ribosomal protein S19), a small single copy (SSC) region of 18,529 bp from ndhF (NAD(P)H dehydrogenase) to ycf1, a pair of inverted repeats (IRs) regions of 25,751 bp from rps19 to pseudogene ycf1 and ranging from ycf1 to rps19, respectively (Figure 1 and Table 1)
The results showed that the bias was significant in usage of synonymous codons except tryptophan and methionine in T. paniculatum as well as A/T ending rich in cp genome

Summary

Introduction

Chloroplasts are the metabolic centers of our world due to the crucial role of converting sunlight into energy and releasing oxygen. The availability of over 2400 sequenced chloroplast genomes (http://www.ncbi.nlm.nih.gov/genomes/) gave us insights to understand the plant biology diversity, evolution, climatic adaptation, DNA barcoding and expression high-value agricultural or biomedical products by genetic engineering [1,2,5,6,7,8,9]. In the Portulacaceae family of the Caryophyllales. It is widely used for many ailments, including cancer, diabetes, hepatic disorders, leishmaniasis and reproductive disorders due to its high concentrations of alkaloids, flavonoids, tannins, steroids, and triterpenes [10,11,12,13,14]. The leaves of T. paniculatum are widely used as a green leafy vegetable for human consumption in many parts of South America, Africa and Asia

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