scholarly journals Comparative Analysis of Chloroplast Genomes of Thalassiosira Species

2021 ◽  
Vol 8 ◽  
Author(s):  
Kuiyan Liu ◽  
Yang Chen ◽  
Zongmei Cui ◽  
Shuya Liu ◽  
Qing Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Primary Productivity ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Negative Impact ◽  
High Specificity ◽  
Evolutionary Analysis ◽  
Chloroplast Genomes ◽  
Genomic Regions

Thalassiosira is a species-rich genus in Bacillariophyta with important ecological contribution to primary productivity but can also pose negative impact on ecology by developing harmful algal blooms (HABs). However, genomic resources of only a few Thalassiosira species are currently available. Here, we constructed complete chloroplast genomes (cpDNAs) of six Thalassiosira strains (representing six Thalassiosira species T. rotula, T. profunda, T. nordenskioeldii, T. tenera, T. weissflogii, and Thalassiosira sp.), and compared them with published cpDNAs of other diatoms. Comparative analysis revealed that Thalassiosira cpDNAs have generally conventional and conserved quadripartite structure with important exceptions. Gene orders of cpDNAs of Thalassiosira sp. (CNS00561) and T. oceanica were different from that of other Thalassiosira species. Additionally, endosymbiotic gene transfers (EGT) were found to occur in the evolution of Thalassiosira cpDNAs. Furthermore, genomic regions of cpDNAs were found to be highly variable, which could be used to construct molecular markers for distinguishing Thalassiosira species with high resolution and high specificity. This study also demonstrated that Thalassiosira species emerged roughly around 51 MYA and diversified 17–28 MYA. Thalassiosira cpDNAs are not only valuable as super-barcode for phylogenetic analysis, but also important for functional and evolutionary analysis of diatoms.

Phylogenetic Analysis of Dinoflagellate Gonyaulax polygramma SteinResponsible for Harmful Algal Blooms Based on the Partial LSU rDNASequence Data

ALGAE ◽  
2006 ◽  
Vol 21 (3) ◽  
pp. 283-286 ◽  
Author(s):  
Keun-Yong Kim ◽  
Young-Soo Kim ◽  
Choul-Hee Hwang ◽  
Chang-Kyu Lee ◽  
Wol-Ae Lim ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Harmful Algal Blooms ◽  
Algal Blooms

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 Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships

2021 ◽  
Vol 12 ◽  
Author(s):  
Jin Xu ◽  
Chen Liu ◽  
Yun Song ◽  
Mingfu Li
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Future Research ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Chloroplast Genomes

The genus Pennisetum (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of Pennisetum (P. alopecuroides, P. clandestinum, P. glaucum, and P. polystachion) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346–138,119 bp, including a large single-copy region (LSC, 79,380–81,186 bp), a small single-copy region (SSC, 12,212–12,409 bp), and a pair of inverted repeat regions (IRs, 22,284–22,372 bp). The overall GC content of these chloroplast genomes was 38.6–38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions (psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL, and rpl32-trnL), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of Pennisetum. The phylogenetic analysis revealed a close relationship between P. polystachion and P. glaucum, followed by P. clandestinum and P. alopecuroides. The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of Pennisetum species.

scholarly journals Rapid detection of Cyanobacteria by recombinase polymerase amplification combined with lateral flow strips

2018 ◽  
Vol 19 (4) ◽  
pp. 1181-1186
Author(s):  
Jingjing Li ◽  
Chunming Wang ◽  
Xin Yu ◽  
Huirong Lin ◽  
Chen Hui ◽  
...  
Keyword(s):  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
High Specificity ◽  
Lateral Flow ◽  
Recombinase Polymerase Amplification ◽  
Routine Measurement ◽  
Cyanobacterial Species ◽  
Polymerase Chain ◽  
Cell Densities ◽  
Thermal Cycler

Abstract Cyanobacteria are one of the major groups of algae causing algal blooms. In this study, we developed a rapid method for detecting Cyanobacteria using a recombinase polymerase amplification (RPA) method coupled with lateral flow (LF) strips. After releasing cyanobacterial DNA from cells using a freeze-cracking method, DNA was amplified using the RPA method. Next, the RPA products were detected using the LF test. LF-RPA successfully amplified the DNA of eight cyanobacterial species and detected their presence in the sample with high specificity, distinguishing them from five non-cyanobacterial species. The method could detect cyanobacterial DNA in water samples containing as low as 0.01 cell/mL Cyanobacteria, making the method more sensitive than polymerase chain reaction (PCR), which required cell densities of at least 104 cell/mL. LF-RPA could amplify and detect cyanobacterial DNA at any temperature in the range 30–45 °C in just 30 min and without the need for a thermal cycler. The method developed in this study is simple, rapid, and effective for on-site testing of Cyanobacteria, which may become a routine measurement in efforts to detect and treat harmful algal blooms.

scholarly journals The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Feng Wen ◽  
Xiaozhu Wu ◽  
Tongjian Li ◽  
Mingliang Jia ◽  
Xinsheng Liu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Species Discrimination ◽  
Evolutionary Analysis ◽  
Variable Regions ◽  
Triterpenoid Saponins ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes

Abstract Background Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. Results A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. Conclusions This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.

scholarly journals Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

Molecules ◽  
2018 ◽  
Vol 23 (2) ◽  
pp. 437 ◽  
Author(s):  
Jianguo Zhou ◽  
Yingxian Cui ◽  
Xinlian Chen ◽  
Ying Li ◽  
Zhichao Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Molecular Structures ◽  
Papaver Rhoeas ◽  
Chloroplast Genomes

scholarly journals Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12173
Author(s):  
Jiajing Sheng ◽  
Xuan She ◽  
Xiaoyu Liu ◽  
Jia Wang ◽  
Zhongli Hu
Keyword(s):  
Comparative Analysis ◽  
Codon Usage ◽  
Related Species ◽  
Influencing Factor ◽  
Model Organisms ◽  
Evolutionary Analysis ◽  
Optimal Codons ◽  
Chloroplast Genomes ◽  
Representative Species ◽  
Usage Patterns

Miscanthus is not only a perennial fiber biomass crop, but also valuable breeding resource for its low-nutrient requirements, photosynthetic efficiency and strong adaptability to environment. In the present study, the codon usage patterns of five different Miscanthus plants and other two related species were systematically analyzed. The results indicated that the cp genomes of the seven representative species were preference to A/T bases and A/T-ending codons. In addition, 21 common high-frequency codons and 4–11 optimal codons were detected in the seven chloroplast genomes. The results of ENc-plot, PR2-plot and neutrality analysis revealed the codon usage patterns of the seven chloroplast genomes are influenced by multiple factors, in which nature selection is the main influencing factor. Comparative analysis of the codon usage frequencies between the seven representative species and four model organisms suggested that Arabidopsis thaliana, Populus trichocarpa and Saccharomyces cerevisiae could be considered as preferential appropriate exogenous expression receptors. These results might not only provide important reference information for evolutionary analysis, but also shed light on the way to improve the expression efficiency of exogenous gene in transgenic research based on codon optimization.

A comparative analysis of the anthropogenic impact and user-pays principle availability in the model areas of the Russian Federation

2020 ◽  
Vol 18 (9) ◽  
pp. 1787-1798
Author(s):  
S.N. Ayusheeva
Keyword(s):  
Environmental Management ◽  
Comparative Analysis ◽  
Russian Federation ◽  
Natural Environment ◽  
Anthropogenic Impact ◽  
Negative Impact ◽  
Economic Behavior ◽  
Environmental Investment ◽  
The Russian Federation ◽  
Comparative Systems

Subject. This article assesses the effectiveness of the existing system of environmental management based on the user-pays principle in terms of reducing the negative impact on the environment. Objectives. The article aims to conduct a comparative analysis of the anthropogenic impact on natural environment components and deficiency payments for pollution in the model areas of the Russian Federation. Methods. For the study, I used the methods of computational, comparative, systems, and structural analyses. Results. Based on the ecological rating of the Russian Federation subjects, the article defines model areas, assesses the degree of anthropogenic impact on the basis of pollution relative rates, and describes the particularities of environmental investment in the selected areas. Conclusions. The system of payments for pollution does not affect the economic behavior of economic entities.

National coastal management challenges and needs

Shore & Beach ◽  
2020 ◽  
pp. 34-43
Author(s):  
Nicole Elko ◽  
Tiffany Roberts Briggs
Keyword(s):  
Coastal Management ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Local Community ◽  
Extreme Event ◽  
Technical Information ◽  
Interdisciplinary Approach ◽  
Beach Erosion ◽  
The U.S

In partnership with the U.S. Geological Survey Coastal and Marine Hazards and Resources Program (USGS CMHRP) and the U.S. Coastal Research Program (USCRP), the American Shore and Beach Preservation Association (ASBPA) has identified coastal stakeholders’ top coastal management challenges. Informed by two annual surveys, a multiple-choice online poll was conducted in 2019 to evaluate stakeholders’ most pressing problems and needs, including those they felt most ill-equipped to deal with in their day-to-day duties and which tools they most need to address these challenges. The survey also explored where users find technical information and what is missing. From these results, USGS CMHRP, USCRP, ASBPA, and other partners aim to identify research needs that will inform appropriate investments in useful science, tools, and resources to address today’s most pressing coastal challenges. The 15-question survey yielded 134 complete responses with an 80% completion rate from coastal stakeholders such as local community representatives and their industry consultants, state and federal agency representatives, and academics. Respondents from the East, Gulf, West, and Great Lakes coasts, as well as Alaska and Hawaii, were represented. Overall, the prioritized coastal management challenges identified by the survey were: Deteriorating ecosystems leading to reduced (environmental, recreational, economic, storm buffer) functionality, Increasing storminess due to climate change (i.e. more frequent and intense impacts), Coastal flooding, both Sea level rise and associated flooding (e.g. nuisance flooding, king tides), and Combined effects of rainfall and surge on urban flooding (i.e. episodic, short-term), Chronic beach erosion (i.e. high/increasing long-term erosion rates), and Coastal water quality, including harmful algal blooms (e.g. red tide, sargassum). A careful, systematic, and interdisciplinary approach should direct efforts to identify specific research needed to tackle these challenges. A notable shift in priorities from erosion to water-related challenges was recorded from respondents with organizations initially formed for beachfront management. In addition, affiliation-specific and regional responses varied, such as Floridians concern more with harmful algal blooms than any other human and ecosystem health related challenge. The most common need for additional coastal management tools and strategies related to adaptive coastal management to maintain community resilience and continuous storm barriers (dunes, structures), as the top long-term and extreme event needs, respectively. In response to questions about missing information that agencies can provide, respondents frequently mentioned up-to-date data on coastal systems and solutions to challenges as more important than additional tools.

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