Characterization of the Complete Chloroplast Genome Sequence of the Socotra Dragon`s Blood Tree (Dracaena cinnabari Balf.)

Celiński, Konrad; Sokołowska, Joanna; Fuchs, Hanna; Maděra, Petr; Wiland-Szymańska, Justyna

doi:10.3390/f13060932

Cited by 3 publications

(3 citation statements)

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“…This article unveils notable distinctions within the protein-coding genes of complete cp sequences from P. cyrtonema and P. odoratum compared to other Polygonatum species. Specifically, the absence of the ribosomal protein gene rps19 in the LSC region, a phenomenon also identified in Ophiopogon and Dracaena , marks a significant variation 66 , 67 . Moreover, the ycf3 and ycf4 genes absent in P. cyrtonema and P. odoratum , while the pafI and pafII genes appear in their close vicinity, respectively.…”

Section: Discussionmentioning

confidence: 81%

Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny

Yan,

Dong,

Gong

et al. 2023

Sci Rep

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The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.

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Section: Discussionmentioning

confidence: 81%

Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny

Yan,

Dong,

Gong

et al. 2023

Sci Rep

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“…& Link L., and Quercus litseoides Dunn [ 67 , 68 ], and were fully encoded by the IR regions in Polystachya adansoniae Rchb.f., Polystachya bennettiana Rchb.f., and Dracaena cinnabari Balf.f. [ 69 , 70 ]. There are several mechanisms that might explain the IR expansion and contraction [ 71 , 72 , 73 ].…”

Section: Discussionmentioning

confidence: 99%

Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications

Ding

Han

et al. 2022

Biology

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The genus Crassula is the second-largest genus in the family Crassulaceae, with about 200 species. As an acknowledged super-barcode, plastomes have been extensively utilized for plant evolutionary studies. Here, we first report 10 new plastomes of Crassula. We further focused on the structural characterizations, codon usage, aversion patterns, and evolutionary rates of plastomes. The IR junction patterns—IRb had 110 bp expansion to rps19—were conservative among Crassula species. Interestingly, we found the codon usage patterns of matK gene in Crassula species are unique among Crassulaceae species with elevated ENC values. Furthermore, subgenus Crassula species have specific GC-biases in the matK gene. In addition, the codon aversion motifs from matK, pafI, and rpl22 contained phylogenetic implications within Crassula. The evolutionary rates analyses indicated all plastid genes of Crassulaceae were under the purifying selection. Among plastid genes, ycf1 and ycf2 were the most rapidly evolving genes, whereas psaC was the most conserved gene. Additionally, our phylogenetic analyses strongly supported that Crassula is sister to all other Crassulaceae species. Our findings will be useful for further evolutionary studies within the Crassula and Crassulaceae.

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“…The chloroplast genome of plants plays a crucial role in elucidating chloroplast functions, species identification, population genetics, phylogenetics, and conservation of plant resources [13][14][15][16]. In this study, we conducted a comprehensive analysis of the complete cp genome sequence of V. japonicum using second-generation sequencing technology.…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome Structural Characterization and Comparative Analysis of Viburnum japonicum (Adoxaceae)

Zhu,

Liu,

et al. 2023

Forests

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Viburnum japonicum (Thunb.) Sprengel is an endangered species endemic to coastal regions of eastern Asia (China, Japan, and South Korea). However, its systematic position has been controversial. In this study, we present the complete chloroplast (cp) genome of V. japonicum (GenBank OP644292) sequenced using the Illumina NovaSeq platform. The cp genome has a total length of 158,606 bp and a G+C contents of 38.08%. It consists of a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs) regions measuring 87,060 bp, 18,510 bp, and 26,516 bp, respectively. A total of 131 genes were identified, including 87 protein-coding genes, 36 transfer RNA genes (tRNAs), and 8 ribosomal RNA genes(rRNAs). Additionally, a total of 44 dispersed repeats were detected, including three types: forward, palindromic, and reverse. Among the 38 SSR loci that were discovered, the majority were mononucleotide loci composed of A/T. Furthermore, we found that 15 genes (accD, atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps12, rps16, trnA-UGC, trnI, trnK-UUU, and trnL-UAA) contain one intron, while clpP and ycf3 have two introns. The relative synonymous codon usage (RSCU) analysis detected 31 high-frequency codons, where A/U bases accounted for 93.55% of the total, indicating an asymmetry in chloroplast gene and a presence for A/U bases. Comparative analysis of genome structure and sequences data of V. japonicum chloroplast genomes in comparison with other closely related species demonstrated a high level of conservation in their structure and organization. Furthermore, three mutation hotspots (psbH, rps19, and trnL) were identified, which could be valuable for future phylogenetic and population genetic research. Phylogenetic analysis revealed that the two accessions of V. japonicum are closely related to a group of V. setigerum, V. erosum, and V. fordiae within the Viburnum genus. In conclusion, this study provides important insights for accurately identifying and understanding the phylogeny of Viburnum species through the complete cp genome sequencing of V. japonicum.

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Characterization of the Complete Chloroplast Genome Sequence of the Socotra Dragon`s Blood Tree (Dracaena cinnabari Balf.)

Cited by 3 publications

References 50 publications

Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny

Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny

Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications

Complete Chloroplast Genome Structural Characterization and Comparative Analysis of Viburnum japonicum (Adoxaceae)

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