The complete chloroplast genome sequence of Camellia granthamiana.
ABSTRACT: Camellia granthamiana is a rare and endangered plant peculiar to China, and a total of 5 plants have been found at present. Based on the next generation sequencing, the whole chloroplast (Cp) genome of (Camellia granthamiana Sealy) of Camellia oleifera was constructed.In this study, the complete chloroplast (cp) genome of Camellia granthamiana was assembled based on next generation sequencing.The cp genome was 157,001?bp in length, including a large single copy (LSC) region of 70,387?bp, a small single copy (SSC) region of 18,296?bp and a pair of inverted repeats (IRs) of 52,082?bp. The genome contained 135 genes, including 90 protein-coding genes, 37 tRNA genes and 8 ribosomal RNA genes. The majority of these gene species occurred as a single copy.
Project description:<i>Camellia japonica</i> is an evergreen tree species with high ornamental value. The complete <i>C. japonica</i> cp genome is 156,606?bp in length and contains a small single-copy region (18,415?bp) and a large single copy ( 86,257?bp) region - separated by a pair of the inverted repeat regions (51,934?bp ). The overall GC content of the <i>C. japonica</i> cp genome is 37.31%. We identified 128 genes in this genome, including 91 protein-coding genes, 29 transfer RNA genes, and 8 ribosomal RNA genes. The maximum-likelihood phylogenetic analysis revealed that <i>C. japonica</i> is closely related to <i>Camellia oleifera</i>.
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>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:<i>Camellia brevistyla</i> is an economic species for its seeds with high oil content and ornamental value, which is cultivated widespreadly across southern China. In this study, the complete chloroplast (cp) genome sequence of <i>C. brevistyla</i> was assembled and annotated in order to future genetic research. The whole cp genome of <i>C. brevistyla</i> is 159,281?bp in size, composed of a small single copy (SSC) region of 15,662?bp and a large single copy (LSC) region of 86,251?bp separated by a pair of inverted repeats (IRs, IRA: 130598: 159281, IRB: 86252: 114935). The overall GC content of <i>C. brevistyla</i> cp genome is 37.19%, with the base content A (31.03%), T (31.78%), C (18.94%), and G (18.25%). Phylogenetic analysis of 20 species based on 74 protein-coding genes shows that <i>C. brevistyla</i> is evolutionarily closest to <i>Camellia danzaiensis</i>.
Project description:<i>Camellia vietnamensis</i> is an economic woody plant producing high-value edible oils, which is commonly found and cultivated in south areas of China. To provide genetic information for future genetic research, we have sequenced and assembled the complete chloroplast (cp) genome of <i>C. vietnamensis</i> based on the Illumina Hiseq platform. The total genome size is 161,958?bp in length with 37% GC, which contains a large single copy (LSC, 86,657?bp) region, a small single copy (SSC, 13,347?bp) region, and a pair of inverted repeat (IRs, 30,977?bp) regions. It is comprised of 81 protein-coding genes, 44 transfer RNAs and 4 ribosomal RNAs. To obtain the phylogeny relationship, the cp genome of <i>C. vietnamensis</i> has been compared with other <i>Camellia</i> species; the results indicate that <i>C. vietnamensis</i> is closely related to <i>C. taliensis</i>. This study provides fundamental information of <i>C. vietnamensis</i> cp genome, and it is valuable to the molecular phylogenetic and genetic diversity analyses in future.
Project description:The <i>Camellia nitidissima</i> is an endangered tree species native to Southwest China with high economic and medicinal values. Genetic information of <i>C. nitidissima</i> would provide good knowledge for the conservation of this wild resource. In this article, we characterized the complete chloroplast genome of <i>C. nitidissima</i> using Illumina sequencing technology. The size of circular genome is 157,247?bp, containing a large single copy (LSC) region of 86,880?bp and a small single copy (SSC) region of 18,258?bp. The LSC region and SSC region are separated by a pair of inverted repeat regions (IRa and IRb), each of 26,068?bp. In total, 136 genes are encoded in this cp genome, including 89 protein-coding genes (81 species), 39 tRNA genes (30 species), and 8 rRNA genes (4 species). The overall G?+?C content of the chloroplast genome is 37.3%. The phylogenetic analysis suggests that <i>C. nitidissima</i> is closely related to <i>C. petelotti</i>.
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:<i>Camellia rhytidophylla</i> is an endangered plant with economic value. Using Illumina sequencing, the chloroplast genome of <i>C. rhytidophylla</i> was sequenced and analyzed in this study. The complete chloroplast genome is 157,073?bp in length, which consisted of a pair of inverted repeat regions of 26,055?bp (IRa and IRb) separated by a large single-copy region (LSC) of 86,680?bp and a small single-copy region (SSC) of 18,283?bp. The <i>C. rhytidophylla</i> chloroplast genome encodes 135 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes. Sequence comparison analysis with the chloroplast sequences of 28 other <i>Camellia</i> plants found that <i>C. rhytidophylla</i> had the closest relationship with <i>C. szechuanensis</i>. This study provides a theoretical basis for the analysis of the distant relationship of <i>Camellia</i>.
Project description:<i>Leucanthemella linearis</i> is an important marsh plant. The complete chloroplast genome sequence of <i>L</i>. <i>linearis</i> was obtained using next generation sequencing. It was 15,1401?bp in length, including a pair of inverted repeat (IR, 24,941?bp) regions separated by a small single copy (SSC, 18,392?bp) sequence and a large single copy (LSC, 83,127?bp) sequence. The cp genome contained 140 genes, consisting of 96 protein-coding genes, 8 rRNA genes and 36 tRNA genes. Twenty-two genes were present in the IR region. Thirty-four SSR sites were detected in the cp genome. Phylogenetic analysis with the reported chloroplast genomes revealed that <i>L</i>. <i>linearis</i> is most closely related to Tribe Heliantheae species. This new data will help to understand the phylogenetic position and biology of the <i>Leucanthemella</i>.
Project description:Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp) genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros 'Jinzaoshi' were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp) in the cp genome of D. 'Jinzaoshi', support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.