The complete chloroplast genome of Sedum emarginatum (Crassulaceae).
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ABSTRACT:
SUBMITTER: Chang H
PROVIDER: S-EPMC7781901 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Sedum tricarpum Makino., is a perennial succulent herb, which was first discovered and established as a new species ten years ago. Here, we report the complete chloroplast genome of S. tricarpum. It shows a typical quadripartite structure with a total length of 149,349 bp, including the large single-copy region (LSC) of 81,644 bp, the small single-copy region (SSC) of 16,643 bp, and two separated inverted regions (IRs) of 25,531 bp, respectively. For the whole genome, there are a total of 131 genes, including 85 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes. The overall GC content of the cp genome is 37.8%. A well-supported phylogenetic tree revealed monophyly formed by S. tricarpum and S. sarmentosum, suggesting a relatively closer phylogenetic relationship with the clade consisting of S. lineare and Graptopetalum amethystinum. The complete chloroplast genome of S. tricarpum provides valuable information for further phylogenetic reconstruction of the Crassulaceae family.
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Project description:The complete chloroplast genome of Sedum lineare Thunberg, a plant widely occurring in most southern provinces of China, is assembled and characterized using Illumina sequencing data in this study. The genome is 149,257 bp in length, containing a large single-copy (LSC) region of 80,963 bp, a short single-copy (SSC) region of 16,648 bp, and two inverted repeat (IR) regions of 25,823 bp. It contains 130 genes, with 85 protein-coding genes, 8 rRNA genes and 37 tRNA genes. Moreover, the phylogenetic tree shows that S. lineare is closely related to Sedum japonicum.
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Project description:Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.
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Project description:Bryophyllum daigremontianum is a very important traditional medicine and ornamental plant. Although Bryophyllum and Kalanchoe have been supported to form a clade, however, lack of chloroplast genomic severely hinders our understanding the phylogenetic relationships between them. In this study, the complete chloroplast genome of B. daigremontianum is first presented. It is 150,058 bp in length consisted a large single-copy (LSC, 82,164 bp) and a small single-copy (SSC, 17,042bp) separated by a pair of inverted repeats (IR, 25,426 bp) including 86 protein-coding genes, 37 tRNA, and 8 rRNA. Phylogenetic analysis supported that B. daigremontianum was closer to K. tomentosa than other species, which showed that chloroplast genome sequences offer a useful resource for future phylogenetic studies of Kalanchoe and Bryophyllum species.
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Project description:The complete chloroplast genome sequence of Phedimus kamtschaticus, which commonly occurs in northeastern Asia was determined. The genome size was 151,652?bp, composed of one pair of inverted repeats (IRs) of 25,977?bp, which were separated by one large single-copy (LSC; 83,010?bp) and one small single-copy (SSC; 16,688?bp) region. The chloroplast genome contained 132 genes, including 88 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content was 37.8%. Phylogenetic analysis of the complete chloroplast genome suggested that P. kamtschaticus was most closely related to Ulleung Island insular endemic P. takesimensis.
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Project description:Sedum ichangensis sp. nov., from Yichang, Hubei province, central China, is described and illustrated. The new species is similar to S. elatinoides and S. rosthornianum in its leaf and carpel morphology and differs in its creeping stems and solitary flowers. The conservation status of S. ichangensis was assessed as Endangered according to the IUCN Red List criteria.
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Project description:Recent years have seen increasing interest in indirect genetic effects, i.e. influences on the phenotype that depend on the genotype of other conspecific individuals; however, the empirical evidence for such effects is still limited, especially in wild plant species. The present study of the clonal herb Sedum album assessed direct and indirect genetic effects on performance-related traits in a 4-year experiment with clonally replicated genotypes, grown in pairs and differing in anthocyanin pigmentation to allow separation of individuals during data collection. In agreement with the existence of indirect genetic effects, the experimentally-paired plants not only expressed their own genotype but were also affected by the genotype of their pair mate. The effect of neighbour genotype explained up to one-fourth of the variation in performance and most likely resulted from competition, imposed by the close physical contact between paired individuals and the limiting conditions used in the garden environment. Indirect genetic effects from competition have the potential to enhance the efficacy of group-level selection relative to individual selection, given the nutrient-poor and spatially-confined substrate available to plants of S. album in the natural habitat.
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Project description:Main conclusionOur study demonstrated that symplasmic communication between Sedum acre seed compartments and the embryo proper is not uniform. The presence of plasmodesmata (PD) constitutes the structural basis for information exchange between cells, and symplasmic communication is involved in the regulation of cell differentiation and plant development. Most recent studies concerning an analysis of symplasmic communication between seed compartments and the embryo have been predominantly performed on Arabidopsis thaliana. The results presented in this paper describe the analysis of symplasmic communication on the example of Sedum acre seeds, because the ultrastructure of the seed compartments and the embryo proper, including the PD, have already been described, and this species represents an embryonic type of development different to Arabidopsis. Moreover, in this species, an unusual electron-dense dome associated with plasmodesmata on the border between the basal cell/chalazal suspensor cells and the basal cell/the endosperm has been described. This prompted the question as to whether these plasmodesmata are functional. Thus, the aim of this study was to describe the movement of symplasmic transport fluorochromes between different Sedum seed compartments, with particular emphasis on the movement between the basal cell and the embryo proper and endosperm, to answer the following questions: (1) are seeds divided into symplasmic domains; (2) if so, are they stable or do they change with the development? The results have shown that symplasmic tracers movement: (a) from the external integument to internal integument is restricted; (b) from the basal cell to the other part of the embryo proper and from the basal cell to the endosperm is also restricted;
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Project description:Crassulaceae are the largest family in the angiosperm order Saxifragales. Species of this family are characterized by succulent leaves and a unique photosynthetic pathway known as Crassulacean acid metabolism (CAM). Although the inter- and intrageneric relationships have been extensively studied over the last few decades, the infrafamilial relationships of Crassulaceae remain partially obscured. Here, we report nine newly sequenced chloroplast genomes, which comprise several key lineages of Crassulaceae. Our comparative analyses and positive selection analyses of Crassulaceae species indicate that the overall gene organization and function of the chloroplast genome are highly conserved across the family. No positively selected gene was statistically supported in Crassulaceae lineage using likelihood ratio test (LRT) based on branch-site models. Among the three subfamilies of Crassulaceae, our phylogenetic analyses of chloroplast protein-coding genes support Crassuloideae as sister to Kalanchoideae plus Sempervivoideae. Furthermore, within Sempervivoideae, our analyses unambiguously resolved five clades that are successively sister lineages, i.e., Telephium clade, Sempervivum clade, Aeonium clade, Leucosedum clade, and Acre clade. Overall, this study enhances our understanding of the infrafamilial relationships and the conservation of chloroplast genomes within Crassulaceae.
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Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads
| PRJNA723268 | ENA