The complete chloroplast genome sequence of the folk medicinal and vegetable plant purslane (<i>Portulaca oleracea</i>L.)

Liu, Xia; Yang, Hongju; Zhao, Jiafeng; Zhou, Boyang; Li, Tongtong; Bai, Xiang

doi:10.1080/14620316.2017.1389308

Cited by 14 publications

(17 citation statements)

References 43 publications

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“…The chloroplast genome of T. paniculatum , a typical quadripartite structure, is 156,929 bp in size, including a LSC region of 86,898 bp ranging from trnH-GUG to rps19 (Ribosomal protein S19), a SSC region of 18,529 bp from ndhF (NAD(P)H dehydrogenase) to ycf1 (hypothetical protein 1 gene), a pair of IR regions of 25,751 bp from rps19 to pseudogene ycf1 and ranging from ycf1 to rps19 , respectively ( Figure 1 and Table 1 ). The GC content of cp genome in the cp total, LSC (large single copy), SSC (small single copy), IRA (inverted repeat A region) and IRB (inverted repeat B region) is 36.79%, 34.6%, 30.5%, 42.7% and 42.7%, respectively ( Table 1 ), which is similar to the cp genome of other Caryophyllales [ 23 , 24 ] and the higher GC content in IR regions. A higher AT representation at the third codon position and second codon position was significant, which is one of the common characteristics of the chloroplast genome [ 26 , 27 , 28 , 29 ].…”

Section: Resultsmentioning

confidence: 55%

“…Fifty six protein-coding and 22 tRNA genes are located in LSC region, but only 12 protein-coding genes and one tRNA are located in the SSC region. Meanwhile, all eight rRNA are sited in IR regions, which has been found to be common in most cp genomes [ 23 , 30 ]. The ycf1 gene is located at the IR and SSC boundary region, the rps19 gene was located at the IR and LSC boundary region.…”

Section: Resultsmentioning

confidence: 99%

“…The Portulacaeae are composed only a single genus of Portulace [ 21 ]. Molecular barcodes based on the chloroplast genome have shown great potential for species discrimination, especially between closely related taxa, but to date, chloroplast genome sequences of only two genus of the Portulacaceae have been analyzed, which are Carnegiea gigantean and Portulaca oleracea [ 22 , 23 , 24 ]. At both the species and population levels, the complete chloroplast genome sequence might enhance our ability to explore reliable barcoding for accurate plant identification [ 6 , 7 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

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

Liu

Yang

et al. 2018

Molecules

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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.

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Section: Resultsmentioning

confidence: 55%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Liu

Yang

et al. 2018

Molecules

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“…However, unlike the saguaro genome (Sanderson et al., ), ndh genes appeared to be present and functional in our C. bigelovii plastome. Another notable difference between the saguaro genome and Cylindropuntia is the placement of ycf1 adjacent to rpl32 , instead of beside ycf2 as in the saguaro plastid genome (Sanderson et al., ) or adjacent to ndhF as in most typical angiosperm plastomes (see Portulaca oleracea ; Liu et al., ). All other assembled Opuntioideae to date show the same placement of ycf1 (L. C. Majure, unpublished data).…”

Section: Discussionmentioning

confidence: 99%

“…Subsequently, we de novo assembled the raw reads from that same accession using the Geneious assembler, using the default settings and 25% of the raw reads, which yielded a more complete plastome (125,158 bp) from two contigs (the two contigs were then joined at the trnF‐ndhJ IGS). This plastome was annotated in Geneious using a database based on the Portulaca oleracea (NC‐036236; Liu et al., ) plastid genome downloaded from GenBank (https://www.ncbi.nlm.nih.gov/genbank/). The fully annotated cholla plastome from C. bigelovii was then used as a reference for mapping raw reads from all taxa sampled, including those sequences downloaded from GenBank.…”

Section: Methodsmentioning

confidence: 99%

Phylogenomics in Cactaceae: A case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts

Majure

Baker

Cloud-Hughes³

et al. 2019

American J of Botany

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Premise Although numerous phylogenetic studies have been conducted in Cactaceae, whole‐plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age, and morphological evolution. Methods We developed a plastome dataset for most known diploid members of the chollas (42 taxa) as well as for other members of Cylindropuntieae. Paired‐end, raw reads from genome skimming were reference‐mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, and were used to build our plastome dataset, which was analyzed using various methods. Results Our plastome dataset resolved the phylogeny of the chollas, including most interspecific and intraspecific relationships. Tribe Cylindropuntieae arose ~18 mya, during the early Miocene in southern South America, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series in Cylindropuntia (e.g., spiny fruit) are mostly homoplasious. Conclusions This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although the chollas s.l. are widespread throughout western North American deserts, their most recent common ancestor likely arose in the Chihuahuan Desert region during the mid‐Miocene, with much of their species diversity arising in the early to mid‐Pliocene, a pattern strikingly similar to those found in other western North American desert groups.

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Intraspecific variation within the Portulaca oleracea L. from Republic of Korea based on chloroplast genomes

Tamboli,

Yang,

Youn

et al. 2024

Plant Biotechnol Rep

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The complete chloroplast genome sequence of the folk medicinal and vegetable plant purslane (Portulaca oleraceaL.)

Cited by 14 publications

References 43 publications

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

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

Phylogenomics in Cactaceae: A case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts

Intraspecific variation within the Portulaca oleracea L. from Republic of Korea based on chloroplast genomes

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