The complete chloroplast genome of Camellia vietnamensis, an economic shrub producing edible seed oil.
ABSTRACT: Camellia vietnamensis 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 C. vietnamensis 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 C. vietnamensis has been compared with other Camellia species; the results indicate that C. vietnamensis is closely related to C. taliensis. This study provides fundamental information of C. vietnamensis cp genome, and it is valuable to the molecular phylogenetic and genetic diversity analyses in future.
Project description:<i>Camellia granthamiana</i> 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 <i>Camellia granthamiana</i> 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 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 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 spp., which are self-incompatible plants, are some of the most important woody species producing edible oil in Southeast Asian countries. However, the demand for camellia oil currently exceeds the supply due to low product yields that have resulted from a decrease in pollination services. Although Camellia osmantha, C. vietnamensis, and C. oleifera are cultivated in South China, little is known about the correspondence between pollinator abundance and pollinator services for this plant genus. In this study, the diversity, daily activity patterns, and pollination effectiveness of insects visiting C. osmantha, C. vietnamensis and C. oleifera were investigated. A total of 24 species, belonging to four orders and 11 families, of visiting insects were identified. Apis cerana cerana Fabricius, Vespa bicolor Fabricius, V. velutina Lepeletier, V. ducalis Smith, and Phytomia zonata Fabricius were the dominant pollinators. The daily activity peaks of the five visiting insects were between 10:00 and 14:00, which may have been related to the pattern of floral resource production (particularly nectar). Cross-pollination by insects significantly increased the fruit production rates of C. osmantha, C. vietnamensis, and C. oleifera. Therefore, the wild bees and flies that pollinate wild and cultivated Camellia plants should be protected in South China.
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>Ampelopsis grossedentata</i> (Hand.-Mazz.) W. T. Wang is rich in flavonoids and also displays excellent pharmacological activities. The phylogenetic relationship between <i>A. grossedentata</i> and other related Vitaceae family members remains unclear. The chloroplast (cp) genome is a useful model for assessing genome evolution. In this study, we assembled the cp genome of <i>A. grossedentata</i> using the high-throughput Illumina pair-end sequencing data and characterized the genome to providing useful information for future genetic studies. The circular cp genome was 162,147?bp in size, including a large single-copy (LSC) region of 89,244?bp and a small single-copy (SSC) region of 18,439?bp, which were separated by two inverted repeat (IR) regions (27,232?bp each). A total of 135 genes were predicted, including 8 ribosomal RNAs (rRNAs), 37 transfer RNAs (tRNAs), and 90 protein-coding genes (PCGs). Furthermore, phylogenetic analysis revealed that <i>A. grossedentata</i> within <i>Ampelopsis</i> genus and formed a different clade from other three congeneric species. This study provides useful information for future genetic study of <i>A. grossedentata</i>.
Project description:BACKGROUND: P. vietnamensis var. fuscidiscus, called "Yesanqi" in Chinese, is a new variety of P. vietnamensis, which was first found in Jinping County, the southern part of Yunnan Province, China. Compared with other Panax plants, this species contains higher content of ocotillol-type saponin, majonoside R2. Despite the pharmacological importance of ocotillol-type saponins, little is known about their biosynthesis in plants. Hence, P. vietnamensis var. fuscidiscus is a suitable medicinal herbal plant species to study biosynthesis of ocotillol-type saponins. In addition, the available genomic information of this important herbal plant is lacking. RESULTS: To investigate the P. vietnamensis var. fuscidiscus transcriptome, Illumina HiSeq™ 2000 sequencing platform was employed. We produced 114,703,210 clean reads, assembled into 126,758 unigenes, with an average length of 1,304 bp and N50 of 2,108 bp. Among these 126,758 unigenes, 85,214 unigenes (67.23%) were annotated based on the information available from the public databases. The transcripts encoding the known enzymes involved in triterpenoid saponins biosynthesis were identified in our Illumina dataset. A full-length cDNA of three Squalene epoxidase (SE) genes were obtained using reverse transcription PCR (RT-PCR) and the expression patterns of ten unigenes were analyzed by reverse transcription quantitative real-time PCR (RT-qPCR). Furthermore, 15 candidate cytochrome P450 genes and 17 candidate UDP-glycosyltransferase genes most likely to involve in triterpenoid saponins biosynthesis pathway were discovered from transcriptome sequencing of P. vietnamensis var. fuscidiscus. We further analyzed the data and found 21,320 simple sequence repeats (SSRs), 30 primer pairs for SSRs were randomly selected for validation of the amplification and polymorphism in 13 P. vietnamensis var. fuscidiscus accessions. Meanwhile, five major triterpene saponins in roots of P. vietnamensis var. fuscidicus were determined using high performance liquid chromatography (HPLC) and evaporative light scattering detector (ELSD). CONCLUSIONS: The genomic resources generated from P. vietnamensis var. fuscidiscus provide new insights into the identification of putative genes involved in triterpenoid saponins biosynthesis pathway. This will facilitate our understanding of the biosynthesis of triterpenoid saponins at molecular level. The SSR markers identified and developed in this study show genetic diversity for this important crop and will contribute to marker-assisted breeding for P. vietnamensis var. fuscidiscus.
Project description:Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants.
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:<h4>Background</h4>Camellia, comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic resolution of the species has proven to be difficult. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. Phylogenomics is an attractive avenue that can be used to reconstruct the tree of life, especially at low taxonomic levels.<h4>Methodology/principal findings</h4>Seven complete chloroplast (cp) genomes were sequenced from six species representing different subdivisions of the genus Camellia using Illumina sequencing technology. Four junctions between the single-copy segments and the inverted repeats were confirmed and genome assemblies were validated by PCR-based product sequencing using 123 pairs of primers covering preliminary cp genome assemblies. The length of the Camellia cp genome was found to be about 157kb, which contained 123 unique genes and 23 were duplicated in the IR regions. We determined that the complete Camellia cp genome was relatively well conserved, but contained enough genetic differences to provide useful phylogenetic information. Phylogenetic relationships were analyzed using seven complete cp genomes of six Camellia species. We also identified rapidly evolving regions of the cp genome that have the potential to be used for further species identification and phylogenetic resolution.<h4>Conclusions/significance</h4>In this study, we wanted to determine if analyzing completely sequenced cp genomes could help settle these controversies of interspecies relationships in Camellia. The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based "barcodes", can be established for a species and then used to unmask interspecies phylogenetic relationships. It reveals that phylogenomics based on cp genomes is an effective approach for achieving phylogenetic resolution between Camellia species.