The complete chloroplast genome of Syzygium acuminatissimum.
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ABSTRACT:
SUBMITTER: Zeng F
PROVIDER: S-EPMC7819109 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Syzygium nervosum A.Cunn. ex DC (also named as Cleistocalyx operculatus) is a member of genus Syzygium mainly distributed in China, Vietnam and some other tropical countries and belongs the family of Myrtaceae. Syzygium nervosum is a popular medicinal plant, some species of genus Syzygium have been used in folk medicine. In this study, we sequenced the sample of Syzygium nervosum and determined its complete chloroplast genome. The complete chloroplast genome of Syzygium nervosum is 158,979 bp in length, and contained a large single copy (LSC) with 88,099 bp in length, a small single copy (SSC) with 18,756 bp in length and two inverted repeat (IR) regions of 26,062 bp each. It includes 85 protein coding genes, 8 rRNA and 37 tRNA, and 37% overall GC content. Each of trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC and ndhA genes contain an intron, the gene clpP and ycf3 contain 2 introns. The phylogenetic position shows that Syzygium nervosum has the closest relationship with Syzygium aromaticum.
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Project description:Syzygium malaccense is native to Malaysia. It is sometimes called the malay apple, malay rose-apple, mountain rose-apple, mountain apple, water apple, or French cashew. The tree is very popular in many tropical and subtropical regions for its fruit and traditional medicine. The first complete chloroplast genome of Syzygium malaccense has been reported in this study. The complete chloroplast genome of Syzygium malaccense is 158,954 bp, composed of four regions: a large single-copy region with a size of 87,991 bp, a small single copy region with a size of 18,793 bp, and two inverted repeat regions with a size of 26,085 bp. The GC content is 36.97%. A total of 132 genes were annotated, including 84 encoding proteins, eight encoding rRNA genes, 37 encoding tRNA genes, and three encoding pseudo genes. Phylogenetic analysis showed that Syzygium aromaticum, Syzygium cumini, and Syzygium forrestii are closely related to Syzygium malaccense.
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Project description:Plants in the genus Syzygium have been widely used as traditional medicine, fruit crops, and ornamental trees. In this study, we reported the complete chloroplast genome of Syzygium jambos (L.) Alston which was known as rose apple. The chloroplast genome of this species is 158541 bp in length, including a pair of inverted repeat regions (IRs) (26076 bp) that is divided by a large single copy area (LSC) (88036 bp) and a small single copy area (SSC) (18353 bp). The circular chloroplast genome of S. jambos contains 132 unique genes, composing of 85 protein-coding genes, 39 tRNA genes and 8 rRNA genes. Phylogenetic analysis indicates that S. jambos is clustered with species in genus Syzygium. This complete chloroplast genome of S. jambos will provide a powerful tool to accelerate breeding, biotechnological and phylogenetic study.
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Project description:Syzygium samarangense (Blume) Merr. et Perry, 1938, commonly known as wax apple, is a Myrtaceae species that is known for its unique fruit shape, flavorful and colorful fruits, medicinal value and increasing economic relevance. In this study, we reported the complete chloroplast genome sequence of S. samarangense. The complete genome is 159,109 bp in length with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,155 bp) and a Small Single Copy region (SSC, 18,796 bp) separated by Inverted Repeat regions (IRs, 26,079 bp). The GC content was 37.0%. It encoded 126 genes, including 81 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The phylogenetic relationships of 20 species inferred that all Syzygium species formed a single cluster belonging to Syzygieae tribe. Our results offer insights into the evolutionary relationship of S. samarangense within Myrtaceae, indicating a closer relationship between S. samarangense and S. forrestii.
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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.
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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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