Characterization of the complete chloroplast genome of <i>Hovenia acerba</i> (Rhamnaceae)

Zhang, Lin; Mao, Run-Li; Bi, Huitao; Shen, Jiemei; Wang, Yihan; Li, Mingwan

doi:10.1080/23802359.2020.1714492

Cited by 8 publications

(8 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast, the least tandem repeats were recorded for R. tanquetii (36). These repeats exhibit a similar pattern as reported previously [ 8 , 9 , 33 , 34 ]. The complex repeats and high numbers are key components in studying the chloroplast genome evolution [ 35 , 36 ].…”

Section: Discussionsupporting

confidence: 88%

Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae)

et al. 2022

View full text Add to dashboard Cite

Background Ziziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman. Despite its potential medicinal uses, little is known regarding its genomic architecture, phylogenetic position, or evolution. Here we sequenced and analyzed the entire chloroplast (cp) genome of Z. hajarensis to understand its genetic organization, structure, and phylogenomic disposition among Rhamnaceae species. Results The results revealed the genome of Z. hajarensis cp comprised 162,162 bp and exhibited a typical quadripartite structure, with a large single copy (LSC) region of 895,67 bp, a small single copy (SSC) region of 19,597 bp and an inverted repeat (IR) regions of 26,499 bp. In addition, the cp genome of Z. hajarensis comprises 126 genes, including 82 protein-coding genes, eight rRNA genes, and 36 tRNA genes. Furthermore, the analysis revealed 208 microsatellites, 96.6% of which were mononucleotides. Similarly, a total of 140 repeats were identified, including 11 palindromic, 24 forward, 14 reverse, and 104 tandem repeats. The whole cp genome comparison of Z. hajarensis and nine other species from family Rhamnaceae showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. Comparative phylogenetic analysis based on the complete cp genome, 66 shared genes and matK gene revealed that Z. hajarensis shares a clade with Z. jujuba and that the family Rhamnaceae is the closest family to Barbeyaceae and Elaeagnaceae. Conclusion All the genome features such as genome size, GC content, genome organization and gene order were highly conserved compared to the other related genomes. The whole cp genome of Z. hajarensis gives fascinating insights and valuable data that may be used to identify related species and reconstruct the phylogeny of the species.

show abstract

Section: Discussionsupporting

confidence: 88%

Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae)

et al. 2022

View full text Add to dashboard Cite

show abstract

“…The phylogenetic tree at low taxonomic levels of Rhamnaceae was reconstructed using 78 orthologous protein-coding genes from 25 Rhamnaceae members and two organisms for the outgroup. As a greater number of Rhamnaceae species were included in the analysis, our phylogenetic tree added up the coverage of phylogenetic relationships between Rhamnaceae species to that of other studies [ 20 , 24 , 54 , 55 ]. Furthermore, the clusters of Rhamnaceae organisms based on codon usage were in line with the molecular phylogenetic tree.…”

Section: Discussionmentioning

confidence: 99%

“…Chinese jujube ( Ziziphus jujuba Mill) and Indian jujube ( Ziziphus mauritiana) fruits are economically important [ 18 ]. Members of genus Hovenia are used for making fine furniture and musical instruments [ 18 – 20 ]. Other species, such as Hovenia dulcis [ 21 ], Ventilago species [ 22 , 23 ] and Ziziphus species [ 24 ], possess medicinal properties.…”

Section: Introductionmentioning

confidence: 99%

Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae

et al. 2023

View full text Add to dashboard Cite

Background Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree is from 13 out of 24 Rhamnaceae chloroplast genomes, and only one chloroplast genome of the genus Ventilago is available. Hence, the phylogenetic relationships in Rhamnaceae remain incomplete, and more representative species are needed. Results The complete chloroplast genome of Ventilago harmandiana Pierre was outlined using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the final genome were confirmed with PCR amplifications and investigation of coverage depth. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar. The clustering based on codon usage was congruent with the molecular phylogenetic tree. The groups of genera in each tribe were in accordance with tribal classification based on molecular markers. We resolved the phylogenetic relationships among six Hovenia species, three Rhamnus species, and two Ventilago species. Our reconstructed tree provides the most complete and reliable low-level taxonomy to date for the family Rhamnaceae. Similar to other higher plants, the RNA editing mostly resulted in converting serine to leucine. Besides, most genes were subjected to purifying selection. Annotation anomalies, including indel calling errors, unaligned open reading frames of the same gene, inconsistent prediction of intergenic regions, and misannotated genes, were identified in the published chloroplast genomes used in this study. These could be a result of the usual imperfections in computational tools, and/or existing errors in reference genomes. Importantly, these are points of concern with regards to utilizing published chloroplast genomes for comparative genomic analysis. Conclusions In summary, we successfully demonstrated the use of comprehensive genomic data, including DNA and amino acid sequences, to build a reliable and high-resolution phylogenetic tree for the family Rhamnaceae. Additionally, our study indicates that the revision of genome annotation before comparative genomic analyses is necessary to prevent the propagation of errors and complications in downstream analysis and interpretation.

show abstract

“…Infructescence nutritional value is far higher than common fruits, because it contains not only fat, protein, and various types of sugar, but also a variety of mineral elements needed by the human body [1,4]. H. acerba fruit medicinal value is vast and is effective for numerous diseases: it inhibits cancer cell growth [5,6]; it has sedative, analgesic and anticonvulsant [3], anti-inflammation, anti-oxidation, anti-aging, and other effects [7]; it contains active components for liver protection [8,9]; it reduces coronary heart disease and improves immunity incidences [10,11]. The chemical components of H. acerba fruit were studied, and a variety of compounds, such as triterpenoid saponins, tannins, flavones, and fatty acids were isolated [7,12].…”

Section: Introductionmentioning

confidence: 99%

“…H. acerba studies have been mainly focused on ecological [28] and biological characteristics [6,8,29], pharmacology [4,12] for active ingredient extraction [1], and cultivation [30]. A few H. acerba germplasm resource studies have been conducted to assess its genetic diversity using ISSR and RAPD molecular markers [17,18]; however, evaluation of quality traits has not received much attention.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Evaluation of Quality Traits of Hovenia acerba Germplasm Resources in Fujian Province

Yang

Chen

Lin

et al. 2023

Forests

View full text Add to dashboard Cite

Hovenia acerba is a precious medicinal and edible tree. We assessed the genetic variation of H. acerba quality traits and conducted a comprehensive germplasm resource evaluation to provide a theoretical basis for breeding edible, medicinal, and edible/medicine combination varieties. We evaluated 31 H. acerba germplasm resources, including 12 infructescence and 8 fruit quality traits using correlation, principal component, and cluster analyses. The results showed that there were significant differences in all quality traits, with an average coefficient of variation greater than 0.20, an average genetic diversity greater than 1.80, and an average repeatability greater than 0.90. The average genetic variation and repeatability of quality traits in infructescence were higher than fruit. Infructescence K, Ca, Mn, Mg, and reducing sugar contents are important indicators in evaluating infructescence and fruit quality traits, and infructescence K, Mg, and reducing sugar contents are also quality innovation indices of H. acerba germplasms. Tannin, protein, and soluble sugar were the most suitable quality components for screening, followed by reducing sugar, starch, fat, total saponins, and total flavones. According to principal component factor scores and cluster analysis results, specific genotypes were selected as breeding materials for infructescence protein, tannin, flavone, reductive sugar, fruit tannin, fat, flavonoid, saponin, protein, and starch. The correlation analysis with environmental factors showed that the total amount of applied water could influence H. acerba infructescence and fruit quality. In conclusion, the variability of H. acerba germplasm resources was rich, and selection potential is large, which is beneficial to germplasm quality innovation and breeding.

show abstract

Characterization of the complete chloroplast genome of Hovenia acerba (Rhamnaceae)

Cited by 8 publications

References 10 publications

Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae)

Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae)

Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae

Comprehensive Evaluation of Quality Traits of Hovenia acerba Germplasm Resources in Fujian Province

Contact Info

Product

Resources

About