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

Li, Mingwan; Ye, Xiaofan; Bi, Huitao

doi:10.1080/23802359.2020.1749177

Cited by 5 publications

(3 citation statements)

References 6 publications

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“…In the ziziphoid clade, there were two groups of Ziziphus species, in which all five Z. jujuba clustered together and formed a sister clade to the one containing Z. mauritiana , Z. spina-christi , and Z. incurva . The recent phylogeny grouped H. acerba MN794429, H. dulcis MT225403, and H. trichocarpa into one clade [ 19 ], which further became a sister to H. acerba MN782301 in our tree.…”

Section: Resultsmentioning

confidence: 93%

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

et al. 2023

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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.

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Section: Resultsmentioning

confidence: 93%

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

et al. 2023

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“… 2016 ); Hovenia dulcis (MT225403) (Li et al. 2020 ); H. trichocarpa (MT225404) (Li et al. 2020 ); Morus Alba (KU355297) (Li et al.…”

Section: Resultsmentioning

confidence: 99%

“… 2020 ); H. trichocarpa (MT225404) (Li et al. 2020 ); Morus Alba (KU355297) (Li et al. 2018 ); Rhamnella rubrinervis (ON881505); Rhamnus globosa (ON009012) (Xie et al.…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome sequence of Rhamnella wilsonii Schneid (Rhamnaceae)

Wang,

An,

2024

Mitochondrial DNA Part B

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Rhamnella wilsonii Schneid 1914 is a member of the Rhamnaceae and endemic to China. In this study, the complete chloroplast genome of R. wilsonii was sequenced and assembled. The complete chloroplast genome was 160,049 bp in length, including a pair of inverted repeats (IRs) of 26,502 bp, one large single copy (LSC) region of 88,274 bp and one small single copy (SSC) region of 18,771 bp. The genome contained 129 genes, including 8 rRNA genes, 37 tRNA genes and 84 protein-coding genes. The overall GC content of the complete chloroplast genome was 37.15%. The phylogenetic analysis demonstrated that R. wilsonii is closely related to R. martinni . This study provides basic information for further studies on the identification and evolution of R. wilsonii and Rhamnella from genomic perspective.

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Sequencing the chloroplast genome of a jujube genotype ( Ziziphus jujuba Mill. 'Fengmiguan') uncovered a 101 bp insertion in the large-single copy region

Zhang

Han

et al. 2023

Mitochondrial DNA Part B

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Characterization of the complete chloroplast genome of two Hovenia species (Rhamnaceae)

Cited by 5 publications

References 6 publications

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

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

The complete chloroplast genome sequence of Rhamnella wilsonii Schneid (Rhamnaceae)

Sequencing the chloroplast genome of a jujube genotype ( Ziziphus jujuba Mill. 'Fengmiguan') uncovered a 101 bp insertion in the large-single copy region

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