Variation among the Complete Chloroplast Genomes of the Sumac Species Rhus chinensis: Reannotation and Comparative Analysis

Xu, Yujie; Wen, Jun; Xu, Shuai; Ren, Zhumei

doi:10.3390/genes13111936

Cited by 4 publications

(2 citation statements)

References 54 publications

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“…Numbers near branches are bootstrap values. Xu et al, 2022). The nucleotide diversity value (Pi) in this study was relatively low compared to other species in the orchid family such as Paphiopedilum (Liu et al, 2022).…”

Section: Genetic Variation In Cp Genomesmentioning

confidence: 61%

“…Additionally, it possesses various pharmacological activities, such as antioxidant, anti-inflammatory, anticancer, and neuroprotective effects (Nguyen et al, 2023b;Wang et al, 2002). The exceptional medicinal value of this herb can be attributed to its chemical composition, which includes phenolic acids, flavonoids, diarylpentanoid, kinsenone, and polysaccharides (Chiang & Lin, 2017;Wang et al, 2002;Xu et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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Complete chloroplast genome of the Jewel Orchid, Anoectochilus formosanus (Orchidaceae) and its relatives

2024

Rev. Biol. Trop.

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Introduction: Anoectochilus formosanus is a highly valuable herb known for its efficacy in treating a wide range of diseases. However, the current methods used to differentiate this species from others within the same genus are not effective due to the high similarity in morphological characteristics and DNA barcode sequences among these species. Objective: Characterization of chloroplast (cp) genome in order to identify potential molecular markers to distinguish this plant at species or isolation levels is necessary. Methods: The complete cp genome was sequenced using next-generation sequencing technology, annotated, and compared with published cp genomes of various species within the Anoectochilus genus. Results: The complete cp genome of A. formosanus is 152 658 bp in size, consisting of a large and small copy of 82 692 bp and 17 346 bp, respectively, separated by reverse repeats of 26 310 bp. Within the cp genome, there are a total of 141 genes, including 92 protein-coding genes, 10 rRNA genes, and 39 tRNA genes. This genome contains a total of 80 simple sequence repeats, with 50 long repeats. Through phylogenetic analysis, a close relationship was observed between A. formosanus in Vietnam and A. formosanus samples originated from China (NC_061756.1). However, genomic comparisons highlighted significant differences between the two cp genomes, specifically in their reverse repeat sequences. Conclusions: These findings reveal distinct variations in the cp genome of A. formosanus in Vietnam, offering valuable insights for the taxonomy, plant identification, breeding, and conservation programs related to this herb in Vietnam.

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Section: Genetic Variation In Cp Genomesmentioning

confidence: 61%

Section: Introductionmentioning

confidence: 99%

Complete chloroplast genome of the Jewel Orchid, Anoectochilus formosanus (Orchidaceae) and its relatives

2024

Rev. Biol. Trop.

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In silico comparative analysis of the complete chloroplast genome sequences in the mulberry family (Moraceae)

NGO,

TRAN,

2024

Korean J. Pl. Taxon

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The mulberry family (Moraceae) encompasses a wide range of angiosperms and includes several important fruit plants, such as jackfruit, breadfruit, and figs, among others. While there have been multiple published complete chloroplast (cp) genomes within this family, there has been no comprehensive study that summarizes the characteristics of these sequences. In the current study, a comprehensive analysis was conducted using a dataset consisting of 32 cp genomes obtained from NCBI GenBank. These genomes belong to 32 species, encompassing 12 genera within the mulberry family. The collected data were used to conduct genomic comparisons and phylogenetic analyses, employing a range of bioinformatics tools. The findings revealed length variations among the cp genomes of different species, ranging from 158,459 bp in Morus mongolica to 162,594 bp in Broussonetia luzonica. Additionally, the study detected structural variations in simple sequence repeat motifs including gene losses. Overall, the phylogenetic results in this study generally supported the existing taxonomy of species within this family, with the exception that Malaisia scandens and Trophis scandens are clustered in the clade of the Broussonetia genus. This investigation provides further evidence of the effectiveness of characterizing the entire cp genome when classifying species and genera within the mulberry family.

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Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae

Huang,

Xu,

Valcárcel

et al. 2024

BMC Genom Data

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Background The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy. Results The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152–156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship. Conclusions Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.

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Variation among the Complete Chloroplast Genomes of the Sumac Species Rhus chinensis: Reannotation and Comparative Analysis

Cited by 4 publications

References 54 publications

Complete chloroplast genome of the Jewel Orchid, Anoectochilus formosanus (Orchidaceae) and its relatives

Complete chloroplast genome of the Jewel Orchid, Anoectochilus formosanus (Orchidaceae) and its relatives

In silico comparative analysis of the complete chloroplast genome sequences in the mulberry family (Moraceae)

Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae

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