scholarly journals SAPROBITY IDENTIFICATION OF HYDROBIONT SPECIES OF VERHNIY KABAN LAKE OF KAZAN BY 18S rRNA MARKER GENE

2021 ◽  
Vol 6(72) (4) ◽  
pp. 127-142
Author(s):  
A. E. Sverdrup ◽  
L. L. Frolova
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Indicator Species ◽  
18S Rrna ◽  
Marker Gene ◽  
Ribosomal Genes ◽  
Molecular Phylogenetic Analysis ◽  
Next Generation ◽  
Molecular Phylogenetic ◽  
Generation Sequencing

The paper presents the results of a study of the hypothetical evolution of unicellular hydrobionts from Verhniy Kaban Lake of Kazan by 18S rRNA marker gene with aim of identifying species saprobity based on molecular phylogenetic analysis. Verhniy Kaban Lake is an isolated freshwater reservoir. Its coastline is relatively smooth except for the northern end, which forms swampy and overgrown bay. To the West of lake an urban settlement is situated and to the East are highway and garden plots. Lake length is about 1 km, average and maximum widths are 245 m and 370 m respectively. Deepest point is 15 m; average depth is 8 m; lake area – 25 hectares. Quality of lake water is classified as polluted. One of methods used for ecological assessment of water reservoirs is the bioindication method based on ability of indicator species to survive in water of certain pollution degree. At present, freshwater hydrobiont species from V.Sladechek’s list (1973) are used as indicators. Indicator species lists expand very slowly due to the long process of experimental observations. At the same time, price drop of the next-generation sequencing technologies allows to identify more organisms and run molecular phylogenetic analysis with aim of identifying species saprobity based on study of hypothetic evolution of hydrobionts by marker genes including 18S rRNA. The advantage of using 18S rRNA/16S rRNA ribosomal genes is that they are present in all organisms. Ribosomal genes are ones of the most conservative genes. Therefore, the systematic position of the organism and the time of divergence with closely related species can be determined via analysis of similarities and differences in rRNA sequences. Molecular phylogenetic trees were constructed by the neighbour joining (NJ) and maximal parsimony (MP) methods for Verhniy Kaban Lake hydrobionts identified with next-generation sequencing method (Illumina) by 18S rRNA marker gene (SRR7510986, SRR7465374, SRR7516513). Phylogenetic analysis of hydrobionts of Verhniy Kaban Lake by 18S rRNA marker gene revealed 12 clusters with a high bootstrap value (68–100 %), containing 12 existing indicator species of hydrobionts and 13 unicellular algae and ciliates – indicator species of different saprobity that did not previously have the status of bioindicators – algae: Diplosphaera mucosa (o-b-saprobity), Mucidosphaerium pulchellum (p-a-saprobity), Dinobryon pediforme (b-mesosaprobity), Gomphoneis minuta (b-mesosaprobity), Nitzschia amphibia (o-b-saprobity), Rhabdonema adriaticum (o-b-saprobity), Synura mammillosa (b-o-saprobity), Cryptomonas ozolini (b-mesosaprobity); ciliates: Astylozoon enriquesi (b-mesosaprobity), Blepharocorys curvigula (p-saprobity), Enchelys gasterosteus (p-saprobity), Monocoronella carnea (a-b-mesosaprobity), Plagiopogon loricatus (b-a-mesosaprobity). Most identified indicator species group near b-mesosaprobity. This indicates ecological state of Verhniy Kaban Lake as polluted by ecological assessments.

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

scholarly journals The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7415
Author(s):  
An Huang ◽  
Shuo Liu ◽  
Haijun Li ◽  
Hongdi Luo ◽  
Qingyong Ni ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Control Region ◽  
Evolutionary Process ◽  
Tree Frog ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Mitogenome Sequence ◽  
Nd5 Gene ◽  
Generation Sequencing

The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.

Reassortant Cache Valley virus associated with acute febrile, non-neurologic illness, Missouri

2021 ◽  
Author(s):  
Molly Baker ◽  
Holly R Hughes ◽  
S Hasan Naqvi ◽  
Karen Yates ◽  
Jason O Velez ◽  
...  
Keyword(s):  
Renal Failure ◽  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Lactic Acidosis ◽  
Adult Male ◽  
Gastrointestinal Symptoms ◽  
Next Generation ◽  
Cache Valley Virus ◽  
Cache Valley ◽  
Generation Sequencing

Abstract An adult male from Missouri sought care for fever, fatigue, and gastrointestinal symptoms. He had leukopenia and thrombocytopenia and was treated for a presumed tickborne illness. His condition deteriorated with respiratory and renal failure, lactic acidosis, and hypotension. Next-generation sequencing and phylogenetic analysis identified a reassortant Cache Valley virus.

The origin of Alopecurus × brachystylus Peterm. according to the results of next-generation sequencing (NGS)

2020 ◽  
Vol 19 (1) ◽  
pp. 5-7
Author(s):  
A. A. Gnutikov ◽  
N. N. Nosov ◽  
E. O. Punina ◽  
A. V. Rodionov
Keyword(s):  
Next Generation Sequencing ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Next Generation ◽  
Illumina Platform ◽  
Its1 Sequence ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

A molecular phylogenetic study of the hybrid species Alopecurus × brachystylus Peterm. and somesupposed ancestral taxa was carried out. Next-generation sequencing (NGS) of the ITS1 sequence and the start of the5.8S rRNA gene was used on the Illumina platform. According to NGS sequencing, genome of the A. × brachystylusforms common subgenomes with representatives of the section Alopecurium: A. geniculatus and A. aequalis, as well asrepresentatives of the type section: A. pratensis, A. arundinaceus, and alpine A. vlassowii. In addition, it was found thatA. vlassowii (section Alopecurus) contains sequences identical to the species of another section, Alopecurium.

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