Complete chloroplast genome of Sphaeropteris brunoniana (Cyatheaceae).
Ontology highlight
ABSTRACT:
SUBMITTER: Zhu M
PROVIDER: S-EPMC7782704 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The chloroplast genome of the tree fern Alsophila podophylla has been completely sequenced. The genome is 166,151?bp in size and features a typical quadripartite structure with the large (LSC, 86,762?bp) and small single copy (SSC, 21,641?bp) regions separated by a pair of inverted repeats (IRs, 28,874?bp each). It encodes 133 genes including 91 protein-coding genes, 33 tRNA genes, eight rRNA genes, and one pseudogene. Maximum-likelihood tree indicates that A. podophylla is sister to A. spinulosa. This work provides a solid molecular resource for surveying phylogeny and chloroplast genomics of ferns.
| S-EPMC7800846 | biostudies-literature
Project description:Alsophila latebrosa is a common and widespread tree fern of Cyatheaceae. Its complete chloroplast genome is first assembled and reported with 155,724 bp in length, including a large single copy (LSC) region of 85,800 bp, a small single copy (SSC) region of 21,620 bp, and a pair of inverted repeats (IRs) of 24,152 bp. The genome has 133 genes, including 89 protein-coding genes, 33 tRNA genes, eight rRNA genes and three pseudogenes. Maximum likelihood approach was employed to construct the phylogenetic relationship among ten ferns including A. latebrosa. The result showed that A. latebrosa was most related to A. costularis as a sister group with 100% bootstrap support. The complete chloroplast genome sequences of A. latebrosa will provide valuable genomic information to further illuminate phylogenetic classification of Cyatheacea.
| S-EPMC8221145 | biostudies-literature
Project description:Abstract The simple sequence repeats (SSRs) of plant chloroplasts show considerable genetic variation and have been widely used in species identification and phylogenetic relationship determination. Whether chloroplast genome SSRs can be used to classify Cyatheaceae species has not yet been studied. Therefore, the chloroplast genomes of eight Cyatheaceae species were sequenced, and their SSR characteristics were compared and statistically analyzed. The results showed that the chloroplast genome structure was highly conserved (genome size: 154,046–166,151 bp), and the gene content (117 genes) and gene order were highly consistent. The distribution characteristics of SSRs (number, relative abundance, relative density, GC content) showed taxon specificity. The primary results were the total numbers of SSRs and mononucleotides: Gymnosphaera (61–67 and 40–47, respectively), Alsophila (121–122 and 95–96), and Sphaeropteris (102–103 and 77–80). Statistical and clustering analyses of SSR characteristics showed that their distribution was consistent with the recent classification of Cyatheaceae, which divided the eight Cyatheaceae species into three genera. This study indicates that the distribution characteristics of Cyatheaceae chloroplast SSRs can provide useful phylogenic information at the genus level. Whether chloroplast genome SSRs can be used to classify Cyatheaceae species has not yet been studied. Therefore, the chloroplast genomes of eight Cyatheaceae species were sequenced by our team, and their SSR characteristics were compared and statistically analyzed. Statistical and clustering analyses of SSR characteristics showed that their distribution was consistent with the recent classification of Cyatheaceae, which divided the eight Cyatheaceae species into three genera.
| S-EPMC8525152 | biostudies-literature
Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads
| PRJNA723268 | ENA
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
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
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.
| S-EPMC6764489 | biostudies-literature
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.
| S-EPMC4873274 | biostudies-literature
Project description:Disporum sessile roots are used as a medicinal herb. To ensure the accurate identification of D. sessile, we sequenced its chloroplast genome using the Illumina MiSeq platform. Results showed that the chloroplast genome of D. sessile is 159,102 bp in size, with a large single-copy (LSC) region (85,456 bp), a small single-copy (SSC) region (17,108 bp), and two inverted repeat (IR) regions (IRa and IRb; 28,269 bp each). Additionally, the chloroplast genome contains 112 unique genes, including 78 protein-coding, four ribosomal RNA, and 30 transfer RNA genes. Phylogenetic analysis revealed that D. sessile is most closely related to Colchicum autumnale.
| S-EPMC7748843 | biostudies-literature