Characterization and Dynamics of Intracellular Gene Transfer in Plastid Genomes of Viola (Violaceae) and Order Malpighiales

Yang, Ji-Young; Park, Seongjun; Gil, Hee-Young; Pak, Jae‐Hong; Kim, Seung‐Chul

doi:10.3389/fpls.2021.678580

Cited by 5 publications

(5 citation statements)

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“…Furthermore, we identified that the genes infA , rpl32 , and rps16 were not present in 17 Viola cp genomes (Table S 1 ). Studies suggest that the cause of the loss of these genes may be due to parallel loss of chloroplast DNA during the evolution of angiosperms [ 45 – 47 ]. There were 17 intron-containing genes in each Viola species analyzed (Table S 1 ).…”

Section: Discussionmentioning

confidence: 99%

Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica

et al. 2022

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Background Viola philippica Cav. is the only source plant of “Zi Hua Di Ding”, which is a Traditional Chinese Medicine (TCM) that is utilized as an antifebrile and detoxicant agent for the treatment of acute pyogenic infections. Historically, many Viola species with violet flowers have been misused in “Zi Hua Di Ding”. Viola have been recognized as a taxonomically difficult genera due to their highly similar morphological characteristics. Here, all common V. philippica adulterants were sampled. A total of 24 complete chloroplast (cp) genomes were analyzed, among these 5 cp genome sequences were downloaded from GenBank and 19 cp genomes, including 2 “Zi Hua Di Ding” purchased from a local TCM pharmacy, were newly sequenced. Results The Viola cp genomes ranged from 156,483 bp to 158,940 bp in length. A total of 110 unique genes were annotated, including 76 protein-coding genes, 30 tRNAs, and four rRNAs. Sequence divergence analysis screening identified 16 highly diverged sequences; these could be used as markers for the identification of Viola species. The morphological, maximum likelihood and Bayesian inference trees of whole cp genome sequences and highly diverged sequences were divided into five monophyletic clades. The species in each of the five clades were identical in their positions within the morphological and cp genome tree. The shared morphological characters belonging to each clade was summarized. Interestingly, unique variable sites were found in ndhF, rpl22, and ycf1 of V. philippica, and these sites can be selected to distinguish V. philippica from samples all other Viola species, including its most closely related species. In addition, important morphological characteristics were proposed to assist the identification of V. philippica. We applied these methods to examine 2 “Zi Hua Di Ding” randomly purchased from the local TCM pharmacy, and this analysis revealed that the morphological and molecular characteristics were valid for the identification of V. philippica. Conclusions This study provides invaluable data for the improvement of species identification and germplasm of V. philippica that may facilitate the application of a super-barcode in TCM identification and enable future studies on phylogenetic evolution and safe medical applications.

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Section: Discussionmentioning

confidence: 99%

Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica

et al. 2022

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“…For example, the mtDNA had multiple losses of ribosomal and succinate dehydrogenase genes, caused by these genes being transferred to the host cell and becoming part of the nuclear genome during plant evolution [ 16 , 17 ]. Some chloroplast genes were also transferred to the nuclear genome during evolution, which is similar to the mitochondrial gene process [ 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules

et al. 2022

BMC Genomics

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Background Okra (Abelmoschus esculentus L. Moench) is an economically important crop and is known for its slimy juice, which has significant scientific research value. The A. esculentus chloroplast genome has been reported; however, the sequence of its mitochondrial genome is still lacking. Results We sequenced the plastid and mitochondrial genomes of okra based on Illumina short reads and Nanopore long reads and conducted a comparative study between the two organelle genomes. The plastid genome of okra is highly structurally conserved, but the mitochondrial genome of okra has been confirmed to have abundant subgenomic configurations. The assembly results showed that okra’s mitochondrial genome existed mainly in the form of two independent molecules, which could be divided into four independent molecules through two pairs of long repeats. In addition, we found that four pairs of short repeats could mediate the integration of the two independent molecules into one complete molecule at a low frequency. Subsequently, we also found extensive sequence transfer between the two organelles of okra, where three plastid-derived genes (psaA, rps7 and psbJ) remained intact in the mitochondrial genome. Furthermore, psbJ, psbF, psbE and psbL were integrated into the mitochondrial genome as a conserved gene cluster and underwent pseudogenization as nonfunctional genes. Only psbJ retained a relatively complete sequence, but its expression was not detected in the transcriptome data, and we speculate that it is still nonfunctional. Finally, we characterized the RNA editing events of protein-coding genes located in the organelle genomes of okra. Conclusions In the current study, our results not only provide high-quality organelle genomes for okra but also advance our understanding of the gene dialogue between organelle genomes and provide information to breed okra cultivars efficiently.

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“… 2019 ), V. selkirkii NC_059909 (unpublished), V. ulleungdoensis NC_050744 (Yang et al. 2021 ), V. albida ON815353 (this study), V. chaerophylloides NC_065000 (Cao et al. 2022 ), V. raddeana NC_041584 (Cheon et al.…”

Section: Resultsmentioning

confidence: 77%

“…However, previous molecular phylogenetic studies of Viola didn’t provide information for the most relative genome to V. albida (Yoo and Jang 2010 ; Yang et al. 2021 ) because trees from these studies showed polytomy or low bootstrap supports. We, therefore, further mapped the raw reads against the three candidate cp genomes [ V. selkirkii (NC_059909), V. chaerophylloides (NC_065000), and V. phalacrocarpa (NC_041583)], respectively.…”

Section: Discussionmentioning

confidence: 99%

“…In order to determine the cp genome of V. albida , the paired-end reads were mapped against the cp genome of V. ulleungdoensis (NC_050744), of which phylogenetic position is closely related to the members of the VIOLA ALBIDA complex (Yoo and Jang 2010 ; Yang et al. 2021 ), with the mapping module in the Geneious prime (v. 11.0.11 + 7; 'medium-low’ sensitivity option; Kearse et al. 2012 ).…”

Section: Methodsmentioning

confidence: 99%

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A complete chloroplast genome sequence of Viola albida Palibin 1899 (Violaceae), a member of VIOLA ALBIDA complex

Moon

Kim

2023

Mitochondrial DNA Part B

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The VIOLA ALBIDA complex is a complicated group with taxonomic problems having continuous leaf variations and composed of taxa related to the following names: Viola albida , V. albida var. takahashii , and V. chaerophylloides. As a first step to understanding the genomic nature of this complex, this study identified the whole chloroplast genome of V. albida . The genome is 157,692 bp in length (36.3% of GC content) and contains four subregions: a large single copy region of 86,220 bp, a small single copy region of 17,248 bp, and a pair of inverted regions of 27,112 bp each. An annotation of the gene identifies 111 unique genes, including 77 protein-coding genes, four rRNA genes, and 30 tRNA genes. The phylogenetic analysis of this genome with selected cp genomes from Viola identifies the close relationship between V. albida and V. ulleungdoensis. It is noteworthy that V. chaerophylloides , traditionally recognized as a member of the VIOLA ALBIDA complex, is genetically distant from V. albida and forms a sister group of all other members of the subsection Patellares . Our genome report is expected to serve as a basis for understanding the identity of the VIOLA ALBIDA complex.

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Characterization and Dynamics of Intracellular Gene Transfer in Plastid Genomes of Viola (Violaceae) and Order Malpighiales

Cited by 5 publications

References 51 publications

Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica

Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica

The complete mitochondrial genome of okra (Abelmoschus esculentus): using nanopore long reads to investigate gene transfer from chloroplast genomes and rearrangements of mitochondrial DNA molecules

A complete chloroplast genome sequence of Viola albida Palibin 1899 (Violaceae), a member of VIOLA ALBIDA complex

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