The complete chloroplast genome sequence of Viola prionantha (Violaceae).
Ontology highlight
ABSTRACT:
SUBMITTER: Duan C
PROVIDER: S-EPMC7782906 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Viola verecunda is a perennial plant native to the mountainous areas of Northeast Asia. Here the complete chloroplast genome of V. verecunda and its phylogenetic relationships to other species within the genus Viola are reported. The complete chloroplast genome of V. verecunda is 157,843 bp in length and circular in structure with four regions: a large single-copy region (86,345 bp), a small single-copy region (17,292 bp), and a pair of inverted repeat regions (27,103 bp each). The chloroplast genome contains 111 unique genes comprising 77 protein-coding, 30 unique tRNA, and 4 unique rRNA genes. Based on the protein-coding gene sequences from eight Viola chloroplast genomes, with Balanops balansae designated as the outgroup, maximum likelihood tree analysis indicates that V. verecunda is more closely related to V. raddeana than to other Viola species. The complete chloroplast genome of V. verecunda contributes to a better understanding of the phylogenetic relationships among Viola species.
| S-EPMC8604497 | biostudies-literature
Project description:Viola Prionantha belongs to the family Violaceae. It has been widely used for a traditional Chinese herb with antibacterial activity and is grown as an early spring ornamental species in China. In this study, we determined the complete chloroplast genome sequence of V. prionantha which forms a circular structure. The whole chloroplast genome was 156,501 bp in length, consisting of a pair of inverted repeats (IR) of 26,404 bp, a large single-copy (LSC) region of 85,689 bp, and a small single-copy (SSC) region of 18,004 bp. We annotated 131 genes, including 84 coding sequences, 8 rRNA sequences, 37 tRNA sequences and 2 pesudogenes. Among the annotated genes, 17 genes contained one or two introns. Furthermore, a phylogenetic analysis revealed that V. prionantha and V. seoulensis clustered together as sisters to other Violaceae species.
| S-EPMC7781978 | biostudies-literature
Project description:We constructed and characterized the chloroplast genome of Viola grypoceras via de novo assembly of Illumina data. The complete circular chloroplast genome is 158,357 bp long and contains four parts: a large single-copy (LSC) region of 86,764 bp, a small single-copy (SSC) region of 17,345 bp, and two inverted-repeat regions (IRa and IRb) of 27,124 bp each. Genome annotation predicted that this genome harbors 111 genes, comprising 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Phylogenetic analysis demonstrated that V. grypoceras shares a close systematic relationship with V. mirabilis and V. websteri by forming a basal clade in the genus Viola.
| S-EPMC9815259 | biostudies-literature
Project description:Viola philippica, as a traditional Chinese medicine, has great value in treating various diseases. Here, we report the chloroplast genome of V. philippica and its phylogenetic feature. The complete chloroplast genome is 156,744 bp in length, assembled from 22,346,570 reads, and its GC contents ratio is 36.26%. Its long single-copy (LSC) region is 85,892 bp. The small single-copy (SSC) region covers 18,006 bp and inverted repeat (IR) is 26,423 bp. It encodes 77 genes, including 43 protein genes, 4 rRNA genes, and 30 tRNA genes. Moreover, according to the phylogenetic analysis for a total of 12 chloroplast sequences, V. philippica demonstrated close relationship within genus Viola.
| S-EPMC7995846 | biostudies-literature
Project description: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.
| S-EPMC10281375 | biostudies-literature
Project description:Viola selkirkii, belonging to the genus Viola, has heart-shaped leaves and pale purple flowers, and it is widely distributed in the Northern Hemisphere, including Europe, North America, and Asia. In this study, the plastid genome of V. selkirkii was sequenced and phylogenetic analysis was performed on 11 Viola plastid genomes. The length of the plastid genome length of V. selkirkii was 156,774 bp, and it was identified as having a typical quadripartite structure with a large single-copy region (85,930 bp), a small single-copy region (17,982 bp), and two inverted repeat regions (26,431 bp each). A phylogenetic analysis was conducted with 77 protein-coding genes from the complete plastid genomes of 11 Viola and nine Salicaceae species; the complete plastid genome of Erythroxylum novogranatense was used as an outgroup. Viola formed a monophyletic clade, and V. selkirkii was closely related to V. ulleungdoensis. These results contribute to the clear identification of the phylogenetic position of V. selkirkii in Viola.
| S-EPMC9245995 | biostudies-literature
Project description:We report the complete chloroplast genomes of four Viola species (V. mirabilis, V. phalacrocarpa, V. raddeana, and V. websteri) and the results of a comparative analysis between these species and the published plastid genome of the congeneric species V. seoulensis. The total genome length of the five Viola species, including the four species analyzed in this study and the species analyzed in the previous study, ranged from 156,507 (V. seoulensis) to 158,162 bp (V. mirabilis). The overall GC contents of the genomes were almost identical (36.2-36.3%). The five Viola plastomes each contained 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Among the annotated genes, 16 contained one or two introns. Based on the results of a chloroplast genome structure comparison using MAUVE, all five Viola plastomes were almost identical. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved among the Viola species. A total of 259 exon, intron, and intergenic spacer (IGS) fragments were compared to verify the divergence hotspot regions. The nucleotide diversity (Pi) values ranged from 0 to 0.7544. The IR region was relatively more conserved than the LSC and SSC regions. The Pi values in ten noncoding regions were relatively high (>0.03). Among these regions, all but rps19-trnH, petG-trnW, rpl16-rps3, and rpl2-rpl23 represent useful molecular markers for phylogenetic studies and will be helpful to resolve the phylogenetic relationships of Viola. The phylogenetic tree, which used 76 protein-coding genes from 21 Malpighiales species and one outgroup species (Averrhoa carambola), revealed that Malpighiales is divided into five clades at the family level: Erythroxylaceae, Chrysobalanaceae, Euphorbiaceae, Salicaceae, and Violaceae. Additionally, Violaceae was monophyletic, with a bootstrap value of 100% and was divided into two subclades.
| S-EPMC6426196 | biostudies-literature
Project description:The complete chloroplast genome of Viola philippica was sequenced, assembled, and annotated. It is a circular form of 156,469 bp in length, which was separated into four distinct regions, a large single-copy (LSC) of 85,668 bp, a small single-copy region (SSC) of 18,001 bp, and two inverted repeats (IR) of 26,400 bp. After annotation, a total of 129 genes were predicted, of which, 84 encode proteins, 8 rRNA, and 37 tRNA. The evolutionary history, inferred using maximum likelihood (ML) method, indicates that V. philippica was grouped within Violaceae, and comprised a clade with Viola seoulensis with 100% Bootstrap value.
| S-EPMC8078920 | biostudies-literature
Project description:Viola kunawarensis Royle is a precious Uygur medicinal material that has anti-fever and detoxifying effects. This study reports the complete chloroplast genome sequence of V. kunawarensis based on Illumina NovaSeq-PE150 platform sequencing reads. The genome is 156,837 bp long and contains a small single-copy (SSC) region of 17,059 bp and a large single-copy (LSC) region of 86,194 bp, separated by two inverted repeats (IRs) of 26,792 bp each. There are 111 unique genes in the chloroplast genome. In this study, V. kunawarensis was confirmed to be most closely related to all comprising Viola taxa except Viola mirabilis and Viola websteri.
| S-EPMC9518287 | biostudies-literature
Project description:Recently, the chloroplast genome of Viola verecunda from a sample collected in Japan has been published. Although the name is often recognized as a taxonomic synonym of Viola arcuata, the genetic identity of the two species has never been compared intensively. We report the complete chloroplast genome sequence of V. arcuata, of which sample was collected from Seoul, Korea. The cp genome of V. arcuata (OM301625) has 157,870 bp in length and is composed of four regions: 86,366 bp of a large single-copy (LSC) region, 17,298 bp of a small single-copy (SSC) region, and 27,103 bp of a pair of inverted repeats (IRs). The complete genome contains 130 genes, including 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. When comparing chloroplast genomes between V. verecunda, and V. arcuata, 34 different loci were recognized: 12 SNPs and 22 indels. In the coding regions, there were two amino acid insertions (ndhI) caused by one base deletion, three synonymous substitutions (ndhF, ccsA, and ndhI), and six nonsynonymous substitutions (matK, rpoC2, ndhF, ycf1, and two rpl2s on each IR region). In non-coding regions, variants of 19 polyN sites, one microsatellite, two insertions, and two SNPs were recognized. Phylogenetic analysis confirms a sister or nearly identical relationship between two genomes. This study will provide the genetic basis for solving a taxonomic problem between V. arcuata and V. verecunda.
| S-EPMC9467595 | biostudies-literature