Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

Zhou, Jianguo; Cui, Yingxian; Chen, Xinlian; Liu, Ying; Xu, Zhichao; Duan, Baozhong; Li, Yonghua; Song, Jingyuan; Yao, Hui

doi:10.3390/molecules23020437

Cited by 85 publications

(80 citation statements)

References 48 publications

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“…Among them, the numbers of penta-SSRs and mono-SSRs were 123 and 87, respectively, and accounted for 77% of the entire SSRs ( Figure 5A). These results are in sharp contrast to previous results regarding other taxa, in which mono-SSRs were the most abundant and penta-SSRs were rarely present [19,41,[43][44][45][46][47]. The largest number of SSRs was located in the LSC (232), followed by the SSC (37) and the IR (3) ( Figure 4B).…”

Section: Distribution Of Large and Simple Sequence Repeatscontrasting

confidence: 97%

Two-Step Contractions of Inverted Repeat Region and Psai Gene Duplication from the Plastome of Croton Tiglium (Euphorbiaceae)

Jo¹,

Kim²

2018

Preprint

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Croton L. (Euphorbiaceae) is a very specious genus and consists of about 1,250 species, mainly distributed in tropical Asia and China. The first complete plastome sequence from the genus, Croton tiglium, is reported in this study (NCBI acc. No. MH394334). The plastome is 150,021 bp in length. The lengths of LSC and SSC are 111,654 bp and 18,167 bp, respectively. However, the length of the IR region is only 10,100 bp and includes only four rrn and four trn genes, and a small part of the ycf1 gene. We propose two-step IR contractions to explain this unique IR region of the C. tiglium plastome. First, the IR contracted from rps19-rpl2 to ycf2-trnL-CAA on the LSC/IRb boundary. Second, the IR contracted from ycf2-trnL-CAA to rrn16-trnV-GAC on the LSC/IRa boundary. In addition, duplicated copies of psaI genes were discovered in the C. tiglium plastome. Both copies were located side by side between accD and ycf4 genes, but one copy was pseudogenized because of a five-basepair (TAGCT) insertion in the middle of the gene following frameshift mutation. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes have two introns. The infA gene is lost. Twelve large repeats were detected in the plastome. All large repeats are located in the LSC region. Also, 272 simple sequence repeats (SSRs) were identified. The penta-SSRs accounted for 45% of total SSRs, followed by mono- (32%), di- (12%), tetra (6%) and tri-SSRs (5%). Most of them were distributed in the large single copy (LSC) region (85%). In addition, 76% of the SSRs were located in the intergenic spacer (IGS). Phylogenetic analysis suggested that C. tiglium is a sister group of Jatropha curcas with 100% bootstrap support. Seven Euphorbiaceae species formed one clade with 100% bootstrap support.

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Section: Distribution Of Large and Simple Sequence Repeatscontrasting

confidence: 97%

Two-Step Contractions of Inverted Repeat Region and Psai Gene Duplication from the Plastome of Croton Tiglium (Euphorbiaceae)

Jo¹,

Kim²

2018

Preprint

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“…In the phylogenetic tree in Figure 1, the posterior probability (PP) of all branch nodes is 1.00. As shown in Figure 1, our research supports that Chelidonium majus and Coreanomecon hylomeconoides are clustered into one clade, which is sister to the clade of the genera Papaver (Zhou et al 2018), Meconopsis, and Lamprocapnos. Meanwhile, the phylogenetic relationship in Papaveraceae was consistent with previous studies and this will be useful data for developing markers for further studies.…”

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confidence: 76%

The complete chloroplast genome sequence of Chelidonium majus (Papaveraceae)

Peng

Wang

et al. 2019

Mitochondrial DNA Part B

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The complete chloroplast genome sequence of Chelidonium majus L. has been presented in this article. The complete chloroplast genome is 159,741 bp in length with 38.7% of GC content, containing a large single copy region (LSC) of 87,698 bp, and a small single copy region (SSC) of 18,573 bp, which were separated by a pair of 26,735 bp inverted repeat regions (IRs). The sequence contained 132 unique genes, including 37 tRNA, 8 rRNA, and 87 protein-coding genes. This plastid genome is the first report for the genus Chelidonium and will be useful data for developing markers for further studies on resolving the relationship within the Papaveraceae.

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“…The whole chloroplast genome contains more effective molecular markers, referred to as DNA barcodes, which are useful for identifying species accurately. Chloroplast genomic sequences provide molecular information that is a good resource for plant systematics, phylogenetic studies, and population genomics [12,13]. Therefore, in recent years, many chloroplast genomes in the family Fabaceae, have been completely sequenced.…”

Section: Introductionmentioning

confidence: 99%

The Complete Chloroplast Genomes of Two Lespedeza Species: Insights into Codon Usage Bias, RNA Editing Sites, and Phylogenetic Relationships in Desmodieae (Fabaceae: Papilionoideae)

Somaratne

Guan

Wang

et al. 2019

Plants

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The genus Lespedeza (tribe: Desmodieae) consists of about 40 species that have high medicinal and economic value. However, in this genus, using morphological characters, the species identification is quite complicated, which can be solved by the analysis of the complete chloroplast genomes. As primary organelle genomes, the complete genome sequences of chloroplasts (cp) provide unique molecular information to study the divergence of species, RNA editing, and phylogeny. Therefore, to the best of our knowledge, for the first time, we sequenced the complete cp genomes of two representative Lespedeza species: Lespedeza davurica and Lespedeza cuneata. The cp genomes of both the species were found to be 149,010 bp in length, exhibiting the typical angiosperm chloroplast structure containing four regions. The Lespedeza cp genomes showed similar conserved gene contents, order, and orientations with a total GC content of 35.0%. A total of 128 genes, including 83 protein-coding genes, 37 tRNAs, and eight rRNAs, were identified from each genome. Unique molecular features of the two Lespedeza cp genome sequences were obtained by performing the analysis of repeats, sequence divergence, codon usage, and predicting the RNA editing sites in addition to phylogenetic analysis with other key genera in tribe Desmodieae. Using the two datasets, the phylogenetic relationship of Lespedeza species among Deasmodieae was discovered, suggesting that whole cp genomes provided useful information for phylogenetic studies of these species.

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Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

Cited by 85 publications

References 48 publications

Two-Step Contractions of Inverted Repeat Region and <em>Psa</em>i Gene Duplication from the Plastome of <em>Croton Tiglium</em> (Euphorbiaceae)

Two-Step Contractions of Inverted Repeat Region and <em>Psa</em>i Gene Duplication from the Plastome of <em>Croton Tiglium</em> (Euphorbiaceae)

The complete chloroplast genome sequence of Chelidonium majus (Papaveraceae)

The Complete Chloroplast Genomes of Two Lespedeza Species: Insights into Codon Usage Bias, RNA Editing Sites, and Phylogenetic Relationships in Desmodieae (Fabaceae: Papilionoideae)

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