Complete Chloroplast Genome Sequence of Decaisnea insignis: Genome Organization, Genomic Resources and Comparative Analysis.
ABSTRACT: Decaisnea insignis is a wild resource plant and is used as an ornamental, medicinal, and fruit plant. High-throughput sequencing of chloroplast genomes has provided insight into the overall evolutionary dynamics of chloroplast genomes and has enhanced our understanding of the evolutionary relationships within plant families. In the present study, we sequenced the complete chloroplast genome of D. insignis and used the data to assess its genomic resources. The D. insignis chloroplast genome is 158,683?bp in length and includes a pair of inverted repeats of 26,167?bp that are separated by small and large single copy regions of 19,162?bp and 87,187?bp, respectively. We identified 83 simple sequence repeats and 18 pairs of large repeats. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited a high A/T content. The D. insignis chloroplast genome bias was skewed towards A/T on the basis of codon usage. A phylogenetic tree based on 82 protein-coding genes of 33 angiosperms showed that D. insignis was clustered with Akebia in Lardizabalaceae. Overall, the results of this study will contribute to better understanding the evolution, molecular biology and genetic improvement of D. insignis.
Project description:<i>Akebia trifoliata</i>, commonly known as 'Bayuezha' in China, has been widely used as traditional Chinese medicinal herbs with a long history. In the present study, the complete chloroplast genome of <i>A. trifoliata</i> was sequenced using Illumina high-throughput sequencing approach. The length of the complete chloroplast genome is 157,952?bp with 38.7% GC content. It contains 131 genes, including 86 protein-coding genes, 37 <i>tRNA</i> genes, and 8 <i>rRNA</i> genes. Phylogenetic analysis indicated that <i>A. trifoliata</i> was closely related to another Lardizabalaceae species, <i>Akebia quinata</i>, which further confirms traditional species classification.
Project description:<i>Akebia trifoliata</i> subsp. <i>australis</i> (Diels) T.Shimizu is a medicinal plant in China. Here, the complete chloroplast (cp) genome sequence of <i>A. trifoliata</i> subsp. <i>australis</i> was assembled and characterized as a resource for future genetic studies. The whole cp genome was 157,952?bp in length, containing of a large single-copy (LSC) region of 86,596?bp, a small single-copy (SSC) region of 19,060?bp, and two inverted repeat (IR) regions of 26,148?bp. The new sequence possessed total 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The nucleotide composition was asymmetric (30.3% A, 19.7% C, 19.0% G and 31.0% T) with an overall GC content of 38.7%. The maximum likelihood phylogenetic analysis based on 10?cp genomes indicated that <i>A. trifoliata</i> subsp. <i>australis</i> was closely related to <i>Akebia trifoliata</i> subsp. <i>trifoliata.</i> However, <i>Akebia quinata</i> was closely related to <i>Stauntonia obovatifoliola</i>.
Project description:<i>Brainea insignis</i> (Hooker) J. Smith, a member of Blechnaceae, is a rare and endangered species in tropical Asia. Here we assembled and annotated the complete chloroplast (cp) genome. It is 149,730?bp in length and encodes 88 protein-coding genes, 36 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. This chloroplast genome sequencing offers a useful resource for future conservation genetics and phylogenetic studies.
Project description:<i>Scutellaria tsinyunensis</i> (Lamiaceae) is an endangered species endemic to Mt. Jinyun of Chongqing, China. In this study, the complete chloroplast (cp) genome of <i>S. tsinyunensis</i> was sequenced and characterized. The cp genome is 152,066?bp in length with a typical quadripartite structure, containing a pair of inverted repeats (IRs) of 25,223?bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region of 84,096?bp and 17,524?bp, respectively. The whole cp genome contains 130 genes, including 86 protein-coding genes, 36 tRNA genes, and eight rRNA genes. The overall GC content of the circular genome is 38.4%, whereas the corresponding values in LSC, SSC, and IR regions are 36.4, 32.6, and 43.6%, respectively. The phylogenetic analysis based on the complete cp genomes of the Lamiaceae family indicated that <i>S. tsinyunensis</i> was closely related to <i>S. insignis</i>.
Project description:Spathiphyllum is a very important tropical plant used as a small, potted, ornamental plant in South China, with an annual output value of hundreds of millions of yuan. In this study, we sequenced and analyzed the complete nucleotide sequence of the Spathiphyllum 'Parrish' chloroplast genome. The whole chloroplast genome is 168,493 bp in length, and includes a pair of inverted repeat (IR) regions (IRa and IRb, each 31,600 bp), separated by a small single-copy (SSC, 15,799 bp) region and a large single-copy (LSC, 89,494 bp) region. Our annotation revealed that the S. 'Parrish' chloroplast genome contained 132 genes, including 87 protein coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. In the repeat structure analysis, we detected 281 simple sequence repeats (SSRs) which included mononucleotides (223), dinucleotides (28), trinucleotides (12), tetranucleotides (11), pentanucleotides (6), and hexanucleotides (1), in the S. 'Parrish' chloroplast genome. In addition, we identified 50 long repeats, comprising 18 forward repeats, 13 reverse repeats, 17 palindromic repeats, and 2 complementary repeats. Single nucleotide polymorphism (SNP) and insertion/deletion (indel) analyses of the chloroplast genome of the S. 'Parrish' relative S. cannifolium revealed 962 SNPs in S. 'Parrish'. There were 158 indels (90 insertions and 68 deletions) in the S. 'Parrish' chloroplast genome relative to the S. cannifolium chloroplast genome. Phylogenetic analysis of five species found S. 'Parrish' to be more closely related to S. kochii than to S. cannifolium. This study identified the characteristics of the S. 'Parrish' chloroplast genome, which will facilitate species identification and phylogenetic analysis within the genus Spathiphyllum.
Project description:As an endangered species, <i>Magnolia kobus</i> is distributed in Jeju island in Korea with only about 500-1000 individuals. In this study, we presented a complete chloroplast genome of <i>M. kobus</i> which is 159,443?bp and has four sub-regions: 87,484?bp of large single copy and 18,783?bp of small single copy regions are separated by 26,588?bp of inverted repeat regions including 113 genes (79 unique genes, four rRNAs and 30 tRNAs). Phylogenetic analysis using chloroplast genomes showed that <i>M. kobus</i> is a sister of <i>M. insignis</i> and <i>M. laevifolia</i> clade.
Project description:Chloroplast genome sequences are very useful for species identification and phylogenetics. Chuanminshen (Chuanminshen violaceum Sheh et Shan) is an important traditional Chinese medicinal plant, for which the phylogenetic position is still controversial. In this study, the complete chloroplast genome of Chuanminshen violaceum Sheh et Shan was determined. The total size of Chuanminshen chloroplast genome was 154,529 bp with 37.8% GC content. It has the typical quadripartite structure, a large single copy (17,800 bp) and a small single copy (84,171 bp) and a pair of inverted repeats (26,279 bp). The whole genome harbors 132 genes, which includes 85 protein coding genes, 37 tRNA genes, eight rRNA genes, and two pseudogenes. Thirty-nine SSR loci, 32 tandem repeats and 49 dispersed repeats were found. Phylogenetic analyses results with the help of MEGA showed a new insight for the Chuanminshen phylogenetic relationship with the reported chloroplast genomes in Apiales plants.
Project description:Salix wilsonii is an important ornamental willow tree widely distributed in China. In this study, an integrated circular chloroplast genome was reconstructed for S. wilsonii based on the chloroplast reads screened from the whole-genome sequencing data generated with the PacBio RSII platform. The obtained pseudomolecule was 155,750 bp long and had a typical quadripartite structure, comprising a large single copy region (LSC, 84,638 bp) and a small single copy region (SSC, 16,282 bp) separated by two inverted repeat regions (IR, 27,415 bp). The S. wilsonii chloroplast genome encoded 115 unique genes, including four rRNA genes, 30 tRNA genes, 78 protein-coding genes, and three pseudogenes. Repetitive sequence analysis identified 32 tandem repeats, 22 forward repeats, two reverse repeats, and five palindromic repeats. Additionally, a total of 118 perfect microsatellites were detected, with mononucleotide repeats being the most common (89.83%). By comparing the S. wilsonii chloroplast genome with those of other rosid plant species, significant contractions or expansions were identified at the IR-LSC/SSC borders. Phylogenetic analysis of 17 willow species confirmed that S. wilsonii was most closely related to S. chaenomeloides and revealed the monophyly of the genus Salix. The complete S. wilsonii chloroplast genome provides an additional sequence-based resource for studying the evolution of organelle genomes in woody plants.
Project description:<i>Meclicope pteleifolia</i> is a traditional medicinal herb and edible plant in Southeast China. Here, we report the complete chloroplast genome of <i>M. pteleifolia</i>. The chloroplast genome is 159,012?bp in length with 38.33% GC content, containing a small single-copy (SSC) region (18,609?bp), a large single-copy (LSC) region (851?bp), and a pair of inverted repeats (IRs: 27,640?bp each). A total of 131 genes were predicted, including 84 protein-coding genes, 8 ribosomal RNA genes, 37 tRNA genes, and 2 pseudogenes. Phylogenetic analysis based on chloroplast genomes of 17 plant species shows that <i>M. pteleifolia</i> is closest to <i>Zanthoxylum</i> and <i>Casimiroa</i>. These complete chloroplast genomes can be subsequently used for researches of Rutaceae.
Project description:The alpine plant Arabis alpina (alpine rock-cress) is a thoroughly studied species in the fields of perennial plant flowering regulation, phylogeography, and adaptation to harsh alpine climatic conditions. We report the complete A. alpina chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The A. alpina cp circular genome is 152,866 bp in length and built of two inverted repeats of 26,933 bp separated by unique regions: a large single copy of 82,338 bp and a small single copy of 17,938 bp. The genome contains 131 genes, some of them being duplicated in the inverted repeats. Seventy-nine unique protein-coding genes were annotated, together with 29 tRNA genes and 4 ribosomal RNA genes. Sequencing and mapping of 23 additional A. alpina DNA samples enabled to gain insight into the intraspecies polymorphism of the sequenced cp genome. Genetic variability among genomes was detected as 44 indels, most of them being located in noncoding regions, and 130 single-nucleotide polymorphisms, 37 of them corresponding to mutations in coding regions. A. alpina chloroplast genome sequence will be helpful in population studies or investigations of chloroplast functions of this alpine plant species.