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The complete chloroplast genome of Petunia exserta (Solanaceae: Petunioideae), an endangered ornamental species.

ABSTRACT: Petunia exserta is an ornamental species on the brink of extinction in the wild. We report here the complete chloroplast genome of P. exserta, which is 156,598 bp in size consisting of a large single-copy region (87,095 bp), a small single-copy region (18,643 bp), and a pair of inverted repeats (25,430 bp for each). The chloroplast (used 'cp' hereafter) genome contains 132 genes, including 8 rRNA genes, 37 tRNA genes, and 87 protein-coding genes. Phylogenetic analysis demonstrated that P. exserta was most closely related to P. hybrida, and they together were closer to Calibrachoa hybrida than other taxa in the Solanaceae family.

SUBMITTER: Sun M

PROVIDER: S-EPMC8366615 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Platycerium wallichii (Polypodiaceae), an endangered and ornamental fern species.

Project description:The complete chloroplast genome of a staghorn fern species (Platycerium wallichii) was sequenced. The total genome was 158,286 bp in length, containing four regions: large single-copy (LSC) region (79,087 bp), small single-copy (SSC) region (21,397 bp), and two inverted repeat regions (IRs; 28,901 bp per each). In total 129 genes were annotated including 88 coding genes, 33 tRNAs, and 8 rRNAs. The overall GC content of the genome is 40.5%. Phylogenetic analysis supported the monophyly of both the subfamily Platycerioideae and the genus Platycerium. The genome data provides crucial information to support the future conservation and horticulture research.

| S-EPMC8276651 | biostudies-literature

The complete chloroplast genome sequence of a popular ornamental plant Calibrachoa hybrida (Solanaceae: Petunioideae).

Project description:Calibrachoa hybrida is a popular ornamental plant with colorful flowers. We present here the complete chloroplast genome sequence of C. hybrida. With a total length of 156,099 bp, it is comprised of a large single-copy (LSC) region of 86,695 bp and a small single-copy (SSC) region of 18,694 bp separated by two inverted repeats (IRs) of 25,355 bp for each. A total of 132 genes were identified, consisting of 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis using complete chloroplast genomes clustered C. hybrida together with petunia into the subfamily Petunioideae within the family Solanaceae.

| S-EPMC7781906 | biostudies-literature

Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species.

Project description:BackgroundPhoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus.ResultsWe sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. We also performed comparative analyses with the cp genomes of P. sheareri and P. sheareri var. oineiensis previously reported. The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively. From the two chloroplast genomes, 131 SSRs were identified and 12 different SSRs located in five protein coding genes. The analysis showed the extremely conserved structure of chloroplast genomes with surprisingly little variations at the LSC/IR and SSC/IR boundaries. Moreover, the mean nucleotide diversity was found to be 0.162% for 77 regions, suggesting an extraordinarily low level of sequence divergence. Four highest divergent regions (trnH-psbA, rps14-trnT, petA-psbJ, ccsA-ndhD) with the percentage of nucleotide diversity higher than 0.50% were identified, which had potential use for species identification and phylogenetic studies.ConclusionThis study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.

| S-EPMC5597560 | biostudies-literature

The complete chloroplast genome of Primula bulleyana, a popular ornamental species.

Project description:Primula bulleyana is a popular ornamental species, with high commercial values. Here, we reported the first chloroplast genome of P. bulleyana. The complete chloroplast genome is 150978 bp, containing a large single-copy (LSC) region of 82873 bp, a small single-copy (SSC) region of 17,741 bp, and a pair of inverted repeats (IRs) regions of 25,182 bp. In total, there are 142 genes, 92 protein-coding genes, 8 rRNA genes, and 38 tRNA genes are annotated in the whole cp genome, including 119 unique genes, 82 unique CDSs, 29 unique tRNAs, and 4 unique rRNAs. The overall GC content of the cp genome is 37.1%. The phylogenetic tree shows that close relationships among P. bulleyana and Primula stenodonta.

| S-EPMC7707575 | biostudies-literature

The complete chloroplast genome sequences of two ornamental Epimedium species (Berberidaceae).

Project description:Both Epimedium sutchuenense Franch. 1894 and E. fargesii Franch. 1894 are perennial herbs with excellent ornamental values due to their showy flowers. However, little molecular research has been done on these species. Here, the complete chloroplast (cp) genome of E. sutchuenense and E. fargesii was analyzed and reported. The cp genome sizes of E. sutchuenense and E. fargesii were 157, 263 and 157, 133 bp, respectively. Both the two cp genomes contained a pair of inverted repeat regions (IRs) (25,782 and 25,796 bp), separated by the small single-copy (SSC) region (17,106 and 17,071 bp) and a large single-copy (LSC) region (88,593 and 88,470 bp). A total of 113 unique genes were annotated in each of the two cp genomes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis supported a close relationship between E. sutchuenense and E. wushanense, while E. fargesii had no clear clustering branch.

| S-EPMC9176344 | biostudies-literature

Characterization of the complete chloroplast genome of an endangered ornamental and medicinal plant Lilium pumilum.

Project description:Lilium pumilum DC. is a useful plant species not only for its showy flowers but also for its edible and medicinal values. Here we report on the complete chloroplast genome sequence of L. pumilum. The chloroplast genome is 152,573 bp in size and includes two inverted repeat regions of 52,984 bp, which is separated by a large single-copy region of 82,009 bp and a small single copy region of 17,580 bp. A total of 130 genes were predicted, including 38 tRNA, 8 rRNA, and 84 protein-coding genes. Phylogenetic analysis placed L. pumilum under the family Liliaceae.

| S-EPMC7748673 | biostudies-literature

The complete chloroplast genome of Capsicum frutescens (Solanaceae).

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

Comparison of Four Complete Chloroplast Genomes of Medicinal and Ornamental Meconopsis Species: Genome Organization and Species Discrimination.

Project description:High-throughput sequencing of chloroplast genomes has been used to gain insight into the evolutionary relationships of plant species. In this study, we sequenced the complete chloroplast genomes of four species in the Meconopsis genus: M. racemosa, M. integrifolia (Maxim.) Franch, M. horridula and M. punicea. These plants grow in the wild and are recognized as having important medicinal and ornamental applications. The sequencing results showed that the size of the Meconopsis chloroplast genome ranges from 151864 to 153816 bp. A total of 127 genes comprising 90 protein-coding genes, 37 tRNA genes and 8 rRNA genes were observed in all four chloroplast genomes. Comparative analysis of the four chloroplast genomes revealed five hotspot regions (matK, rpoC2, petA, ndhF, and ycf1), which could potentially be used as unique molecular markers for species identification. In addition, the ycf1 gene may also be used as an effective molecular marker to distinguish Papaveraceae and determine the evolutionary relationships among plant species in the Papaveraceae family. Futhermore, these four genomes can provide valuable genetic information for other related studies.

| S-EPMC6646306 | biostudies-literature

Complete chloroplast genome of Lycium ferocissimum (Solanaceae), a species native to South Africa.

Project description:Lycium ferocissimum, known as African boxthorn or boxthorn, is a shrub in the Solanaceae family. In this study, we characterized the complete chloroplast (cp) genome sequence of L. ferocissimum using genome skimming data. It had a circular mapping molecular with the length of 155,894 bp, with a large single-copy region (LSC, 86,536 bp) and a small single-copy region (SSC, 18,406 bp) separated by a pair of inverted repeats (IRs, 25,476 bp). The cp genome encodes 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 20 duplicated genes in the IR regions. The phylogenetic analysis indicated that L. ferocissimum is sister to the other three Lycium species.

| S-EPMC7748727 | biostudies-literature

The complete chloroplast genome of an endangered species Cymbidium mastersii (Orchidaceae).

Project description:Cymbidium mastersii Griff. & Lindl. is an endangered orchid. In this study, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. mastersii. The cp genome sequence of C. mastersii was 155,362?bp in length. It included one large single-copy region (LSC, 84,465?bp), one small single-copy region (SSC, 20,647?bp), and two inverted repeat regions (IRs, 25,125?bp). The cp genome encoded 130 genes, of which 107 were unique genes (80 protein-coding genes, 23 tRNAs, and 4 rRNAs). The maximum-likelihood phylogenetic analysis showed that C. mastersii was a sister of C. erythraeum and C. nanulum.

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