The complete chloroplast genome sequence of Camellia sinensis cv. Dahongpao: a most famous variety of Wuyi tea (Synonym: Thea bohea L.).
ABSTRACT: Here, combining PacBio and Illumina sequencing data, we reported the complete chloroplast genome of the first Wuyi tea (Bohea), Camellia sinensis cv. Dahongpao (DHP) with very high economic value. The chloroplast genome was 157,077?bp in length, with a large single copy (LSC) region of 86,633?bp, a small single-copy (SSC) region of 18,282?bp, separated by two inverted repeat (IR) regions of 26,081?bp each. It contained a total of 137 genes, with an overall GC content of 37.29%. The phylogenetic analysis showed that DHP was sister to C. sinensis cv. Longjing.
Project description:Flavonoids are a kind of essential substance for the human body because of their antioxidant properties and extremely high medicinal value. Citrus reticulata "Dahongpao" (DHP) is a special citrus variety that is rich in flavonoids, however little is known about its systematic flavonoids profile. In the present study, the presence of flavonoids in five important citrus varieties, including DHP, Citrus grandis Tomentosa (HZY), Citrus ichangensis Swingle (YCC), Citrus sinensis (L.) Osbeck (TC), and Citrus reticulata 'Buzhihuo' (BZH), was determined using a UPLC-ESI-MS/MS-based, widely targeted metabolome. Results showed that a total of 254 flavonoid metabolites (including 147 flavone, 39 flavonol, 21 flavanone, 24 anthocyanins, 8 isoflavone, and 15 polyphenol) were identified. The total flavonoid content of peels from DHP was the highest. DHP could be clearly separated from other samples through clustering analysis and principal component analysis (PCA). Further, 169 different flavonoid metabolites were observed between DHP peels and the other four citrus peels, and 26 down-regulated differential metabolites displayed important biological activities in DHP. At the same time, a unique flavonoid component, tricin 4'-O-syringyl alcohol, was only found in DHP, which could be used as a marker to distinguish between other varieties. This work might facilitate a better understanding of flavonoid metabolites between DHP peels and the other four citrus peels and provide a reference for its sufficient utilization in the future.
Project description:<i>Hosta plantaginea</i> is an important ornamental and horticultural plant endemic to China. In this study, we generated complete chloroplast genome of <i>H. plantaginea</i> using high-throughput sequencing. The complete chloroplast sequence is a circular molecule of 157,091?bp in size, consisting of a large single copy (LSC, 86,061?bp) and a small single copy (SSC; 18,282?bp) separated by a pair of inverted repeats (IRs; 26,374?bp), The total GC content is 37.8%, with 35.9, 31.7, and 43.0% in LSC, SSC, and IRs, respectively. A total of 132 genes are annotated, including 84 protein-coding genes, 38 tRNAs, 8 rRNAs, and 2 pseudogenes. The phylogenetic analysis revealed that <i>H. plantaginea</i> was formed to be the early diverging species within <i>Hosta</i>.
Project description:Tea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. In this study, we de novo assembled the chloroplast (cp) and mitochondrial (mt) genomes of C. sinensis var. assamica cv. Yunkang10 into a circular contig of 157,100?bp and two complete circular scaffolds (701719 bp and 177329 bp), respectively. We correspondingly annotated a total of 141 cp genes and 71 mt genes. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878?bp and 149?bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ~4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an important resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.
Project description:<i>Celtis sinensis</i> Pers. is a popular garden landscape tree in riparian areas and a valuable resistant tree in many extreme environments. Here, we determined the first complete chloroplast genome of <i>C. sinensis</i> using high-throughput sequencing technology. Our results showed the chloroplast genome of <i>C.sinensis</i> was 159,092?bp long and displayed a typical quadripartite structure consisting of a pair of inverted repeats with a length of 26,895?bp and separating by two single-copy regions (LSC, 86,085?bp and SSC, 19,217?bp). Besides, the chloroplast genome of <i>C. sinensis</i> totally contained 131 genes, including 87 protein coding genes, 36 transfer RNAs and eight ribosomal RNAs. Additionally, a maximum likelihood phylogenetic analysis based on the 19 chloroplast genomes demonstrated the monophyly of Cannabaceae and <i>C. sinensis</i> formed a sister clade to <i>Celtis biondii</i>.
Project description:<i>Sycopsis sinensis</i> is a species of the genus <i>Sycopsis</i> Oliv in the Hamamelidaceae, and it is a native broadleaved evergreen woody plant species in China. Here, we sequenced, assembled, and analyzed the complete chloroplast (cp) genome of <i>S. sinensis</i>. The chloroplast genome of <i>S. sinensis</i> was 159,093?bp with 38.02% GC content, including a large single-copy (LSC) region of 87,841?bp, a small single-copy (SSC) region of 18,792?bp and two equal length inverted repeat (IR) regions of 26,230?bp. And, it contained 131 genes, including 37 tRNA genes, 8 rRNA genes, and 86 mRNA genes. Phylogenetic analysis strongly shows that S. sinensis has a close relationship with <i>Distylium macrophyllum</i>, whose posterior probability is 1.0.
Project description:The complete chloroplast genome sequence of <i>Camellia sinensis L.</i> cultivar Sangmok was determined using high-throughput sequencing technology. We sequenced Sangmok chloroplast genome and performed comparative with 21 published other <i>Camellia</i> and species from different genus for phylogenetic analysis. Chloroplast genome was 153,044?bp in length, containing a pair of 24,627?bp inverted repeat (IR) regions, which were separated by small and large single-copy regions (SSC and LSC) of 19,155 and 64,665?bp, respectively. The chloroplast genome contained 97 genes (63 protein-coding genes, 29 <i>tRNA</i> genes, and 5 <i>rRNA</i> genes). The overall GC content of the chloroplast genome was 37.2%. The phylogenetic analysis among species in number of the genus <i>Camellia</i> provided that <i>C. sinensis L.</i> cultivar Sangmok is closely related to KJ806277 <i>Camellia pubicosta</i>.
Project description:Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.
Project description:<i>Spiranthes sinensis</i> is an important medicinal plant of <i>Spiranthes</i> family and is currently in an endangered state. To better guide the systematic classification of <i>S. sinensis</i>, the complete genome of its chloroplast was sequenced and characterized. The complete chloroplast genome is 152,786?bp in length and contains a large single copy (LSC) region of 83,446?bp, a small single copy (SSC) region of 17,938?bp, and two inverted repeat (IR<sub>A</sub> and IR<sub>B</sub>) regions of 25,701?bp. The genome encodes 132 genes (112 unique genes), including 86 protein-coding genes (78 unique genes), 8 rRNA genes (4 unique genes), and 38 tRNA genes (30 unique genes). The total GC content of plasmid genome is 36.18%. Phylogenetic results indicated that <i>S. sinensis</i> is more closely related to <i>Ludisia discolor</i>, <i>Goodyera schlechtendaliana</i>, <i>Goodyera fumata</i>, and <i>Goodyera procera</i>. The study enriches the plasmid genomic information of <i>S. sinensis</i> and is of great significance for the genetic protection of this species.
Project description:The complete chloroplast genome sequence of <i>Hippophae rahmnoides</i> subsp. <i>sinensis</i> was characterized from Illumina pair-end sequencing. The chloroplast genome of <i>H. rahmnoides</i> subsp. <i>sinensis</i> was 156,355?bp in length, containing a large single-copy region (LSC) of 84,002?bp, a small single-copy region (SSC) of 19,055?bp, and two inverted repeat (IR) regions of 26,649?bp. The overall GC content is 36.6%, while the corresponding values of the LSC, SSC, and IR regions are 64.5%, 69.2%, and 60.1%, respectively. The genome contains 131 complete genes, including 88 protein-coding genes, 38 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). The neighbour-joining phylogenetic analysis showed that <i>H. rahmnoides</i> subsp. <i>sinensis</i> and <i>H. rahmnoides</i> clustered together as sisters to other <i>H. rahmnoides</i> species.
Project description:Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.