The complete chloroplast genome of Chimonobambusa purpurea (Bambusatae).
ABSTRACT: Chimonobambusa purpurea is one of the important bamboo species in southwest of China. We studied the complete chloroplast (cp) genome of C. purpurea in this study. The cp genome of C. purpurea (GenBank accession: MW030500) was 139,574 bp in length, including a large single-copy (LSC) region of 83,171 bp, a small single-copy (SSC) region of 12,811 bp, and a pair of inverted repeated (IR) regions of 21,796 bp. And the genome contained 133 genes, including 86 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Based on 30 cp genomes, we used the phylogenetic analysis to build phylogenetic tree, indicating that C. purpurea is closely related to C. tumidissinoda.
Project description:<i>Chimonobambusa hejiangensis</i> is of the unique edible bamboo specie of high quality in China. We studied the complete chloroplast(cp) genome of <i>C. purpurea</i> in this study. The cp genome of <i>C. hejiangensis</i> (GenBank accession: MW186792) was 138,911 bp in length, including a large single-copy (LSC) region of 82,498 bp, a small single-copy (SSC) region of 12,743 bp and a pair of inverted repeated (IR) regions of 21,835 bp. The genome contained 133 genes, including 86 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Based on 39 cp genomes, we used the phylogenetic analysis to build phylogenetic tree, indicating that <i>C. hejiangensis</i> is closely related to <i>C. tumidissinoda</i>. Also, the phylogenetic relationship of lineages might be (Hsuehochloa + (((Shibataea clade + Arundinaria clade) + Indocalamus wilsonii) + ((Bergbambos + Indocalamus) + (((African alpine bamboos + Gaoligongshania) + (Chimonocalamus + Kuruna))+(Thamnocalamus + Phyllostachys clade))))). It could be devoted to phylogenetic analysis of Arundinarieae.
Project description:<i>Chimonobambusa hejiangensis</i> is a kind of bamboo that has excellent edible and economic value, which is endemic to southwest China. The study used next-generation sequencing to obtain the complete chloroplast (cp) genome sequence of <i>C. hejiangensis</i>. The cp genome of <i>C. hejiangensis</i> has a total length of 138,908 bp, and consisted of an 82,495-bp large single-copy region, an 12,743-bp small single-copy region, and two 21,835-bp IR regions. In total, 112 unique genes were found in the cp genome, including 77 protein coding, 31 tRNA, and 4 rRNA genes. Phylogenetic analysis indicated that <i>C.hejiangensis</i> and <i>C. tumidissinoda</i> are sister species within the <i>Arundinarieae</i> genus, where <i>Chimonocalamus</i> and <i>Ampelocalamus</i> are more closely related to them.
Project description:<i>Chimonobambusa quadrangularis</i> (Fenzl) Makino is one of the 'Square Bamboo' due to its square-shaped culm. However, as an edible bamboo, there is no genomic information reported so far. In this study, we reported and characterized the first plastome of <i>C. quadrangularis</i> based on Illumina Hiseq sequencing. The plastome exhibited a typical angiosperm circular structure, containing four regions: large single-copy region (LSC: 83,125 bp), small single-copy region (SSC: 12,811 bp), and a pair of inverted repeat regions (IR: 21,802 bp). The plastome consisted of 139,540 bp in size, with 82 protein-coding genes, 39 tRNA genes, and eight rRNA genes. The total nucleotide composition consisted of 30.16% A, 30.97% T, 19.25% C, and 19.63% G. The G + C content of the whole plastome was 38.88%. Phylogenetic analysis based on the complete plastomes of six species indicated that <i>C. quadrangularis</i> was closed to <i>C. hejiangensis</i>. The plastome is helpful for studying the evolution of beneficial adaptations and developing bioremediation and biomedical science.
Project description:<i>Chimonobambusa sichuanensis</i> is an ornamental shrubby bamboo endemic to southern China. In this study, the complete chloroplast genome (cpDNA) sequence of <i>Chimonobambusa sichuanensis</i> was first reported. The cpDNA is 139,594 bp in length, including a small single-copy (SSC) region of 12,820 bp and a large single-copy (LSC) region of 83,196 bp, which were separated by a pair of inverted repeat (IR) regions of 21,789 bp. The genome contains 140 genes, consisting of 93 protein-coding genes, seven ribosomal RNA (rRNA) genes, and 40 transfer RNA (tRNA) genes. The phylogenetic analysis showed that <i>C. sichuanensis</i> is highly clustered in the <i>Phyllostachys</i> clade, sister to <i>C. tumidissinoda</i>.
Project description:<i>Schnabelia tetrodonta</i> is a medicinal plant used in traditional Chinese medicine. However, the molecular biology data of the species was too scarce to bioprospect the medicinal species. In this study, the first complete chloroplast genome (cp) of <i>S. tetrodonta</i> was sequenced and assembled based on the next generation sequencing. The cp genome is 157,004 bp in length, including a large single-copy (LSC) region of 83,605 bp, a small single-copy (SSC) region of 36,899 bp, and a pair of inverted repeat (IR) regions of 18,250 bp each. The genome encodes 134 genes, including 90 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The GC content of whole genome is 37.80%. The phylogenetic analysis based on 20 complete cp sequences (19 genome sequences from the Teucrioideae of Lamiaceae and an outgroup of <i>Ipomoea purpurea</i>) revealed that <i>S. tetrodonta</i> was closely related to <i>S. oligophylla.</i>
Project description:Ipomoea L. is the largest genus within the Convolvulaceae and contains 600-700 species. Ipomoea species (morning glories) are economically valuable as horticultural species and scientifically valuable as ecological model plants to investigate mating systems, molecular evolution, and both plant-herbivore and plant-parasite interactions. Furthermore, the dried seeds of I. nil or I. purpurea are used in Korean traditional herbal medicines. In this study, chloroplast (cp) genomes were sequenced from six Ipomoea species, namely, I. nil and I. purpurea and, for the first time, I. triloba, I. lacunosa, I. hederacea, and I. hederacea var. integriuscula. The cp genomes were 161,354-161,750 bp in length and exhibited conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 transfer RNA genes, and 4 ribosomal RNA genes. The gene order, content, and orientation of the six Ipomoea cp genomes were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the six Ipomoea cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (petN-psbM, trnI-CAU-ycf2, ndhH-ndhF, psbC-trnS, and ccsA-ndhD). In addition, the protein-coding genes accD, cemA, and ycf2 exhibited high sequence variability and were under positive selection (Ka/Ks > 1), indicating adaptive evolution to the environment within the Ipomoea genus. Phylogenetic analysis of the six Ipomoea species revealed that these species clustered according to the APG IV system. In particular, I. nil and I. hederacea had monophyletic positions, with I. purpurea as a sister. I. triloba and I. lacunosa in the section Batatas and I. hederacea and I. hederacea var. integriuscula in the section Quamoclit were supported in this study with strong bootstrap values and posterior probabilities. We uncovered high-resolution phylogenetic relationships between Ipomoeeae. Finally, indel markers (IPOTY and IPOYCF) were developed for the discrimination of the important herbal medicine species I. nil and I. purpurea. The cp genomes and analyses in this study provide useful information for taxonomic, phylogenetic, and evolutionary analysis of the Ipomoea genome, and the indel markers will be useful for authentication of herbal medicines.
Project description:Plant mitochondrial (mt) genomes possess several complex features, including a variable size, a dynamic genome structure, and complicated patterns of gene loss and gain throughout evolutionary history. Studies of plant mt genomes can, therefore, provide unique insights into organelle evolution. We assembled the complete Salix purpurea L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. The pseudo-molecule obtained has a typical circular structure 598,970 bp long, with an overall GC content of 55.06%. The S. purpurea mt genome contains 52 genes: 31 protein-coding, 18 tRNAs, and three rRNAs. Eighteen tandem repeats and 404 microsatellites are distributed unevenly throughout the S. purpurea mt genome. A phylogenetic tree of 23 representative terrestrial plants strongly supports S. purpurea inclusion in the Malpighiales clade. Our analysis contributes toward understanding the organization and evolution of organelle genomes in Salicaceae species.
Project description:The first complete chloroplast (cp) genome of <i>Indofevillea khasiana</i> was reported in this study. The <i>I. khasiana</i> cp genome was 159,238 bp in size, with two inverted repeat (IR) regions of 26,275 bp separated by a large single copy (LSC) region of 88,538 bp and a small single copy (SSC) region of 18,150 bp. The cp genome of this species contained 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content was 36.9%. Phylogenetic analysis based on the cp genome sequences suggests that <i>I. khasiana</i> is sister to the rest species of subfam. Cucurbitoideae.