Comparative and phylogenetic analysis based on chloroplast genome of Heteroplexis (Compositae), a protected rare genus.

BACKGROUND: Heteroplexis Chang is an endangered genus endemic to China with important ecological and medicinal value. However, due to the lack of genetic data, our conservation strategies have repeatedly been delayed by controversial phylogenetic (molecular) relationships within the genera. In this study, we reported three new Heteroplexis chloroplast (cp.) genomes (H. vernonioides, H. impressinervia and H. microcephala) to clarify phylogenetic relationships between species allocated in this genus and other related Compositae. RESULTS: All three new cp. genomes were highly conserved, showing the classic four regions. Size ranged from 152,984 - 153,221 bp and contained 130 genes (85 protein-coding genes, 37 tRNA, eight rRNA) and two pseudogenes. By comparative genomic and phylogenetic analyses, we found a large-scale inversion of the entire large single-copy (LSC) region in H. vernonioides, H. impressinervia and H. microcephala, being experimentally verified by PCR. The inverted repeat (IR) regions showed high similarity within the five Heteroplexis plastomes, showing small-size contractions. Phylogenetic analyses did not support the monophyly of Heteroplexis genus, whereas clustered the five species within two differentiated clades within Aster genus. These phylogenetic analyses suggested that the five Heteroplexis species might be subsumed into the Aster genus. CONCLUSION: Our results enrich the data on the cp. genomes of the genus Heteroplexis, providing valuable genetic resources for future studies on the taxonomy, phylogeny, and evolution of Aster genus.

Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China.

Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.

Complete chloroplast genome of Kadsura coccinea (Lem.) A.C.Sm. (Schisandraceae): genome structure and evolution.

Kadsura coccinea (Lem.) A.C.Sm. in the Schisandraceae family is woody vine plant, which produce edible red fruits that are rich in nutrients and antioxidant activities. Herein, we assembled the complete chloroplast genome of Kadsura coccinea by next-generation sequencing technologies. The complete chloroplast genome sequence of Kadsura coccinea is 145,413 base pairs (bp) in length, including a pair of inverted repeat regions (IRs, 16,431 bp), one large single-copy region (LSC, 94,511 bp), one small single-copy region (SSC, 18,040 bp). Besides, the complete chloroplast genome contains 126 genes in total, including 82 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that Kadsura coccinea has the closest relationship with Kadsura longipedunculata. Our study lay a foundation for further research of Kadsura coccinea.

The complete chloroplast genome of Keteleeria davidiana var. calcarea (Pinaceae), an endangered species endemic to China.

Keteleeria davidiana var. calcarea is an endangered tree with considerable economic potential that used as timber wood for furniture and house construction. However, the natural population of K. davidiana var. calcarea is very fragmented, which is the cause for its low genetic diversity. In this study, we report the complete chloroplast genome of K. davidiana var. calcarea using Illumina sequencing. The chloroplast genome size is 117,670 bp in length, harboring a pair of very short inverted repeats (IRs) of 262 bp separated by a large single copy (LSC) sequence of 64,634 bp and a small single copy (SSC) sequence of 53,078 bp. The chloroplast genome K. davidiana var. calcarea contains 113 genes (74 protein genes, 35 tRNA genes, and 4 rRNA genes) and the overall GC content is 38.6%. The maximum likelihood phylogenetic analysis shows that K. davidiana var. calcarea is clustered with K. davidiana in genus Keteleeria. This complete chloroplast genome will help us to understand the evolution of K. davidiana var. calcarea and lays the foundations for future studies in this species conservation.

Complete chloroplast genome sequence of Maytenus guangxiensis (celastraceae), a rare and critically endangered species endemic to China.

Maytenus guangxiensis (Celastraceae) is a rare and critically endangered species endemic to China. Here, we first report and characterize its complete chloroplast genome sequence based on Illumina paired-end sequencing data. The complete plastid genome was 157,102 bp, which contained inverted repeats (IR) of 26,476 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 85,559 bp and 18,591 bp, respectively. The cpDNA contains 130 genes, comprising 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of the plastome is 37.3%. The phylogenetic analysis of 19 selected chloroplast genomes demonstrated that M. guangxiensis was close to the species Catha edulis.

The complete chloroplast genome of Vatica guangxiensis S.L. Mo (Dipterocarpaceae): genome structure and evolution.

Vatica guangxiensis S.L. Mo is an evergreen large tree of Dipterocarpaceae. Herein, we assembled the complete chloroplast genome of Vatica guangxiensis by next-generation sequencing technologies. The complete chloroplast genome sequence of Vatica guangxiensis is 151,010 base pairs (bp) in length, including a pair of inverted repeat regions (IRs, 23,827 bp), one large single-copy region (LSC, 83,353 bp), one small single-copy region (SSC, 20,003 bp). Besides, the complete chloroplast genome contains 123 genes in total, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that Vatica guangxiensis has the closest relationship with Vatica mangachapoi. Our study lay a foundation for further research of Vatica mangachapoi.

Species Quantification in Complex Herbal Formulas-Vector Control Quantitative Analysis as a New Method.

Product mislabeling and/or species fraud in Traditional Chinese Medicine (TCM) not only decrease TCM quality, but also pose a potential health issue to the end user. Up to now, methods to control TCM quality have been developed to detect specific metabolites or identify the original species. However, species quantification in complex herbal formulas is rarely concerned. Here, we reported a simple Vector Control Quantitative Analysis (VCQA) method for flexible and accurate multiplex species quantification in traditional Chinese herbal formulas. We developed PCR-based strategy to quickly generate the integrated DNA fragments from multiple targeted species, which can be assembled into the quantitative vector in one round of cloning by Golden Gate ligation and Gateway recombination technique. With this method, we recruited the nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region for the quantification of Ligusticum sinense "Chuanxiong," Angelica dahurica (Hoffm.) Benth. & Hook.f. ex Franch. & Sav., Notopterygium incisum K. C. Ting ex H. T. Chang, Asarum sieboldii Miq., Saposhnikovia divaricata (Turcz.) Schischk., Nepeta cataria L., Mentha canadensis L., and Glycyrrhiza uralensis Fisch. ex DC. in ChuanXiong ChaTiao Wan, a classic Chinese herbal formula with very long historical background. We found that, firstly, VCQA method could eliminate the factors affecting such as the variations in DNA extracts when in combination with the use of universal and species-specific primers. Secondly, this method detected the limit of quantification of A. sieboldii Miq. in formula products down to 1%. Thirdly, the stability of quality of ChuanXiong ChaTiao Wan formula varies significantly among different manufacturers. In conclusion, VCQA method has the potential power and can be used as an alternative method for species quantification of complex TCM formulas.

Complete chloroplast genome sequence of Liquidambar formosana, an ancient subtropical landscape plant to China.

Liquidambar formosana (Hamamelidaceae) is a tertiary relic species widely distributed in subtropical areas, and is a common endemic broad-leaved tree species in south China. Here, we report and describe for the first time the complete chloroplast genome of L. formosana based on Illumina double-ended sequencing data. The complete plastid genome was 160,425 bp, which contained inverted repeats (IR) of 26,266 bp separated by a large single-copy (LSC) and a small single-copy (SSC) of 88,971 bp and 18,922 bp, respectively. The cpDNA contains 132 genes, comprising 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the plastome is 37.9%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that L. formosana was close to the species Sinowilsonia henryi.

Complete chloroplast genome of Paphiopedilum emersonii (Orchidaceae).

Paphiopedilum emersonii is an endemic terrestrial orchid in China. In this study, the chloroplast genome of P. emersonii was determined from BGISEQ-500 sequencing data. The total chloroplast genome was 162,590 bp in length, consisting of a large single-copy region (LSC, 87,852 bp), a small single-copy region (SSC, 870 bp), and two inverted repeat regions (IRA and IRB, 36,934 bp, each). The complete chloroplast genome contains 131 genes, including 81 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. In addition, the phylogenetic analysis indicates that P. emersonii was sister to Paphiopedilum micranthum. The chloroplast genome will contribute to the research and conservation of P. emersonii.

Current knowledge of bermudagrass responses to abiotic stresses.

Bermudagrass (Cynodon spp.) is a common turfgrass found in parks, landscapes, sports fields, and golf courses. It is also grown as a forage crop for animal production in many countries. Consequently, bermudagrass has significant ecological, environmental, and economic importance. Like many other food crops, bermudagrass production also faces challenges from various abiotic and biotic stresses. In this review we will focus on abiotic stresses and their impacts on turfgrass quality and yield. Among the abiotic stresses, drought, salinity and cold stress are known to be the most damaging stresses that can directly affect the production of turfgrass worldwide. In this review, we also discuss the impacts of nutrient supply, cadmium, waterlogging, shade and wear stresses on bermudagrass growth and development. Detailed discussions on abiotic stress effects on bermudagrass morphology, physiology, and gene expressions should benefit our current understanding on molecular mechanisms controlling bermudagrass tolerance against various abiotic stresses. We believe that the rapid development of transcriptomics and proteomics, as well as bermudagrass stable transformation technologies will promote the production of new bermudagrass cultivars with desirable tolerance against abiotic stresses.

The complete chloroplast genome sequence of Helixanthera parasitica (Loranthaceae).

The complete chloroplast genome of Helixanthera parasitica from China was analyzed using next-generation sequencing. The plastome of H. parasitica is a typical quadripartite structure with a length of 125,021 bp, which contained inverted repeats (IR) of 22,752 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 73,151 bp and 6,366 bp, respectively. The cpDNA contains 105 genes, comprising 67 protein-coding genes, 30 tRNA genes, and 8 rRNA genes. The overall GC content of the plastome is 36.5%. Phylogenetic analysis showed that H. parasitica was closely related to the Tolypanthus maclurei.

Complete chloroplast genome of Toona sinensis (Meliaceae), a goluptious 'tree vegetables'.

Toona sinensis, also known as Xiangchun in Chinese, is a popular 'tree vegetables' and famous medicinal plant with good economic value. In our study, we sequenced the complete chloroplast (cp) genome of T. sinensis using the llumina sequencing platform. The cp genome of T. sinensis is a characteristic four-party structure with a length of 157,228 bp, which contains two 26,994 bp inverted repeats (IRs), an 85,971 bp large single copy (LSC), and a 17,269 bp small single copy (SSC). We identified a total of 126 genes, of which clouding 82 protein-coding genes, 36 tRNA genes, and eight rRNA genes. The phylogenetic analysis showed that T. sinensis was closely related to the congeneric T. ciliata.

The complete chloroplast genome sequence of Scurrula parasitica (Loranthaceae).

Scurrula parasitica Linn. is a hemiparasitic shrub distributed in southern China and Southeast Asian countries. Here, we report and characterize the complete plastid genome sequence of S. parasitica in an effort to provide genomic resources useful for the phylogenetic studies for Santalales. The complete chloroplast genome of S. parasitica was 122,599 bp in total sequence length, which containing two inverted repeats (IRs) of 23,137 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 70,237 bp and 6,088 bp, respectively. The cpDNA contains 105 genes, comprising 67 protein-coding genes, 30 tRNA genes, 8 rRNA genes. The overall GC content of the plastome is 37.2%. Phylogenetic analysis with 17 species revealed that S. parasitica was closely related to the congeneric species S. notothixoides.

Complete chloroplast genome sequence of Heteroplexis incana (Asteraceae), a rare species endemic to China.

Heteroplexis incana (Asteraceae) is a rare species endemic to China. Here, we report and characterize the complete chloroplast genome sequence of H. incana based on Illumina paired-end sequencing data. The complete plastid genome was 152,605 bp in length, which contained two inverted repeats (IRs) of 24,954 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,427 bp and 18,270 bp, respectively. The cpDNA contains 132 genes, comprising 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes. The overall GC content of the plastome is 37.3%. The phylogenetic analysis of 17 selected chloroplast genomes demonstrated that Heteroplexis incana was closely related to Aster indicus.

Complete chloroplast genome sequence of Taxillus chinensis (Loranthaceae): a hemiparasitic shrub in South China.

Taxillus chinensis (DC) Danser, which is a hemiparasitic shrub distributed in southern China and Southeast Asian countries, is wildly used in various traditional Chinese medicine prescriptions. In this study, the complete chloroplast genome of the T. chinensis was assembled from the whole genome Illumina sequencing data. The complete plastome is a typical quadripartite structure with a length of 121,305 bp, which contained two inverted repeats (IRs) of 22,460 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 70,295 bp and 6090 bp, respectively. The plastome contains 106 genes, comprising 66 protein-coding genes, 28 tRNA genes, eight rRNA genes, and four processed pseudogenes. The overall GC content of the plastome is 37.4%, which is unevenly distributed across the whole chloroplast genome. The phylogenetic analysis shows that T. chinensis was closely related to the congeneric species T. sutchuenensis.

Complete chloroplast genome sequence of Semiliquidambar cathayensis (hamamelidaceae), a rare and endangered species endemic to China.

Semiliquidambar cathayensis (Hamamelidaceae) is a rare and endangered species endemic to China. Here, we first report and characterize the complete chloroplast genome sequence of S. cathayensis based on Illumina paired-end sequencing data. The complete plastid genome was 160,406 bp in length, which contained two inverted repeats (IRs) of 26,282 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 88,920 bp and 18,922 bp, respectively. The cpDNA contains 132 genes, comprising 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes and one processed pseudogene. The overall GC content of the plastome is 37.9%. The phylogenetic analysis of 20 selected chloroplast genomes demonstrated that S. cathayensis was close to the species Liquidambar formosana.

Complete chloroplast genome sequence of Heteroplexis sericophylla (Asteraceae), a rare and vulnerable species endemic to China.

Heteroplexis sericophylla (Asteraceae) is a rare and vulnerable species endemic to China. Here, we report and characterize the complete chloroplast genome sequence of H. sericophylla based on Illumina paired-end sequencing data. The complete plastid genome was 152,629 bp in length, which contained two inverted repeats (IRs) of 24,954 bp separated by a large single-copy (LSC) and a small single-copy (SSC) of 84,427 bp and 18,294 bp, respectively. The cpDNA contains 131 genes, comprising 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes and one processed pseudogene. The overall GC content of the plastome is 37.3%. The phylogenetic analysis of 17 selected chloroplast genomes demonstrated that H. sericophylla was close to congeneric species H. incana.

Complete chloroplast genome sequence of Annamocarya sinensis (Juglandaceae), an endangered perennial plant.

Annamocarya sinensis (Juglandaceae) is a tertiary relict tree restricted to southeastern China and northern Vietnam. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 160,065 bp, which contained inverted repeats (IR) of 25,786 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 89,759 bp and 18,734 bp, respectively. The cpDNA contains 130 genes, comprising 85 protein-coding genes, 36 tRNA genes, 8 rRNA genes, and one processed pseudogene. The overall GC content of the plastome is 36.3%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that A. sinensis was close to the species Carya kweichowensis.

Complete chloroplast genome sequence of Zanthoxylum nitidum (Rutaceae), an important medicinal shrub.

Zanthoxylum nitidum (Rutaceae) is a scandent prickly shrub and widely distributed in South China. It's well known for its valuable medicinal values due to contains some important secondary metabolites. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 157,253 bp, which contained inverted repeats (IR) of 27,618 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,382 bp and 17,635 bp, respectively. The cpDNA contains 132 genes, comprising 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes. The overall GC content of the plastome is 38.5%. The phylogenetic analysis of 20 selected chloroplast genomes demonstrated that Z. nitidum is closely related to the congeneric Z. bungeanum.

Complete chloroplast genome sequence of Gynostemma pentaphyllum (Cucurbitaceae), a perennial medicinal herb.

Gynostemma pentaphyllum (Cucurbitaceae) is a perennial medicinal herb widely distributed in China. It's well known for its medicinal values due to contains important medicinal components gypenosides. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 154,457 bp, which contained inverted repeats (IR) of 25,603 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,998 bp and 18,253 bp, respectively. The cpDNA contains 132 genes, comprising 81 protein-coding genes, 37 tRNA genes, 8 rRNA genes and six processed pseudogenes. The overall GC content of the plastome is 37.1%. The phylogenetic analysis of 17 selected chloroplast genomes demonstrated that G. pentaphyllum is closely related to the congeneric G. compressum.