The complete chloroplast genome of copper-tolerance plant Elsholtzia splendens.
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ABSTRACT:
SUBMITTER: Ding L
PROVIDER: S-EPMC7706683 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Elsholtzia fruticosa is an ornamental plant with high medicinal value. In this study, we sequenced and analyzed the complete chloroplast (cp) genome of the species. The complete cp sequence is 151,550 bp, including the large single-copy (LSC) region of 82,778 bp, the small single-copy (SSC) region of 17,492 bp, and a pair of invert repeats (IRs) regions of 25,640 bp. It encodes 132 unique genes in total, including 87 protein-coding genes, 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). The comparative analysis of complete cp genomes showed that the genomic structure and gene order of E. fruticosa cps were conserved. The sequences of rps15, rps19, ycf1, ycf3, ycf15, psbL, psaI, trnG-UCC, trnS-GCU, trnR-UCU, trnL-UAG, trnP-UG, and trnL-UAA serve as hotspots for developing the DNA barcoding of Elsholtzia species. There are 49 SSR loci in the cp genome of E. fruticosa, among which the repeat numbers of mononucleotide, dinucleotide, trinucleotide, tetranucleotide, and pentanucleotides SSR are 37, 9, 3, 0, and 0, respectively. A total of 50 repeats were detected, including 15 forward repeats, seven reverse repeats, 26 palindromic repeats, and two complementary repeats. Phylogenetic analysis based on the complete cp genome and protein-coding DNA sequences of 26 plants indicates that E. fruticosa has a dose relationship with E. splendens and E. byeonsanensis.
| S-EPMC9980026 | biostudies-literature
Project description:The complete chloroplast genome sequence of Elsholtzia densa was analysed. The results indicated that the size of the chloroplast genome was 149,095 bp in length with a large single-copy region (LSC) of 81,497 bp, a small single-copy region (SSC) of 17,364 bp, and a pair of inverted repeat (IR) regions of 25,117bp. The overall GC content of the cpDNA genome was 37.86%, while the corresponding values of the LSC, SSC, and IR regions were 35.96%, 31.92%, and 43.16%, respectively. A total of 132 functional genes were identified, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood phylogenetic tree suggested that E. densa was closely related to the species in the family Labiatae.
| S-EPMC7748739 | biostudies-literature
Project description:Elsholtzia byeonsanensis M. Kim. is an endemic species in Korea, and its leaves are distinguished from other taxa of Elsholtzia by the leathery texture. In this study, we first presented the complete chloroplast genome of E. byeonsanensis. The complete chloroplast genome was 150,628 bp, including a large-single copy region (LSC) of 82,738 bp, a small-single copy region (SSC) of 17,492 bp, and a pair of inverted repeat regions (IRs) of 25,199 bp. It contained 112 genes including 78 protein-coding genes, four rRNA, and 30 tRNA genes. The phylogenetic analysis indicated that E. byeonsanensis and E. splendens formed a monophyletic clade and showed a close relationship. The complete chloroplast genome of E. byeonsanensis will provide useful information for phylogenetic and evolutionary studies.
| S-EPMC9754010 | biostudies-literature
Project description:BACKGROUND AND AIMS: Copper (Cu) is an essential micronutrient for plants. However, excess amounts of Cu are toxic and result in a wide range of harmful effects on the physiological and biochemical processes of plants. Cell wall has a crucial role in plant defense response to toxic metals. To date, the process of cell wall response to Cu and the detoxification mechanism have not been well documented at the proteomic level. METHODS: An recently developed 6-plex Tandem Mass Tag was used for relative and absolute quantitation methods to achieve a comprehensive understanding of Cu tolerance/detoxification molecular mechanisms in the cell wall. LC-MS/MS approach was performed to analyze the Cu-responsive cell wall proteins and polysaccharides. KEY RESULTS: The majority of the 22 up-regulated proteins were involved in the antioxidant defense pathway, cell wall polysaccharide remodeling, and cell metabolism process. Changes in polysaccharide amount, composition, and distribution could offer more binding sites for Cu ions. The 33 down-regulated proteins were involved in the signal pathway, energy, and protein synthesis. CONCLUSIONS: Based on the abundant changes in proteins and polysaccharides, and their putative functions, a possible protein interaction network can provide new insights into Cu stress response in root cell wall. Cu can facilitate further functional research on target proteins associated with metal response in the cell wall.
| S-EPMC4207692 | biostudies-literature
Project description:Bacterial communities of rhizospheric soils play an important role in the tolerance and uptake of metal-tolerant/hyperaccumulating plants to metals, e.g. the Cu-tolerant Elsholtzia splendens native to China. In this work, pyrosequencing of the bacterial 16S rRNA gene was firstly applied to investigate the rhizospheric bacterial community of E. splendens grown at Cu contaminated sites. The 47 phyla including 11 dominant phyla (>1%) in E. splendens rhizosphere were presented. The effects of Cu and other environmental factors (total organic carbon, total nitrogen and pH) on the rhizospheric bacterial community were studied comprehensively. The phyla abundances were affected by the environmental factors to different extent, and we found pH, instead of Cu concentration, influenced UniFrac distance significantly and was identified as the most important environmental factor affecting bacterial community. In addition, the influence of environmental factors on gene profiles was explored according to the predicted metagenomes obtained by PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states). Our study illustrates a view about Cu-tolerant E. splendens rhizospheric bacterial communities (composition, diversity and gene profiles) and their influencing factors, giving a hand for the understanding on bacterial community is formed and affected in rhizosphere.
| S-EPMC5080579 | biostudies-literature
Project description:Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant.
| S-EPMC3584094 | biostudies-literature
Project description:The complete chloroplast genome sequence of Maianthemum dilatatum is sequenced and analyzed. The chloroplast genome is 156,921 bp, with 36.7% GC content. A pair of inverted repeats of 26,468 bp is separated by a large single-copy region (85,554 bp) and a small single-copy region (18,431 bp). It encodes 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Of 132 individual genes, 19 genes are duplicated in the IR regions, while 14 genes are encoded with one intron and three genes with two introns.
| S-EPMC7799983 | biostudies-literature
Project description:Pogostemon cablin, the natural source of patchouli alcohol, is an important herb in the Lamiaceae family. Here, we present the entire chloroplast genome of P. cablin. This genome, with 38.24% GC content, is 152,460 bp in length. The genome presents a typical quadripartite structure with two inverted repeats (each 25,417 bp in length), separated by one small and one large single-copy region (17,652 and 83,974 bp in length, respectively). The chloroplast genome encodes 127 genes, of which 107 genes are single-copy, including 79 protein-coding genes, four rRNA genes, and 24 tRNA genes. The genome structure, GC content, and codon usage of this chloroplast genome are similar to those of other species in the family, except that it encodes less protein-coding genes and tRNA genes. Phylogenetic analysis reveals that P. cablin diverged from the Scutellarioideae clade about 29.45 million years ago (Mya). Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to high AT content in the chloroplast genome. Complete sequences and annotation of P. cablin chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.
| S-EPMC4926354 | biostudies-literature
Project description:Sophora tonkinensis belongs to genus Sophora of the Fabaceae family. It is mainly distributed in the ridge and peak regions of limestone areas in western China and has high medicinal value and important ecological functions. Wild populations of S. tonkinensis are in danger and need urgent conservation. Furthermore, wild S. tonkinensis resources are very limited relative to the needs of the market, and many adulterants are present on the market. Therefore, a method for authenticating S. tonkinensis and its adulterants at the molecular level is needed. Chloroplast genomes are valuable sources of genetic markers for phylogenetic analyses, genetic diversity evaluation, and plant molecular identification. In this study, we report the complete chloroplast genome of S. tonkinensis. The circular complete chloroplast genome was 154,644 bp in length, containing an 85,810 bp long single-copy (LSC) region, an 18,321 bp short single-copy (SSC) region and two inverted repeat (IR) regions of 50,513 bp. The S. tonkinensis chloroplast genome comprised 129 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The structure, gene order and guanine and cytosine (GC) content of the S. tonkinensis chloroplast genome were similar to those of the Sophora alopecuroides and Sophora flavescens chloroplast genomes. A total of 1,760 simple sequence repeats (SSRs) were identified in the chloroplast genome of S. tonkinensis, and most of them (93.1%) were mononucleotides. Moreover, the identified SSRs were mainly distributed in the LSC region, accounting for 60% of the total number of SSRs, while 316 (18%) and 383 (22%) were located in the SSC and IR regions, respectively. Only one complete copy of the rpl2 gene was present at the LSC/IRB boundary, while another copy was absent from the IRA region because of the incomplete structure caused by IR region expansion and contraction. The phylogenetic analysis placed S. tonkinensis in Papilionoideae, sister to S. flavescens, and the genera Sophora and Ammopiptanthus were closely related. The complete genome sequencing and chloroplast genome comparative analysis of S. tonkinensis and its closely related species presented in this paper will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.
| S-EPMC7385175 | biostudies-literature
Project description:Alseodaphne hainanensis is an endangered species with inhabiting dense forest along valleys, and it is one of the representative species of tropical rain forest in Hainan Island. In this paper, we reported and characterized the complete chloroplast genome sequence of the species assembled from short reads generated by Illumina sequencing. The size of chloroplast was 152,829 bp, a pair of inverted repeats (IRs) separating a large single copy and a small single copy, the size of IRs, LSC and SSC were 20,036 bp, 93,872 bp and 18,885 bp, respectively. A total of 129 genes were predicted, including 81 protein-coding genes, 38 tRNA, 8 rRNA, and 2 pseudogene. Phylogenetic analysis confirmed the position of A. hainanensis within the order Laurales.
| S-EPMC7687619 | biostudies-literature