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The re-sequencing of complete chloroplast genome of Cinnamomum camphora (Lauraceae) from Quanzhou, China.

ABSTRACT: Cinnamomum camphora is a precious species for its significance of timber. It is also the main component of the subtropical evergreen broad-leaved forest. We report a chloroplast genome of C. camphora from Quanzhou, China. The complete chloroplast genome is 152,730 bp in length consisting of a pair of inverted repeat (IR) regions of 19,968 bp, a small single-copy (SSC) region of 18,874 bp, and a large single-copy (LSC) region of 93,706 bp, respectively. The chloroplast genome encoded 116 genes, including 79 protein-coding genes, 36 tRNA genes, and eight rRNA genes. This result will provide useful genomic basis for the phylogenetic research of Lauraceae.

SUBMITTER: Qiu MY

PROVIDER: S-EPMC7748760 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species.

Project description:Cinnamomum camphora, a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized as herbal medicines and essential oils. Here, we reported the complete sequencing of the chloroplast genome of Cinnamomum camphora using illumina technology. The chloroplast genome of Cinnamomum camphora is 152,570 bp in length and characterized by a relatively conserved quadripartite structure containing a large single copy region of 93,705 bp, a small single copy region of 19,093 bp and two inverted repeat (IR) regions of 19,886 bp. Overall, the genome contained 123 coding regions, of which 15 were repeated in the IR regions. An analysis of chloroplast sequence divergence revealed that the small single copy region was highly variable among the different genera in the Lauraceae family. A total of 40 repeat structures and 83 simple sequence repeats were detected in both the coding and non-coding regions. A phylogenetic analysis indicated that Calycanthus is most closely related to Lauraceae, both being members of Laurales, which forms a sister group to Magnoliids. The complete sequence of the chloroplast of Cinnamomum camphora will aid in in-depth taxonomical studies of the Lauraceae family in the future. The genetic sequence information will also have valuable applications for chloroplast genetic engineering.

| S-EPMC5609524 | biostudies-literature

The complete chloroplast genome of Cinnamomum camphora (L.) Presl., a unique economic plant to China.

Project description:Cinnamomum camphora (Lauraceae) Presl. is a unique economic plant to China. The complete chloroplast (cp) genome was sequenced and assembled by using Illumina paired-end reads data. The circular cp genome is 152,729 bp in size, including a pair of inverted repeat (IRs) regions of 20,074 bp, a large single copy (LSC) region of 93,688 bp and a small single copy (SSC) region of 18,893 bp. The genome contains 127 unique genes, including 83 protein-coding genes (PCGs), 36 transfer RNA genes (tRNAs), and 8 ribosomal RNA genes (rRNAs). Besides, 19 genes possess a single intron, while another three genes (ycf3, rps12, and clpP) have a couple of introns. The GC content of entire C. camphora cp genome, LSC, SSC, and IR regions are 39.2, 38.0, 33.9, and 44.4%, respectively. Phylogenetic analysis based on the concatenated coding sequences of cp PCGs showed that C. camphora and Cinnamomum verum are closely related with each other within the genus of cinnamomum.

| S-EPMC7687621 | biostudies-literature

The complete chloroplast genome of Cinnamomum pittosporoides reveals its phylogenetic relationship in Lauraceae.

Project description:Cinnamomum pittosporoides is an important timber plant endemic to southwest of China. In the present study, we sequenced the complete chloroplast genome of C. pittosporoides and used the data to reveal the species phylogenetic in Lauraceae. The complete chloroplast genome showed a circular genome of 152,730?bp size with 39.2% GC content. The genome is of typical structure and contains a pair of inverted repeat (IR) regions with 20,074?bp, separated by one large single-copy (LSC) with 93,722?bp and one small single-copy (SSC) regions with 18,860?bp. The genome contained 116 genes, including 82 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A phylogenetic tree reconstructed based on 26 chloroplast genomes reveals that C. pittosporoides is most related with C. chago in Lauraceae.

| S-EPMC7707191 | biostudies-literature

The complete chloroplast genome sequence of Cinnamomum septentrionale (Lauraceae) from Sichuan Province, China, a medicinal plant and phylogenetic analysis.

Project description:Cinnamomum septentrionale is a commercially important timber tree and wild spice plant classified in the Lauraceae. Here we sequenced the complete plastid genome of C. septentrionale to contribute to its phylogenetics and bioinformatics. The chloroplast genome of C. septentrionale is 152,729 bp in length and includes a large single copy (LSC) region of 93,639 bp, a small single copy (SSC) region of 18,858 bp, and two inverted repeat (IR) regions of 20,114 bp. The GC content of LSC, SSC, IR and the whole genome is 37.9%, 33.8%, 44.4%, and 39.1%, respectively. There are 128 genes, including 84 protein-coding, 36 tRNA, and eight rRNA genes. The phylogenetic analysis resolved C. septentrionale in a sister position to C. glanduliferum. The complete chloroplast genome sequence of C. septentrionale provides valuable genomic information for future systematic studies on Cinnamomum.

| S-EPMC8386741 | biostudies-literature

The chloroplast genome of aromatic plants Cinnamomum burmanni (Lauraceae).

Project description:Cinnamomum burmanni (Nees et T. Nees) Blume is a valuable aromatic timber tree of the genus Cinnamomum Tree in the family Lauraceae. To better determine its phylogenetic location with respect to the other Cinnamomum species, the complete chloroplast genome of C. burmanni was sequenced. The total chloroplast genome size is 152,775 bp, consisting of a pair of inverted repeats (IRa/b) with a length of 20,092 bp separated by a large single-copy region (LSC) and a small single-copy region (SSC) which are 93,687 and 18,903 bp, respectively. The overall GC content of the cp genome is 39.1%. Further, maximum-likelihood phylogenetic analysis with K3Pu + F+I model was performed using eleven complete plastomes of the Lauraceae, which revealed that C. burmanni is closely related to C. verum.

| S-EPMC7707236 | biostudies-literature

The re-sequencing and re-assembly of complete chloroplast genome of Melastoma dodecandrum (Melastomataceae) from Fujian, China.

Project description:The plant genus Melastoma of the family Melastomataceae is comprised of nine species and one variety in China. Melastoma dodecandrum is the only creeping species of this genus. Previous study has reported the complete chloroplast genome of M. dodecandrum from Guangzhou, China, but there may be some differences between plant populations from different regions. Herein, we reported the complete chloroplast genome of M. dodecandrum from Fuzhou, China, which was assembled from Pacbio and whole genome data was sequenced. The sequence has a circular molecular length of 156,598?bp and contained 129 genes. Phylogenetic analysis indicated that M. dodecandrum was closely related to M. candidum in Melastomataceae. The study aims to provide insights for the future studies on the differences in molecular evolution level between plant populations of M. dodecandrum and taxonomy of Melastoma.

| S-EPMC7687374 | biostudies-literature

The complete plastid genome of Chinese cinnamon, Cinnamomum aromaticum Nees (Lauraceae).

Project description:Cinnamomum aromaticum has long been recognized and cultivated in tropical and subtropical Asia for their aromatic bark to produce cinnamon. We reported for the first time the complete plastid genome of C. aromaticum and reconstructed its phylogenetic position. The complete plastid genome is 152,754 bp in length with a quadripartite organization: a large single copy (LSC) region of 93,706 bp and a small single copy (SSC) region of 18,916 bp. Each of the two inverted repeat regions (IRa and IRb) is 20,066 bp. We recovered 128 functional genes, including 84 protein-coding genes, 36 tRNA genes and 8 rRNA genes. The phylogenetic analysis suggested that C. aromaticum and two samples of C. camphora forms a strongly supported clade, which is sister to another cinnamon species of C. verum native to Sri Lanka with strong ultrafast bootstrap support.

| S-EPMC7707532 | biostudies-literature

Characterization of the chloroplast genome of the family Lauraceae plant species, Cinnamomum cassia.

Project description:The fruit of Cinnamomum cassia is an important spice material and its branch is a common Chinese herbal medicine as the family Lauraceae. In this study, we reported the complete chloroplast genome of C. cassia. The chloroplast genome of C. cassia with length of 152,675?bp is a characteristic quadripartite structure. The length of the inverted-repeats regions (IRs), large single-copy (LSC) region, and small single-copy (SSC) region of C. cassia was 20,068?bp, 93,663 and 18,876?bp. The chloroplast genome of C. cassia contains 124 genes, which includes 80 protein-coding genes (PCGs), 36 transfer RNA genes (tRNAs) and 8 ribosomal RNA genes (rRNAs). The overall nucleotide content of the chloroplast genome: 30.0% A (Adenine), 30.8% T (Thymine), 19.7% C (Cytosine), 19.5% G (Guanine), and 39.2% GC content. Evolutionary relationship result showed that Cinnamomum cassia was most closely related to Cinnamomum parthenoxylon in the family Lauraceae by the Neighbor-Joining (NJ) method.

| S-EPMC7707686 | biostudies-literature

The complete chloroplast genome sequence of China Lindera praecox (Lauraceae) and intra-species diversity.

Project description:Lindera praecox is a signature composition in the broadleaved deciduous forest of East China and Japan. Presently, the complete chloroplast (cp) genome of this species was sequenced, assembled, and annotated. It is 152,818 bp in length and encodes 85 protein-coding genes, 36 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated intraspecific varieties within L. praecox species collected in China and Japan. This chloroplast genome sequencing offers genetic background for resources conservation and phylogenetic studies.

| S-EPMC8253210 | biostudies-literature

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

Project description:BACKGROUND:Phoebe (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. RESULTS:We 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. CONCLUSION:This study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.

| S-EPMC5597560 | biostudies-literature

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