scholarly journals Sequences analysis of chloroplast psbA-trnH region in Citrus L. (Rutaceae) species from the Aegean region of Turkey

2021 ◽  
Vol 20 (2) ◽  
pp. e877
Author(s):  
Emre Sevindik ◽  
Gaye Zeynep Canbolat ◽  
İlayda İrem Moral ◽  
Monika Sujka
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Sequence Data ◽  
Citrus Species ◽  
Sequencing Data ◽  
Aegean Region ◽  
Maximum Likelihood Phylogenetic Tree ◽  
Sequences Analysis

In this study, sequences analysis of some Citrus species distributed in Turkey's Aegean region was based on the cpDNA psbA-trnH  region. The sequences for psbA-trnH regions of the outgroups were retrieved from NCBI GenBank. Genomic DNA was isolated from healthy and green leaves. Total genomic DNA was extracted using GeneMark DNA isolation Plant Kit. The psbA-trnH region was amplified using primers psbA and trnH. DNA sequences were edited using the Sequencher 5.4.6. Sequencing data were analyzed using MEGA 6.0 software. Maximum likelihood (ML) tree was created to determine the relationships between Citrus taxa.  cpDNA psbA-trnH  sequences ranged between 426 and 470 nucleotides. Maximum likelihood phylogenetic tree is composed of two clades. The divergence values differed between 0.000 and 0.012. According to the results of the study, the separation of Citrus species in phylogenetic tree obtained with psbA-trnH sequence data was realized. However, it has been found that cpDNA psbA-trnH sequence populations of species belong together. In addition, the phylogenetic relationship between the sequence data of some species belonging to the Rutaceae family taken from NCBI and Citrus species was revealed.

scholarly journals Molecular characterization based on chloroplast (trnl-f) DNA sequence of the apple genotypes in Ardahan/Turkey

2019 ◽  
Vol 48 (4) ◽  
pp. 1099-1106
Author(s):  
Emre Sevindik ◽  
Zehra Tuğba Murathan ◽  
Sümeyye Filiz ◽  
Kübra Yalçin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nucleotide Composition ◽  
Neighbor Joining ◽  
Sequencing Data ◽  
F Region ◽  
Phylogenetic Studies

Genetic diversity among Turkish apple genotypes in Ardahan province was conducted based on cpDNA trnL-F sequences. Apple genotypes were plotted on a phylogenetic tree where Pyrus x bretschneideri was used as the outgroup. The plant samples were collected from different locations and genomic DNA was isolated from healthy and green leaves. For sequence in trnL-F region trnLe and trnFf primers were used. Later obtained DNA sequences were edited using the BioEdit and FinchTV. Sequencing data were analyzed using MEGA 6.0 software. Neighbor joining and bootstrap trees were constructed in order to verify the relationships among the apple genotypes. Phylogenetic tree consisted of two clades. The divergence values of trnL-F sequences differed between 0.000 and 0.005. Average nucleotide composition was 38.3 T, 14.9 C, 31.9 A and 14.9% G. The phylogenetic tree constructed based on trnL-F region sequences was nearly parallel to prior phylogenetic studies on apple genotypes.

scholarly journals Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kuldeepsingh A. Kalariya ◽  
Ram Prasnna Meena ◽  
Lipi Poojara ◽  
Deepa Shahi ◽  
Sandip Patel
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Competitive Inhibition ◽  
Sequence Data ◽  
Homology Model ◽  
Squalene Synthase ◽  
Gymnema Sylvestre ◽  
Gardenia Jasminoides ◽  
Ramachandran Plots ◽  
Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

Strelitziana sarbhoyi sp. nov. (Strelitzianaceae, Chaetothyriales), from North-Western Himalayas, India, described based on morphology and molecular phylogeny

Phytotaxa ◽  
2019 ◽  
Vol 427 (1) ◽  
pp. 51-59
Author(s):  
SHIWALI RANA ◽  
SANJAY KUMAR SINGH ◽  
PARAS NATH SINGH
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Culture Collection ◽  
Fungal Culture ◽  
Western Himalayas ◽  
Holotype Specimen ◽  
North Western

Strelitziana sarbhoyi is established as a new species to accommodate a phylloplane fungus isolated from Mallotus philippensis collected from Kangra region of North-Western Himalayas, Himachal Pradesh. The identity of the fungus is confirmed based on the asexual-morphs, cultural characteristics and phylogenetic analyses of the internal transcribed spacer (ITS) rDNA and partial nuclear ribosomal 28S large subunit (LSU) sequence data. The placement of S. sarbhoyi in the phylogenetic tree was determined based on DNA sequences from authenticated isolates of Strelitziana. Strelitziana sarbhoyi shows nearly 94% similarity with other known species of Strelitziana. Area description is provided for the proposed taxon along with microscopic images, and a phylogenetic tree. This is probably the first report of Strelitziana from India. Holotype specimen (dried voucher culture) is deposited in the Ajrekar Mycological Herbarium (AMH), and an ex-type culture is deposited in National Fungal Culture Collection of India (NFCCI).

scholarly journals ADOPS - Automatic Detection Of Positively Selected Sites

2012 ◽  
Vol 9 (3) ◽  
pp. 18-32 ◽  
Author(s):  
David Reboiro-Jato ◽  
Miguel Reboiro-Jato ◽  
Florentino Fdez-Riverola ◽  
Cristina P. Vieira ◽  
Nuno A. Fonseca ◽  
...  
Keyword(s):  
Amino Acid ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Sequence Data ◽  
Automatic Detection ◽  
Acid Sites ◽  
Nucleotide Sequence Data ◽  
Software Applications ◽  
Codon Substitution ◽  
Positively Selected Sites

Summary Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models. Therefore, a significant effort is made in order to prepare input files for the different software applications and in the analysis of the output of every analysis. In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software. It was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data. An example of the usefulness of such a pipeline is given by showing, under different conditions, positively selected amino acid sites in a set of 54 Coffea putative S-RNase sequences. ADOPS software is freely available and can be downloaded from http://sing.ei.uvigo.es/ADOPS.

scholarly journals Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 847-854
Author(s):  
Linda Cardle ◽  
Luke Ramsay ◽  
Dan Milbourne ◽  
Malcolm Macaulay ◽  
David Marshall ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Simple Sequence Repeats ◽  
Genomic Dna ◽  
Sequence Data ◽  
Average Frequency ◽  
Dna Sequence Data ◽  
Ssr Frequency ◽  
Copy Dna ◽  
Simple Sequence

Abstract The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSRs was one every 6.04 kb in genomic DNA, decreasing to one every 14 kb in ESTs. SSR frequency and type differed between coding, intronic, and intergenic DNA. Similar frequencies were found in other plant species. On the basis of these findings, an approach is proposed and demonstrated for the targeted isolation of single or multiple, physically clustered SSRs linked to any gene that has been mapped using low-copy DNA-based markers. The approach involves sample sequencing a small number of subclones of selected randomly sheared large insert DNA clones (e.g., BACs). It is shown to be both feasible and practicable, given the probability of fortuitously sequencing through an SSR. The approach is demonstrated in barley where sample sequencing 34 subclones of a single BAC selected by hybridization to the Big1 gene revealed three SSRs. These allowed Big1 to be located at the top of barley linkage group 6HS.

Studies on Parmulariaceae I. A phylogeny based on available sequence data; introducing Parmulariales ord. nov., and Hemigraphaceae, Melaspileellaceae and Stictographaceae fam. nov.

Phytotaxa ◽  
2018 ◽  
Vol 369 (2) ◽  
pp. 63 ◽  
Author(s):  
DONG-QIN DAI ◽  
LI-ZHOU TANG ◽  
CHAO LIU ◽  
HAI-BO WANG ◽  
KEVIN D. HYDE
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Tree ◽  
Type Species ◽  
Sequence Data ◽  
Sensu Stricto ◽  
New Order ◽  
Bayesian Analyses ◽  
Phylogenic Analysis ◽  
The Family

The family Parmulariaceae comprises three polyphyletic genera, but with very little data in GenBank and is presently placed in the order Asterinales. In this study, we re-analyze the available sequence data for taxa of the family and re-examine the type species of Hemigrapha, Inocyclus and Parmularia. The phylogenetic tree generated from maximum likelihood and Bayesian analyses of combined LSU-SSU sequence data demonstrate the relationships among Hemigrapha, Inocyclus and Parmularia species, and the relations of Buelliella, Karschia, Labrocarpon, Lembosia, Melaspileella, Melaspileopsis and Stictographa. We introduce Parmulariales ord. nov. to accommodate Parmulariaceae and the order Asterinales accommodates Asterinaceae, Asterotexaceae, Hemigraphaceae fam. nov., Melaspileellaceae fam. nov. and Stictographaceae fam. nov. Notes for each new order and families are provided. We confirm that Asterinaceae sensu lato is distant from Asterinaceae sensu stricto in the phylogenic analysis. The classification presented here is provisional, as more species are needed to re-collected and sequenced. We expect further support for our ordinal and familial lineages, as well as further novel lineages.

scholarly journals Pattern Matching for DNA Sequencing Data Using Multiple Bloom Filters

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Maleeha Najam ◽  
Raihan Ur Rasool ◽  
Hafiz Farooq Ahmad ◽  
Usman Ashraf ◽  
Asad Waqar Malik
Keyword(s):  
Dna Sequencing ◽  
Dna Sequence ◽  
Pattern Matching ◽  
Dna Sequences ◽  
Sequence Data ◽  
Bloom Filters ◽  
Sequencing Data ◽  
Dna Sequence Data ◽  
Efficient Data ◽  
Improved Accuracy

Storing and processing of large DNA sequences has always been a major problem due to increasing volume of DNA sequence data. However, a number of solutions have been proposed but they require significant computation and memory. Therefore, an efficient storage and pattern matching solution is required for DNA sequencing data. Bloom filters (BFs) represent an efficient data structure, which is mostly used in the domain of bioinformatics for classification of DNA sequences. In this paper, we explore more dimensions where BFs can be used other than classification. A proposed solution is based on Multiple Bloom Filters (MBFs) that finds all the locations and number of repetitions of the specified pattern inside a DNA sequence. Both of these factors are extremely important in determining the type and intensity of any disease. This paper serves as a first effort towards optimizing the search for location and frequency of substrings in DNA sequences using MBFs. We expect that further optimizations in the proposed solution can bring remarkable results as this paper presents a proof of concept implementation for a given set of data using proposed MBFs technique. Performance evaluation shows improved accuracy and time efficiency of the proposed approach.

Sign in / Sign up

Export Citation Format

Share Document