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The complete chloroplast genome of Petasites japonicus (Siebold & Zucc.) Maxim. (Asteraceae).

ABSTRACT: The complete chloroplast (cp) genome sequence of Petasites japonicus (Asteraceae) was determined. The cp genome is 150,445 bp and consists of a large single-copy region (82,910 bp), a small single-copy region (17,907 bp), and a pair of inverted repeats (24,814 bp). It encodes a set of 114 genes, consisting of 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic inference confirmed that P. japonicus is sister to the genus Ligularia in the tribe Senecioneae of Asteraceae.

SUBMITTER: Hashimoto T

PROVIDER: S-EPMC8635567 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of Xylosma racemosa (Siebold & Zucc.) Miq. (Salicaceae).

Project description:Xylosma racemosa (Siebold & Zucc.) Miq. which plays an important role in ecology, medicine and economy, is a deciduous species of Salicaceae. In this paper, we sequenced, assembled, and annotated the chloroplast (cp) genome of X. racemosa (Siebold & Zucc.) Miq. by using the sequencing data from Illumina Novaseq platform. The complete cp genome of X. racemosa is 157,262 bp in length, containing a large single-copy (LSC) region of 84,289 bp, and a small single-copy (SSC) region of 17,817 bp. It contains 131 genes, including 8 rRNA genes, 37 tRNAs genes and 86 protein-coding genes. The GC content of X. racemosa cp genome is 36.74%. The phylogenetic analysis suggests that X. racemosa is a sister species to Xylosma congesta in Salicaceae.

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The complete chloroplast genome of Alniaria alnifolia (Siebold and Zucc.) Rushforth, 2018.

Project description:Alniaria alnifolia (Siebold and Zucc.) Rushforth, 2018 (alternative name: Sorbus alnifolia) belongs to the genus Alniaria of the family Rosaceae and is widely distributed in northern China, Korea, and Japan. It is an essential resource used in the construction, pharmaceuticals, and food industries. It is also used to treat various diseases, such as fever, hyperglycemia, rash, asthma, bronchitis, constipation, leprosy, anemia, and other skin ailments. In this study, we sequenced a sample of A. alnifolia and determined its complete chloroplast genome. The chloroplast genome of A. alnifolia has a circular structure with a length of 159,855 bp, which includes a small single-copy region (19,409 bp), a large single-copy region (87,628 bp), and two inverted repeats (26,409 bp). The sequence had 130 genes, including 85 protein-coding genes, eight rRNA genes, and 37 tRNA genes, and the overall GC content was 36.6%. The genes trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC, and ndhA contained one intron; genes clpP and ycf3 contained two introns. Phylogenetic results showed that A. alnifolia had the closest relationship with Sorbus folgneri (MK161058).

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The complete chloroplast genome of Elaeocarpus japonicus Sieb. et Zucc. (Elaeocarpaceae).

Project description:The complete chloroplast genome of Elaeocarpus japonicus Sieb. et Zucc. was reported in this study. The cp genome was 157,639 bp in length including two inverted repeats (IRs) of 27,437 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 85,784 bp and 16,981 bp, respectively. The GC content was 37.2%. The genome encoded 111 functional genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic tree showed that E. japonicus representing Elaeocarpaceae is sister to Averrhoa carambola representing Oxalidaceae with strong support.

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The complete chloroplast genome of Saussurea medusa maxim. (Asteraceae), an alpine Tibetan herb.

Project description:Saussurea medusa is an important traditional Tibetan medicinal plant in China. In this study, we assembled the complete chloroplast (cp) genome of S. medusa. The complete S. medusa chloroplast genome is a circular molecular structure of 152,257 bp in length with coding GC 37.93%, consisting of two inverted repeats (25,204 bp) separated by a large single-copy region (83,334 bp) and a small single-copy region (18,515 bp). The complete chloroplast genome of S. medusa contained 130 genes, including 87 protein-coding genes, 35 tRNA genes, and eight rRNA genes. Phylogenetic analysis shows that S. medusa is most closely related to Saussurea inversa and Saussurea pseudoleucoma. The complete chloroplast genome sequence of S. medusa facilitates the phylogenetic studies of Asteraceae.

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The complete chloroplast genome sequence of Berchemia racemosa Siebold & Zucc. (Rhamnaceae), a rare plant species in Korea.

Project description:Berchemia racemosa Siebold & Zucc., 1845 is a rare species distributed in restricted areas in the western Korean peninsula. In this study, the complete chloroplast genome (plastome) of B. racemosa was sequenced and assembled by Illumina paired-end sequencing. The plastome of B. racemosa was 161,187 bp in length and was quadripartite in structure, including a large single-copy (LSC) region of 89,503 bp, a small single-copy (SSC) region of 18,214 bp, and two inverted repeats of 26,735 bp. The GC content was 37.2%. The plastome of B. racemosa contains 130 genes, including eight ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and 85 protein-coding genes. Phylogenetic analysis using complete genome sequences showed that B. racemosa is most closely related to Berchemia flavescens.

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The complete chloroplast genome of Epimedium sagittatum (Sieb. Et Zucc.) Maxim. (Berberidaceae), a traditional Chinese herb.

Project description:Epimedium sagittatum is an important traditional medicinal plant in China. In this study, we assembled the complete chloroplast (cp) genome of E. sagittatum. The whole cp genome of E. sagittatum is 157,114?bp in length, comprising a pair of inverted repeat (IR) regions (25,775?bp) separated by a large single copy (LSC) region (88,507?bp) and a small single copy (SSC) region (17,057?bp). The E. sagittatum cp genome contains 133 genes, of which 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 5 pseudogenes. Phylogenetic analysis shows that E. sagittatumis closely clustered with E. lishihchenii. This genome provides a wealth of information for distinguishing of Epimedium species.

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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.

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The complete chloroplast genome of Rhamnus crenata Siebold & Zuccarini (Rhamnaceae).

Project description:Rhamnus crenata Siebold & Zuccarini is deciduous shrub or small tree plant that widely distributed in temperate and tropical regions of East to Southeast Asia. It has a chloroplast genome structure similar to that of other species of Rhamnus. It is 160,454 bp in size, including a large single-copy (LSC) region of 88,884 bp, a small single-copy (SSC) region of 18,734 bp and a pair of inverted repeats (IRs) of 26,418 bp. A total of 122 genes were annotated, including 80 protein-coding genes, 38 transfer RNA (tRNA) genes, and 4 rRNA genes. The overall GC content is 30.71%. Phylogenetic analysis shows that R. crenata is clustered with R. taquetii and R. globosa.

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The complete chloroplast genome of Spiraea mongolica Maxim.

Project description:The complete chloroplast genome of Spirea mongolica Maxim. was sequenced and assembled. It is a circular form of 155949 bp in length, which was separated into four distinct regions, a large single copy (LSC) of 84375 bp, a small single copy region (SSC) of 18894 bp, two inverted repeats (IR) of 26340 bp. After annotation, a total of 115 genes were predicted, of which, 70 encode proteins, 8 rRNA, 37 tRNA. The evolutionary history, inferred using Neighbour-Joining method, indicates that S. mongolica was grouped within Rosaceae, and comprised a clade with Spirea blumei G.Don, another species in Spirea, with 100% BS value.

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The complete chloroplast genome of Castanea crenata Sieb. & Zucc.

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