Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characteristic and phylogenetic analyses of chloroplast genome for Mentha haplocalyx (Lamiaceae).

ABSTRACT: Mentha haplocalyx is an important medicinal and edible plant. Now, the complete chloroplast (cp) genome of M. haplocalyx was assembled and annotated. The cp genome of M. haplocalyx was 152,048 bp and contained two short inverted repeat regions (25,608 bp) which were separated by a small single copy region (17,654 bp) and a large single copyregion (83,179 bp). The cp genome encodes 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes and 4 ribosomal RNA genes. The topology of the phylogenetic tree showed that M. haplocalyx and M. spicata formed a monophyletic clade and clustered together with genus Dracocephalum.

SUBMITTER: He SL

PROVIDER: S-EPMC7510601 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characteristic and phylogenetic analyses of chloroplast genome for Mentha haplocalyx (Lamiaceae).

He Shui-Lian SL Yang Yang Y Tian Yang Y

Mitochondrial DNA. Part B, Resources 20200519 3

Mentha haplocalyx is an important medicinal and edible plant. Now, the complete chloroplast (cp) genome of M. haplocalyx was assembled and annotated. The cp genome of M. haplocalyx was 152,048 bp and contained two short inverted repeat regions (25,608 bp) which were separated by a small single copy region (17,654 bp) and a large single copyregion (83,179 bp). The cp genome encodes 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes and 4 ribosomal RNA ...[more]

PMID: 33366931

Similar Datasets

Chloroplast genome characteristic, comparative and phylogenetic analyses in Capsicum (Solanaceae).

Project description:BackgroundCapsicum (Solanaceae) is a globally important vegetable crop and is also used therapeutically in traditional medicine systems. However, little is known of the genetic variation within the commonly grown cultivars, the evolutionary relationships and differences in the chloroplast (cp.) genomes between Capsicum species remain unclear.ResultsThe cp. genomes of 32 Capsicum varieties in three species from 6 countries were investigated. The cp. genome of Capsicum was found to be ~ 156 kb in length and to contain 113 unique genes, of which 79 encoded proteins, 30 encoded transfer tRNAs, and 4 were for ribosomal RNAs. The 32 varieties that we chose for study represented 13 genotypes, containing a total of 608 indels, 83 SNPs, 47 SSRs and 281-306 repeat sequences. We then included several previously sequenced Capsicum cp. genomes, and found that the nine investigated species showed a number of differences in the characteristics of the four IR boundaries, and it was the non-coding regions that contained the most variable regions. We conducted a phylogenetic reconstruction using the cp. genomes of 43 representative species of Solanaceae, and the resulting phylogeny generally reflected the currently accepted classification, with the species of the pungent group having close relationship with one another.ConclusionsThis study provides a comprehensive analysis of Capsicum chloroplast genomes, revealing significant variations in IR boundaries and other genomic features. These findings enhance our understanding of Capsicum evolution and genetic diversity.

| S-EPMC11542203 | biostudies-literature

Characteristic and phylogenetic analyses of chloroplast genome for an endangered species Manglietia lucida (Magnoliaceae).

Project description:Manglietia lucida is a threatened horticultural plant in Yunnan province of China. Now, the complete chloroplast (cp) genome of M. lucida was assembled. The cp genome of M. lucida was 160,134 bp in length and contained two short inverted repeat regions (26,595 bp), which were separated by a small single copy region (18,825 bp) and a large single copy region (88,119 bp). The cp genome encodes 108 unique genes, including 74 protein-coding genes, 30 transfer RNA genes and 4 ribosomal RNA genes. The topology of the phylogenetic tree showed that M. lucida was not formed a monophyletic clade but clustered together with genus Magnolia.

| S-EPMC7687554 | biostudies-literature

The complete chloroplast genome sequence of Plectranthus hadiensis (Lamiaceae) and phylogenetic analysis

Project description: Not available

| S-EPMC10557565 | biostudies-literature

Characteristic and phylogenetic analyses of chloroplast genome for Ephedra monosperma (Ephedraceae), an important medicinal species.

Project description:Ephedra monosperma is an important medicinal plant of Ephedra (Ephedraceae). The complete chloroplast genome of E. monosperma was assembled from Illumina pair-end sequence reads. The whole chloroplast (cp) genome is 109,548 bp in length and presents a quadripartite structure consisting of two copies of inverted repeat (IR) regions (20,398) separated by a large single copy (LSC) region (60,674 bp) and a small single copy (SSC) region (8078 bp). The cp genome of E. monosperma encodes a total of 118 genes, including 73 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of E. monosperma cp genome is 36.6%. A maximum likelihood (ML) phylogenetic analysis revealed that E. monosperma was close to Ephedra equisetina. The ML tree also showed Ephedraceae appeared more closely related to Gnetaceae than to the other families in Gymnospermae.

| S-EPMC7889279 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Salvia karwinskii (Lamiaceae).

Project description:Salvia karwinskii Benth. 1835 is a perennial herb in the Lamiaceae family native in Mexico and Central America. The complete chloroplast (cp) genome of S. karwinskii was sequenced using the Illumina platform and assembled for the first time. The complete plastid genome of S. karwinskii was 150,907 bp in length including a large single-copy (LSC) region of 82,205 bp, a small single-copy (SSC) region of 17,538 bp, and a pair of inverted repeat (IR) regions of 25,582 bp. The total GC content of this genome was 38.05%, and that of LSC, SSC, and IR regions was 36.22%, 31.77%, and 43.14%, respectively. The cp genome contained 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The maximum-likelihood phylogenetic tree was constructed with 38 complete cp genomes, supporting a close relationship between S. karwinskii and a 10 species lineage, all of which belong to the subg. Calosphace of Salvia. The cp genome of S. karwinskii provides a foundation for further studies on genetic diversity and improving the classification system of Salvia.

| S-EPMC9336470 | biostudies-literature

Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora.

Project description:Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data of Polyspora are scarce, and the gene evolution and interspecific relationship are still unclear. In this study, we sequenced and annotated Polyspora chrysandra cp genome and combined it with previously published genomes for other Chinese Polyspora species. The results showed that cp genomes of six Chinese Polyspora varied in length between 156,452 bp (P. chrysandra) and 157,066 bp (P. speciosa), but all contained 132 genes, with GC content of 37.3%, and highly similar genes distribution and codon usage. A total of eleven intergenic spacer regions were found having the highest levels of divergence, and eight divergence hotspots were identified as molecular markers for Phylogeography and genetic diversity studies in Polyspora. Gene selection pressure suggested that five genes were subjected to positive selection. Phylogenetic relationships among Polyspora species based on the complete cp genomes were supported strongly, indicating that the cp genomes have the potential to be used as super barcodes for further analysis of the phylogeny of the entire genus. The cp genomes of Chinese Polyspora species will provide valuable information for species identification, molecular breeding and evolutionary analysis of genus Polyspora.

| S-EPMC9512918 | biostudies-literature

Characteristic and phylogenetic analyses of chloroplast genome for Syringa komarowii C.K.Schneid. (Oleaceae) from Huoditang, China, an important horticultural plant.

Project description:The genus Syringa (Oleaceae) comprises some of the most important cultivated horticultural trees worldwide. Syringa komarowii, is one of these important horticultural plants. We sequenced the complete chloroplast (cp) genomes of S. komarowii (previously identified as var. reflexa) using Illumina Hiseq X Ten platform. The cp genome exhibits a typical quadripartite structure with 158,020 bp in length, which consists of two copies of inverted repeat (IR) regions (25,676 bp) separated by a large single copy (LSC) region (87,628 bp) and a small single copy (SSC) region (19,040 bp). The cp genome of S. komarowii encodes a total of 132 genes, including 88 protein-coding genes, 36 tRNA genes and 8 rRNA genes. A maximum likelihood (ML) phylogenetic analysis resolved that S. komarowii in a clade with S. wolfii and S. yunnanensis. The ML tree also showed Syringa appeared more closely related to Ligustrum than to the other genera in the Oleaceae.

| S-EPMC8081327 | biostudies-literature

Complete chloroplast genomes of two mint species (Lamiaceae) from Al-Madinah, Saudi Arabia: phylogenetic and genomic comparative analyses.

Project description:The genus Mentha encompasses mint species cultivated for their essential oils, which are formulated into a vast array of consumer products. However, the systematics of the genus Mentha is very complicated and still uncertain. This is largely because of the presence of frequent interspecific hybridization, variation in chromosome number, cytomixis, polymorphism in morphology and essential oil composition under different environmental conditions, colonial mutant propagation, as well as the occurrence of polyploidy, aneuploidy, and nothomorphs. Here, we present the plastome assemblies for a wilt-resistant Saudi Arabian accession of Mentha longifolia (L.) Huds and an alien hybrid Mentha × verticillata L. which are 152,078 bp and 152,026 bp in length, respectively, and exhibited large single-copy (LSC) and small single-copy (SSC) regions separated by a pair of inverted repeat regions. The chloroplast genome of M. longifolia has 133 annotated genes, including 88 protein-coding genes and 37 tRNAs while M. × verticillata has 133 annotated genes, including 87 protein-coding genes and 38 tRNAs. Both cp genomes have eight rRNA genes. Phylogenetic analysis using a total chloroplast genome DNA sequence of 17 species revealed that M. longifolia sequenced in this study did not form a sister relationship with M. longifolia from another study. This opens a window for further investigations.

| S-EPMC9586595 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Salvia oxyphora Briq. 1896 (Nepetoideae, Lamiaceae).

Project description:Salvia oxyphora Briq. 1896 is a perennial herb in the family Lamiaceae native to Central Bolivia. In this study, the chloroplast genome of S. oxyphora was sequenced using the Illumina platform and was assembled for the first time. The complete plastid genome of S. oxyphora was 151,014 bp in length including a large single-copy (LSC) region of 82,293 bp, a small single-copy (SSC) region of 17,531 bp, and a pair of inverted repeats (IR) regions of 25,595 bp. The total GC content of this genome was 38.04%, and that of LSC, SSC and IR regions was 36.21%, 31.80% and 43.13%, respectively. A total of 114 unique genes of this genome have been annotated, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The maximum likelihood phylogenetic tree was constructed with 51 complete chloroplast genomes, illustrating the close relationship of S. oxyphora to the Brazil's native medicinal species S. splendens. The chloroplast genome of S. oxyphora provides a foundation for further studies on the adaptive evolution and genetic diversity of the genus Salvia.

| S-EPMC9318231 | biostudies-literature

Complete chloroplast genome sequence and phylogenetic analysis of Clerodendrum japonicum (Thunb.) Sweet (Ajugoideae, Lamiaceae).

Project description:Clerodendrum japonicum (Thunb.) Sweet belongs to the genus Clerodendrum in the family Lamiaceae. It is an important medicinal plant with great ornamental and economic value. We sequenced and analyzed the complete chloroplast genome of C. japonicum by Illumina sequencing in this study. The full length of the complete chloroplast genome is 152,215 bp, containing a pair of inverted repeat regions of 25,705 bp (IRa and IRb) separated by a large single-copy region (LSC) of 83,491 bp and a small single-copy region (SSC) of 17,314 bp. The C. japonicum chloroplast genome encodes 131 genes, comprising 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene. This study will be useful for further study on population, phylogenetic, and molecular genetic studies of this medicinal plant.

| S-EPMC8259852 | biostudies-literature