Comprehensive Analysis of Rhodomyrtus tomentosa Chloroplast Genome

Huang, Yuying; Yang, Zerui; Huang, Song; An, Wenli; Li, Jing; Zheng, Xiasheng

doi:10.3390/plants8040089

Cited by 27 publications

(22 citation statements)

References 46 publications

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“…We found most of the repeats in the LSC region compared to SSC and IR regions. These results are also in agreement with several other studies of angiosperms [36,46,47,48,49].…”

Section: Discussionsupporting

confidence: 93%

Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots

Iram

Hayat

Tahir

et al. 2019

Plants

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Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.

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“…We found most of the repeats in the LSC region compared to SSC and IR regions. These results are also in agreement with several other studies of angiosperms [36,46,47,48,49].…”

Section: Discussionsupporting

confidence: 93%

Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots

Iram

Hayat

Tahir

et al. 2019

Plants

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“…Besides, the position of intron-exon junctions of the genes coding proteins, ribosomal RNAs (rRNAs), and transfer RNAs (tRNAs) was con rmed with BLASTN and tRNAscan v1.23 programs [ 60 ]. The notes were manually corrected when necessary and veri ed using GENEROUS R8.0.2 by realigning with references [ 61 ]. The physical circular cp genome maps were generated by the OGDrawV1.2 software.…”

Section: Assembly Annotation and Analysismentioning

confidence: 99%

Comparative Chloroplast Genome Analysis of Impatiens Species (Balsaminaceae) in the Karst Area of China: Insights Into Genome Evolution and Phylogenomic Implications.

Luo

Huang

Sun

et al. 2021

Preprint

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Background: Impatiens, a controversial and complex genus, which belongs to the family Balsaminaceae with approximately 1000 species. The genus is well known for economical, medicinal, ornamental, and horticultural values. However, Due to the morphological features and insufficient genomic resources, their analyses of germplasm identification and molecular phylogeny are very limited. Results: We have sequenced the chloroplast genomes of six different species (I. chlorosepala, I. fanjingshanica, I. guizhouensis, I. linearisepala, I. loulanensis, and I. stenosepala) in the karst area of China and compared them with previously published species and the monospecific sister Hydrocera triflora belonging to Balsaminaceae family. We comtrasted the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships. The 12 complete chloroplast genomes of the Balsaminaceae species ranged in size from 151,538 bp (I. fanjingshanica) to 154,189bp (H. triflora ) encoded 114 total distinct genes except for I. glandulifera and H. triflora, including 81 protein-coding, 29 transfer RNA genes(tRNA), and 4 ribosomal RNA genes (rRNA). Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were found. Divergent hotspots regions psbK-psbI,trnT-GGU-psbD, rpl36-rps8, rpoB-trnC-GCA, trnK-UUU-rps16, trnQ-UUG, trnP-UGG-psaJ, trnT-UGU-trnL-UAA, and ycf4-cemA were identified in the 12 Balsaminaceae chloroplast genomes, which could be suitable for species identification and phylogenetic studies. Additionally, phylogenetic relationships based on Maximum likelihood (ML) and Bayesian inference (BI) among whole chloroplast genomes showed that H. triflora was the basal group in Balsaminaceae and I. guizhouensis was the basal group in impatiens species. Besides this, cultivated species(I. balsamina, I. hawkeri, and I. walleriana) were clustered together. Conclusion: Our study provides detailed information about nucleotide diversity hotspots and characterized types of repeats, which can be used for developing molecular markers applicable in Balsaminaceae species. And also we reconstructed and analyzed the relationships of some impatiens species and discovered their status based on the complete chloroplast genomes. The current study might provide valuable significant genomic information for the systematics and evolution in the Balsaminaceae.

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“…Extensive genes were transferred from plastids to the nucleus during evolution. In most land plants, the plastid genome (plastome) is a circular biological macromolecule with a typical quadripartite structure [13,14,15]. In higher plants, compared with hundreds or thousands of tandem repeats in nuclear ribosomal RNA genes [16,17,18], typical plastid rRNA genes are characterized by a pair of inverted rrn operons, which show the gene order of rrn16 , rrn23 , rrn4.5 , and rrn5 [19].…”

Section: Introductionmentioning

confidence: 99%

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Ding

Zhu

Dong

et al. 2019

Plants

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The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.

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Comprehensive Analysis of Rhodomyrtus tomentosa Chloroplast Genome

Cited by 27 publications

References 46 publications

Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots

Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots

Comparative Chloroplast Genome Analysis of Impatiens Species (Balsaminaceae) in the Karst Area of China: Insights Into Genome Evolution and Phylogenomic Implications.

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

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