The complete chloroplast genome of Waldheimia glabra.
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ABSTRACT:
SUBMITTER: Hai W
PROVIDER: S-EPMC8266245 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Bougainvillea glabra is one of the most popular ornamental and landscaping plants planted in tropical and subtropical regions. The brightly colored bracts, long florescence and strong stress resistance make B. glabra perfect ornamental horticulture plant. Bougainvillea plants have been frequently hybridized, resulting in more than 400 varieties. To investigate the chloroplast genome will help us to understand the biological diversity and stress resistance of Bougainvillea plants better. Here, we report the complete chloroplast genome of B. glabra, which is 154,542 bp in length, including a large single copy (LSC) region of 85,695 bp and a small single copy (SSC) region of 18,077 bp, separated by a pair of identical inverted repeat regions (IRs) of 25,385 bp each. A total of 128 genes were identified, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 12 chloroplast genomes showed that B. glabra, accompanied with its sister species B. spectabilis, formed a base clade in Nyctaginaceae which was close to Pisonia aculeata. This study will be helpful for better understanding of the genetic diversity and stress resistance of Bougainvillea plants.
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Project description:Potentilla glabra Lodd is an important traditional Chinese medicine, which is widely distributed in many areas of China. It has a variety of pharmacological activities and has been drunk as a tea for a long time. Therefore, it has great economic, research, and social value. However, no plastid genome has been reported to date. Here, we report species of this genus complete chloroplast genome of Potentilla glabra Lodd. The chloroplast genome of Potentilla glabra Lodd is found to be 152,900 bp in length with 37.24% GC contents. The cp genome sequences contained 130 genes, including 84 mRNA genes, 37 tRNA, eight rRNA genes, and one pseudogenes, respectively. A phylogenetic tree reconstructed by 42 chloroplast genomes reveals that Potentilla glabra Lodd is most related with Potentilla parvifolia. The complete chloroplast genome of these plants will be benefit for studies on the general characteristics and evolution of the Potentilla family genome.
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Project description:Sarcandra glabra is a perennial evergreen subshrub, with high ornamental and medicinal value. Using the Illumina high-throughput sequencing data, its chloroplast genome is well assembled and characterized. The complete chloroplast genome is 158,872 bp in length with a typical quadripartite structure: a pair of inverted repeats (IRs) of 26,122 bp for each, an 88,182 bp large single-copy (LSC) region and an 18,445 bp small single-copy (SSC) region. It was composed of 128 genes and they were identified 84 coding genes, 8 rRNA genes, 36 tRNA genes. Phylogenetic analysis confirmed that the position of S. glabra lay within the order Chloranthales instead of Piperales simply according to classical morphological taxonomy.
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Project description:Bougainvillea glabra is an ornamental plant that is domesticated in many tropical and sub-tropical countries. The focus on its breeding programmes has overshadowed genetic studies of this important species. In this study, we reported on the complete chloroplast (cp) genome of B. glabra. The cp genome is 154,763?bp in size, comprised of a large single copy (LSC) region of 85,921?bp, a small single copy (SSC) region of 18,018?bp, and a pair of inverted repeat (IR) regions of 25,412?bp each. A total of 131 genes were predicted, including 37 tRNA, 8 rRNA, and 86 protein-coding genes. Phylogenetic analysis revealed that B. glabra is placed under Nyctaginaceae and sister to B. spectabilis under a strong bootstrap support.
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Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads
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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:Abstract Agave angustifolia is commonly used for the production of bacanora, a kind of fermented and distilled beverage in Mexico. In the present study, we have successfully assembled its chloroplast genome. The full length of the genome is 157,274 bp with the GC content of 37.84%. There is a large single copy region (LSC) of 85,895 bp, a pair of inverted repeat regions (IR) of 26,575 bp and a small single copy region (SSC) of 18,229 bp in the genome. A total of 132 genes are annotated in the cp genome. Among these, there are 86 protein-coding genes, 38 tRNAs and 8 rRNAs. Phylogenetic analysis reveals that A. angustifolia is closely related with A. H11648.
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Project description:Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the result that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis.
| S-EPMC7769439 | biostudies-literature
Project description:Premise:A new set of primers was developed for sequencing of whole chloroplast genomes of Magnolia species and gap-filling of unfinished genomes. Methods and Results:Two hundred and fifty primers were newly designed based on two previously reported chloroplast genomes from two different genera in Magnoliaceae. A total of 134 primer pairs, including the ones developed in this study and 18 previously reported ones, were enough to cover the entire chloroplast genome sequences in Magnoliaceae. Four species from different sections of Magnolia (M. dealbata, M. fraseri var. pyramidata, M. liliiflora, and M. odora) were used to show the general application of these primers to chloroplast genome sequencing in Magnolia. Conclusions:Using the developed primers, four Magnolia chloroplast genomes were successfully assembled. These results show the utility of these primers across Magnolia and their potential use for phylogenetic studies, DNA barcoding, and population genetics in this group.
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Project description:PREMISE OF THE STUDY:We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper. METHODS AND RESULTS:Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792-bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single-copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions. CONCLUSIONS:The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species.
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