Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Cuscuta pentagona Engelm.

ABSTRACT: Cuscuta pentagona is a parasitic plant whose seeds are often mixed with the seeds of medicinal Cuscuta species. To facilitate the identification of C. pentagona seeds, we generated the complete chloroplast genome sequence of C. pentagona Engelm. using the Illumina MiSeq platform. The complete chloroplast genome is 86,380?bp long, with a 50,958?bp LSC region, a 7022?bp SSC region, and two inverted repeat (IRa and IRb) regions comprising 14,200?bp. The chloroplast genome consists of 85 unique genes, 57 protein-coding genes, four ribosomal RNA (rRNA) genes, and 24 transfer RNA (tRNA) genes. Two gene families, NADH oxidoreductases and RNA polymerase-related genes, are absent in this genome. Phylogenetic analysis revealed that C. pentagona is closely related to C. reflexa and C. exaltata, with strong support values.

SUBMITTER: Park I

PROVIDER: S-EPMC7800224 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Cuscuta pentagona Engelm.

Park Inkyu I Yang Sungyu S Kim Wook Jin WJ Noh Pureum P Lee Hyun Oh HO Moon Byeong Cheol BC

Mitochondrial DNA. Part B, Resources 20180426 2

Cuscuta pentagona is a parasitic plant whose seeds are often mixed with the seeds of medicinal Cuscuta species. To facilitate the identification of C. pentagona seeds, we generated the complete chloroplast genome sequence of C. pentagona Engelm. using the Illumina MiSeq platform. The complete chloroplast genome is 86,380 bp long, with a 50,958 bp LSC region, a 7022 bp SSC region, and two inverted repeat (IRa and IRb) regions comprising 14,200 bp. The chloroplast genom ...[more]

PMID: 33474226

Similar Datasets

Complete chloroplast genomes of five Cuscuta species and their evolutionary significance in the Cuscuta genus.

Project description:BackgroundCuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast (cp) genome in Cuscuta species and their relationship with subgenera or sections, thus, providing important information on the evolution of Cuscuta species.ResultsIn the present study, we identified the whole cp genomes of C. epithymum, C. europaea, C. gronovii, C. chinensis and C. japonica, and then constructed a phylogenetic tree of 23 Cuscuta species based on the complete genome sequences and protein-coding genes. The complete cp genome sequences of C. epithymum and C. europaea were 96,292 and 97,661 bp long, respectively, and lacked an inverted repeat region. Most cp genomes of Cuscuta spp. have tetragonal and circular structures except for C. epithymum, C. europaea, C. pedicellata and C. approximata. Based on the number of genes and the structure of cp genome and the patterns of gene reduction, we found that C. epithymum and C. europaea belonged to subgenus Cuscuta. Most of the cp genomes of the 23 Cuscuta species had single nucleotide repeats of A and T. The inverted repeat region boundaries among species were similar in the same subgenera. Several cp genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh, rpo, psa, psb, pet, and rbcL), which could have gradually caused the plants to lose the ability to photosynthesize.ConclusionOur results enrich the data on cp. genomes of genus Cuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the cp genome of Cuscuta species.

| S-EPMC10251547 | biostudies-literature

Cuscuta Species Identification Based on the Morphology of Reproductive Organs and Complete Chloroplast Genome Sequences.

Project description:The genus Cuscuta (Convolvulaceae) comprises well-known parasitic plants. Cuscuta species are scientifically valuable, as their life style causes extensive crop damage. Furthermore, dried seeds of C. chinensis are used as a Korean traditional herbal medicine. Despite the importance of Cuscuta species, it is difficult to distinguish these plants by the naked eye. Moreover, plastid sequence information available for Cuscuta species is limited. In this study, we distinguished between C. chinensis and C. japonica using morphological characterisation of reproductive organs and molecular characterisation of chloroplast genomes. The differences in morphological characteristics of reproductive organs such as style, stigma, infrastaminal scale, seed shape and testa ornamentation were useful for distinguishing between C. japonica and C. chinensis. Analysis of chloroplast genomes revealed drastic differences in chloroplast genome length and gene order between the two species. Although both species showed numerous gene losses and genomic rearrangements, chloroplast genomes showed highly similar structure within subgenera. Phylogenetic analysis of Cuscuta chloroplast genomes revealed paraphyletic groups within subgenera Monogynella and Grammica, which is consistent with the APG IV system of classification. Our results provide useful information for the taxonomic, phylogenetic and evolutionary analysis of Cuscuta and accurate identification of herbal medicine.

| S-EPMC6600609 | biostudies-literature

Keteleeria cyclolepis complete chloroplast genome

Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads

| PRJNA723268 | ENA

Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales.

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.

| S-EPMC3799696 | biostudies-literature

The complete chloroplast genome of Agave angustifolia

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.

| S-EPMC8547807 | biostudies-literature

Complete chloroplast genome comparisons for Pityopsis (Asteraceae).

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

Complete chloroplast genome of Ophiorrhiza baviensis Drake

Project description:Ophiorrhiza baviensis chloroplast, complete genome

| PRJEB57743 | ENA

The complete chloroplast genome of solanum pimpinellifolium

Project description:The chloroplast genome were assembled and annotated for solanum pimpinellifolium

| PRJEB40533 | ENA

The complete chloroplast genome of Ormosia ferruginea

Project description:Chloroplast genome of Ormosia ferruginea

| PRJEB51808 | ENA

Primers for complete chloroplast genome sequencing in Magnolia.

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.

| S-EPMC6764489 | biostudies-literature