scholarly journals The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae

2019 ◽  
Vol 20 (12) ◽  
pp. 2886 ◽  
Author(s):  
Ming Yan ◽  
Xueqing Zhao ◽  
Jianqing Zhou ◽  
Yan Huo ◽  
Yu Ding ◽  
...  
Keyword(s):  
Genetic System ◽  
Punica Granatum ◽  
Fruit Trees ◽  
Specific Model ◽  
Sequence Diversity ◽  
Codon Usage Pattern ◽  
Phylogenetic Position ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
A Site

Pomegranates (Punica granatum L.) are one of the most popular fruit trees cultivated in arid and semi-arid tropics and subtropics. In this study, we determined and characterized three complete chloroplast (cp) genomes of P. granatum cultivars with different phenotypes using the genome skimming approach. The complete cp genomes of three pomegranate cultivars displayed the typical quadripartite structure of angiosperms, and their length ranged from 156,638 to 156,639 bp. They encoded 113 unique genes and 17 are duplicated in the inverted regions. We analyzed the sequence diversity of pomegranate cp genomes coupled with two previous reports. The results showed that the sequence diversity is extremely low and no informative sites were detected, which suggests that cp genome sequences may be not be suitable for investigating the genetic diversity of pomegranate genotypes. Further, we analyzed the codon usage pattern and identified the potential RNA editing sites. A comparative cp genome analysis with other species within Lythraceae revealed that the gene content and organization are highly conserved. Based on a site-specific model, 11 genes with positively selected sites were detected, and most of them were photosynthesis-related genes and genetic system-related genes. Together with previously released cp genomes of the order Myrtales, we determined the taxonomic position of P. granatum based on the complete chloroplast genomes. Phylogenetic analysis suggested that P. granatum form a single clade with other species from Lythraceae with a high support value. The complete cp genomes provides valuable information for understanding the phylogenetic position of P. gramatum in the order Myrtales.

scholarly journals Comparative analysis of whole chloroplast genomes of Ligusticum sinense and L. jeholense, Umbelliferae

2020 ◽  
Author(s):  
Shijie Wang ◽  
Tingting Zhang ◽  
Liang Xu ◽  
Zhilai Zhan ◽  
Guihua Bao ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Higher Plants ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Atpase Subunit ◽  
Gene Group ◽  
Gene Variation ◽  
Chloroplast Genomes ◽  
The Difference ◽  
Cp Genome

Abstract Background Gaoben has a long history of application as medicine. There are few records of Liaogaoben in ancient books. The varieties of Ligusticum in practical application are confused. Therefore, it is very important to identify Ligusticum accurately. The phylogenetic position of Ligusticum in Umbelliferae needs to be determined. It is also of great significance to analyze the phylogeny of Ligusticum in Umbelliferae the difference of somatic genome. Methods Chloroplast (cp) genomic DNA was extracted from two species of Ligusticum and sequenced on Hiseq4000 light source. The sequence was assembled into contrags by soapenovo 2.04, aligned with reference genome by blast, and then corrected manually. Genereanation is performed by online dogma tools. The general characteristics of cp genomes of two species were analyzed, and compared with the relative species. The DNA of chloroplasts of higher plants is double stranded covalently closed loop molecule, and its length varies with species. According to the assembly genome sequence of the sequenced samples, combined with the prediction results of the coding genes, the genome of the samples was displayed in circles. After alignment, the evolutionary tree was constructed based on the single nucleotide polymorphism (SNP) of cp genome in 31 species by ML method. Results The whole chloroplast genome of Gaoben and Liaogaoben is 148,515 bp and 148,493 bp, both of which contain IR (IRa and IRb) LSC and SSC. 127 genes have been annotated, including 83 protein coding genes, 8 tRNA and 36 rRNA of all species, and 28 coding genes in IR region. There are six genes in the ATPase subunit of photosynthesis gene group, and there are obvious differences in the types of introns in NADH dehydrogenase subunit between them. In the comparative analysis of Pi value, two significant gene variation points are petG gene and psaL-ycf4 gene. The phylogenetic tree of the whole cp genome of SNP Umbelliferae was constructed, including 28 Umbelliferae and 3 Ligusticum. Conclusions In this study, the cp genomic characteristics of Ligusticum sinense and L. jeholense were identified, which provided a theoretical basis and documentation for the identification and phylogenetic analysis of Ligusticum.

Effect of Humic Preparation ‟BIO-Don” on the Content Nutrients in the Soil and the Quality of Cherries

2021 ◽  
pp. 52-58
Author(s):  
Olga S. Bezuglova ◽  
Artem E. Popov ◽  
Marina N. Dubinina ◽  
Pavel N. Skripnikov
Keyword(s):  
Work Experience ◽  
Fruit Trees ◽  
Soluble Solids ◽  
Experimental Site ◽  
Control Option ◽  
Mobile Phosphorus ◽  
Open Ground ◽  
Working Solution ◽  
A Site

The work deals with the study of the influence of humic preparation ‟BIO-Don” on indicators of soil fertility, the enzymatic activity of Сalcic Chernozem (Pachic) at the experimental site, as well as on the productivity and quality of fruit crops, for example, cherries varieties Talisman and Vasilisa in terms of work experience in the open ground in the territory of «Agrofirm “the Red garden”». Treatment of fruit trees was carried out once by drip irrigation in a dosage of 300 l/ha of working solution with a concentration of gp 0.008 g/l for carbon, soil samples were taken before treatment, two weeks and a month after the application of the humic preparation, a site without the use of “BIO-Don” was used as a control option. The treatment of plants with a humic preparation increases the activity of the enzymes catalase, invertase and phosphatase, especially during the period of mass ripening of fruits. Accordingly, at the same time, the content of mobile phosphorus and exchangeable potassium decreases, which is due to the increased removal of these elements by plants. Chemical analysis of fruit products for the content of soluble solids and titrated acidity revealed a statistically significant increase in these indicators in fruits from areas treated with humic preparation, which is manifested by their greater taste saturation.

scholarly journals Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics

2018 ◽  
Vol 19 (12) ◽  
pp. 3780 ◽  
Author(s):  
Dingxuan He ◽  
Andrew Gichira ◽  
Zhizhong Li ◽  
John Nzei ◽  
Youhao Guo ◽  
...  
Keyword(s):  
Genome Structure ◽  
Morphological Data ◽  
Basal Angiosperm ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Gene Data ◽  
High Degree

The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.

scholarly journals Effect of rejuvenation pruning on the growth, productivity and disease incidence in declining trees of pomegranate (Punica granatum L.) cv. Kandhari Kabuli

2018 ◽  
Vol 10 (1) ◽  
pp. 358-362
Author(s):  
D. P. Sharma ◽  
Niranjan Singh
Keyword(s):  
Bacterial Blight ◽  
Disease Incidence ◽  
Fruit Size ◽  
Punica Granatum ◽  
Fruit Trees ◽  
Fruit Weight ◽  
Shoot Length ◽  
Marketable Yield ◽  
Disease Attack ◽  
Punica Granatum L

Pruning of fruit trees is an important aspect for the improvement of fruit quality and to minimize the pests and disease attack. Pruning was performed in the month of December in seven year old unpruned trees of Punica granatum cv. Knadhdri Kabuli having many interfering branching and a heavy infestation of bacterial blight orchard. The pruning treatments viz., T1: Retention of 15cm fruiting shoot length, T2: Retention of 30cm fruiting shoot length, T3: Retention of 45cm fruiting shoot length, T4: Retention of 60cm fruiting shoot length and T5: control (No heading back and no thinning) plant. The results of the present investigation revealed that among different pruning treatment, the best results in terms of shoot extension (56.34 cm), fruit size (Diameter 9.66 cm and Length 9.65 cm, fruit weight (278.50 g), marketable yield (10.25 kg) and fruit qualities were in fruits from T1 and T2 where retention of 15cm fruiting shoot length respectively and retention of 30cm fruiting shoot length were maintained. However, maximum fruit set (54.73%) was recorded in control, and it decreased with increasing pruning intensity. The pruning treatments also proved beneficial in controlling bacterial blight on fruit (12.86%) and leaf surface (26.60%) to some extent.

scholarly journals Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2137 ◽  
Author(s):  
Xiang-Xiao Meng ◽  
Yan-Fang Xian ◽  
Li Xiang ◽  
Dong Zhang ◽  
Yu-Hua Shi ◽  
...  
Keyword(s):  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Chloroplast Genomes ◽  
Close Relationship ◽  
Cp Genome ◽  
Sanguisorba Officinalis

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

scholarly journals Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1143 ◽  
Author(s):  
Hang Ran ◽  
Yanyan Liu ◽  
Cui Wu ◽  
Yanan Cao
Keyword(s):  
Genomic Structure ◽  
Phylogenetic Analyses ◽  
Sister Relationship ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Flora Of China ◽  
Phylogenetic Resolution ◽  
Sister Relationships ◽  
Phylogenomic Analyses ◽  
Cp Genome

Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.

Taiwan-Specific Model for VS30 Prediction Considering Between-Proxy Correlations

2018 ◽  
Vol 34 (4) ◽  
pp. 1973-1993 ◽  
Author(s):  
On Lei Annie Kwok ◽  
Jonathan P. Stewart ◽  
Dong Youp Kwak ◽  
Pang-Li Sun
Keyword(s):  
Ground Motion ◽  
Prediction Models ◽  
Site Response ◽  
Specific Model ◽  
Weighted Mean ◽  
Response Models ◽  
Database File ◽  
A Site ◽  
Gradient Effects ◽  
Model Weighting

Ergodic site response models are generally conditional on the time-averaged shear wave velocity in the upper 30 m ( V S30). Ground motion databases contain many recordings from Taiwan, and because of site characterization efforts, 56% of recording sites have V S30 derived from measurements. We develop proxy-based V S30 prediction models, one application of which is for the remaining 44% of Taiwan sites. Our approach, which can be suitable for other regions, differs from previous studies in which proxies are based on detailed geologic categories and possible within-category topographic gradient effects. Instead, we use three broad, age-based geologic categories, and for the youngest category of Holocene and Quaternary undivided sediments, we propose models conditioned on gradient and elevation. We also adapt a geomorphic terrain-based method, thus providing two V S30-prediction models. We describe a model weighting scheme that combines the models in consideration of their relative dispersions and correlation, producing a weighted mean and standard deviation natural-log V S30. Included as an electronic supplement is a profile database file and a site database with site parameters for Taiwan ground motion stations.

scholarly journals Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qiu-jie Li ◽  
Na Su ◽  
Ling Zhang ◽  
Ru-chang Tong ◽  
Xiao-hui Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Medicinal Value ◽  
Cp Genome

AbstractPulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.

scholarly journals Comparative analysis of chloroplast genomes indicated different origin for Indian Tea (Camellia assamica) cv TV-1 as compared to Chinese tea

2020 ◽  
Author(s):  
Hukam C. Rawal ◽  
Abhishek Mazumder ◽  
Sangeeta Borchetia ◽  
Biswajit Bera ◽  
S. Soundararajan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Morphological Characteristics ◽  
African Countries ◽  
Chloroplast Genomes ◽  
Assam Tea ◽  
Cp Genome ◽  
Indian Tea ◽  
Simple Sequence ◽  
Different Origin

AbstractTea is an important plantation crop of some Asian and African countries. Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China joining area, yet specific origin of China and Assam tea are not yet clear. In the present study, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus. Cp genome based phylogenetic analysis indicated that Indian Assam Tea, TV-1 formed a different group from that of China tea, indicating that TV-1 might have undergone different domestication and hence owe different origin. The simple sequence repeats (SSRs) analysis and codon usage distribution pattern also supported the clustering order in the cp genome based phylogenetic tree.

scholarly journals Comparative Chloroplast Genome Analysis of Medicinally Important Veratrum (Melanthiaceae) in China: Insights into Genomic Characterization and Phylogenetic Relationships

2020 ◽  
Author(s):  
Ying-min Zhang ◽  
Li-jun Han ◽  
Ying-Ying Liu ◽  
Cong-wei Yang ◽  
Xing Tian ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Blood Stasis ◽  
Genome Comparison ◽  
Phylogenetic Study ◽  
Species Classification ◽  
Chloroplast Genomes ◽  
Genomic Characterization ◽  
Cp Genome

Abstract Background: Veratrum is a genus of perennial herbs that are widely used as traditional Chinese medicine for emetic, resolving blood stasis and relieve pain. However, the species classification and the phylogenetic relationship of the genus Veratrum have long been controversial due to the complexity of morphological variations. Knowledge on the infrageneric relationships of the genus Veratrum can be obtained from their chloroplast genome sequences and increase the taxonomic and phylogenetic resolution.Methods: Total DNA was extracted from ten species of Veratrum and subjected to next-generation sequencing. The cp genome was assembled by NOVOPlasty. Genome annotation was conducted using the online tool DOGMA and subsequently corrected by Geneious Prime. Then, genomic characterization of the Veratrum plastome and genome comparison with closely related species was analyzed by corresponding software. Moreover, phylogenetical trees were reconstructed, based on the 29 plastomes by maximum likelihood (ML) and Bayesian inference (BI) methods.Results: The whole plastomes of Veratrum species possess a typical quadripartite structure, ranging from 151,597 bp to 153,711 bp in size and comprising 135 genes. The gene order, content, and genome structure were nearly identical with a few exceptions across the Veratrum chloroplast genomes. The total number of simple sequence repeats (SSRs) ranged from 31 to 35, and of large sequence repeats (LSRs) ranged from 65 to 71. Seven highly divergent regions (rpoB-trnC, trnT-trnL, trnS-trnG, psbC-psbZ, psbI, ycf1, and ndhF) were identified that can be used for DNA barcoding in the genus of Veratrum. Phylogenetic analyses based on 29 plastomes strongly supported the monophyly of Veratrum. The circumscription and relationships of infrageneric taxa of Veratrum were well evaluated with high resolutions. Conclusions: Our study identified and analyzed the cp genome features of ten Veratrum species, and suggested high effectivity of chloroplast complete genome in resolving generic circumscription in Veratrum. These results will facilitate the identification, taxonomy, and utilization of Veratrum plants as well as the phylogenetic study of Melanthiaceae simultaneously.

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