The complete chloroplast genome sequence of economical standard tea plant, Camellia sinensis L. cultivar Sangmok, in Korea.
ABSTRACT: The complete chloroplast genome sequence of Camellia sinensis L. cultivar Sangmok was determined using high-throughput sequencing technology. We sequenced Sangmok chloroplast genome and performed comparative with 21 published other Camellia 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 tRNA genes, and 5 rRNA genes). The overall GC content of the chloroplast genome was 37.2%. The phylogenetic analysis among species in number of the genus Camellia provided that C. sinensis L. cultivar Sangmok is closely related to KJ806277 Camellia pubicosta.
Project description:<i>Camellia sinensis var. sinensis</i> cultivar Tieguanyin (TGY) is an important Oolong tea variety in China. In this study, we reported a complete chloroplast (cp) genome based on the Illumina sequencing technology and combined <i>de novo</i> and reference-guided assembly strategies. The complete cp genome of 'TGY' displayed the regular quadripartite structure: a total of 157,126?bp in length, comprising a large single-copy (LSC, 86,904?bp) region, a small single-copy (SSC, 18,532?bp) region, and a pair of inverted repeats (IRs, 26,095?bp) regions. A lot of 132 predicted genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content is 37.3%. Maximum likelihood (ML) phylogenetic tree involving 18 cp genomes of the <i>Camellia</i> genus revealed a relatively independent event of local domestication among three types of cultivars. The complete cp genome of 'TGY' provides an insight into tea plants for further understanding evolutionary research on tea plants.
Project description:Here, combining PacBio and Illumina sequencing data, we reported the complete chloroplast genome of the first Wuyi tea (<i>Bohea</i>), <i>Camellia sinensis</i> cv. <i>Dahongpao</i> (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 <i>C. sinensis</i> cv. <i>Longjing</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:Camellia is an economically, ecologically and phylogenetically valuable genus in the family Theaceae. The frequent interspecific hybridization and polyploidization makes this genus phylogenetically and taxonomically under controversial and require detailed investigation. Chloroplast (cp) genome sequences have been used for cpDNA marker development and genetic diversity evaluation. Our research newly sequenced the chloroplast genome of Camellia japonica using Illumina HiSeq X Ten platform, and retrieved five other chloroplast genomes of Camellia previously published for comparative analyses, thereby shedding lights on a deeper understanding of the applicability of chloroplast information. The chloroplast genome sizes ranged in length from 156,607 to 157,166 bp, and their gene structure resembled those of other higher plants. There were four categories of SSRs detected in six Camellia cpDNA sequences, with the lengths ranging from 10 to 17bp. The Camellia species exhibited different evolutionary routes that lhbA and orf188, followed by orf42 and psbZ, were readily lost during evolution. Obvious codon preferences were also shown in almost all protein-coding cpDNA and amino acid sequences. Selection pressure analysis revealed the influence of different environmental pressures on different Camellia chloroplast genomes during long-term evolution. All Camellia species, except C. crapnelliana, presented the identical rate of amplification in the IR region. The datasets obtained from the chloroplast genomes are highly supportive in inferring the phylogenetic relationships of the Camellia taxa, indicating that chloroplast genome can be used for classifying interspecific relationships in this genus.
Project description:Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36-rps8, rps16-trnQ, trnH-psbA and ndhC-trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.
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>Incarvillea sinensis</i> Lam. is the type of the genus <i>Incarvillea</i> Juss., and it is widely distributed, relative to other members of the genus. In this paper, we sequenced, assembled and annotated the chloroplast genome of <i>Incarvillea sinensis</i>. The complete chloroplast genome is 162,088 bps in size, with overall GC content of 39.4%. We annotated 113 unique genes in the plastome sequence, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis based on chloroplast genome sequences resulted in a different resolution on the relationships among subgenera from the former.
Project description:<i>Sloanea sinensis</i> (Hance) Hu is a tree species and member of the Elaeocarpaceae family. It's an excellent commercial tree species which has a relatively high net growth as forests. Here, we report the complete chloroplast genome sequence of a <i>Sloanea</i> genus for the first time. The complete chloroplast sequence of <i>S. sinensis</i> is 158,001?bp in length, including a large single copy region (LSC: 88,481?bp) and a small single copy region (SSC: 17,481?bp), the latter of which is separated by a pair of inverted repeat regions (IRs: 26,051?bp). Phylogenetic analysis indicates that the Elaeocarpaceae is a family within the Oxalidales may be more appropriate than belongs to Malvales as traditional plant taxonomy.
Project description:Camellia oleifera is one of the four largest woody edible oil plants in the world with high ecological and medicinal values. Due to frequent interspecific hybridization, it was difficult to study its genetics and evolutionary history. This study used C. oleifera that was collected on Hainan Island to conduct our research. The unique island environment makes the quality of tea oil higher than that of other species grown in the mainland. Moreover, a long-term geographic isolation might affect gene structure. In order to better understand the molecular biology of this species, protect excellent germplasm resources, and promote the population genetics and phylogenetic studies of Camellia plants, high-throughput sequencing technology was used to obtain the chloroplast genome sequence of Hainan C. oleifera. The results showed that the whole chloroplast genome of C. oleifera in Hainan was 156,995 bp in length, with a typical quadripartite structure of a large single copy (LSC) region of 86,648 bp, a small single copy (SSC) region of 18,297 bp, and a pair of inverted repeats (IRs) of 26,025 bp. The whole genome encoded a total of 141 genes (115 different genes), including 88 protein-coding genes, 45 tRNA genes, and eight rRNA genes. Among these genes, nine genes contained one intron, two genes contained two introns, and four overlapping genes were also detected. The total GC content of Hainan C. oleifera's chloroplast genome was 37.29%. The chloroplast genome structure characteristics of Hainan C. oleifera were compared with mainland C. oleifera and those of the other eight closely related Theaceae species; it was found that the contractions and expansions of the IR/LSC and IR/SSC regions affected the length of chloroplast genome. The chloroplast genome sequences of these Theaceae species were highly similar. A comparative analysis indicated that the Theaceae species were conserved in structure and evolution. A total of 51 simple sequence repeat (SSR) loci were detected in the chloroplast genome of Hainan C. oleifera, and all Camellia plants did not have pentanucleotide repeats, which could be used as a good marker in phylogenetic studies. We also detected seven long repeats, the base composition of all repeats was biased toward A/T, which was consistent with the codon bias. It was found that Hainan C. oleifera had a similar evolutionary relationship with C. crapnelliana, through the use of codons and phylogenetic analysis. This study can provide an effective genomic resource for the evolutionary history of Theaceae family.
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.