scholarly journals Extended snake venomics by top-down in-source decay: Investigating the newly discovered Anatolian Meadow viper subspecies, Vipera anatolica senliki

2019 ◽  
Author(s):  
Benjamin-Florian Hempel ◽  
Maik Damm ◽  
Mrinalini ◽  
Bayram Göçmen ◽  
Mert Karış ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Comparative Analysis ◽  
Disulfide Bond ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Venom Gland ◽  
Top Down ◽  
Venom Toxin ◽  
Snake Venomics ◽  
Insight Into

AbstractHerein we report on the venom proteome of Vipera anatolica senliki, a recently discovered and hitherto unexplored subspecies of the critically endangered Anatolian Meadow viper endemic to the Antalya Province of Turkey. Integrative venomics, including venom gland transcriptomics as well as complementary bottom-up and top-down proteomic analyses, were applied to fully characterize the venom of V. a. senliki. Furthermore, the classical top-down venomics approach was extended to elucidate the venom proteome by an alternative in-source decay (ISD) proteomics workflow using the reducing matrix 1,5-diaminonaphthalene (1,5-DAN). Top-down ISD proteomics allows for disulfide bond mapping as well as effective de novo identification of high molecular weight venom constituents, both of which are difficult to achieve by commonly established top-down approaches. Venom gland transcriptome analysis identified 42 venom transcript annotations from 13 venom toxin families. Relative quantitative snake venomics revealed snake venom metalloproteinases (svMP, 42.9%) as the most abundant protein family, followed by several less dominant toxin families. Online mass profiling and top-down venomics provide a detailed insight into the venom proteome of V. a. senliki and facilitates a comparative analysis of venom variability for the closely related subspecies, V. a. anatolica.TOC Figure

scholarly journals Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0134824 ◽  
Author(s):  
Jun Duan ◽  
Tim Ladd ◽  
Daniel Doucet ◽  
Michel Cusson ◽  
Kees vanFrankenhuyzen ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Transcriptome Analysis ◽  
De Novo Assembly ◽  
Functional Annotation ◽  
De Novo ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis

scholarly journals Transcriptome analysis of Euonymus europaeus fruits at different stages of development

2020 ◽  
Author(s):  
O. S. Pavlenko ◽  
N. S. Sadovskaya ◽  
O. N. Mustafayev ◽  
Yu. V. Akashkina ◽  
I. V. Goldenkova-Pavlova
Keyword(s):  
Comparative Analysis ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Globular Embryo ◽  
Mature Fruit ◽  
Stages Of Development ◽  
Euonymus Europaeus

The transcript Euonymus europaeus was collected de novo. A comparative analysis of transcriptomes from the stage of the globular embryo and the mature fruit made it possible to identify key DGAT genes at the contrasting stages of the development of E. europaeus fruits.

scholarly journals Snake venom gland cDNA sequencing using the Oxford Nanopore MinION portable DNA sequencer

2015 ◽  
Author(s):  
John F Mulley ◽  
Adam D Hargreaves
Keyword(s):  
Error Correction ◽  
Single Molecule ◽  
De Novo ◽  
Venom Gland ◽  
Sequencing Error ◽  
Cdna Sequencing ◽  
Venom Toxin ◽  
Oxford Nanopore ◽  
Illumina Data ◽  
Corrected Data

Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper, Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0-2% with hybrid error correction and 3% with de novo error correction. Our corrected data provides full coding sequences and 5' and 3' UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species.

scholarly journals Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1441 ◽  
Author(s):  
Adam D. Hargreaves ◽  
John F. Mulley
Keyword(s):  
Error Correction ◽  
Single Molecule ◽  
De Novo ◽  
Venom Gland ◽  
Sequencing Error ◽  
Cdna Sequencing ◽  
Venom Toxin ◽  
Oxford Nanopore ◽  
Illumina Data ◽  
Corrected Data

Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper,Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0–2% with hybrid error correction and 3% withde novoerror correction. Our corrected data provides full coding sequences and 5′ and 3′ UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species.

Molecular insight into the metabolic activities of a protein-rich micro alga, Arthrospira platensis by de novo transcriptome analysis

2018 ◽  
Vol 45 (5) ◽  
pp. 829-838 ◽  
Author(s):  
Venkatesh Kumaresan ◽  
Anbazahan Sannasimuthu ◽  
Mariadhas Valan Arasu ◽  
Naif Abdullah Al-Dhabi ◽  
Jesu Arockiaraj
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Arthrospira Platensis ◽  
De Novo Transcriptome ◽  
Metabolic Activities ◽  
Protein Rich ◽  
Insight Into

De novo transcriptome analysis of Ammopiptanthus nanus and its comparative analysis with A. mongolicus

Trees ◽  
2017 ◽  
Vol 32 (1) ◽  
pp. 287-300 ◽  
Author(s):  
Fei Gao ◽  
Huayun Li ◽  
Zihua Xiao ◽  
Chunxiang Wei ◽  
Jinchao Feng ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Transcriptome Analysis ◽  
De Novo ◽  
De Novo Transcriptome ◽  
Ammopiptanthus Nanus

scholarly journals De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: a comprehensive venom gland transcriptome analysis from an ant species

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 987 ◽  
Author(s):  
Wafa Bouzid ◽  
Marion Verdenaud ◽  
Christophe Klopp ◽  
Frédéric Ducancel ◽  
Céline Noirot ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Venom Gland ◽  
De Novo Sequencing ◽  
Tetramorium Bicarinatum

scholarly journals Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker Bacterium Lonsdalea populi

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 246
Author(s):  
Xiaomeng Chen ◽  
Rui Li ◽  
Yonglin Wang ◽  
Aining Li
Keyword(s):  
Genome Sequence ◽  
Extracellular Enzymes ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Hybrid Poplars ◽  
A Genome ◽  
Conserved Genes ◽  
Genomic Characterization ◽  
Molecular Bases ◽  
Insight Into

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.

scholarly journals Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fengbin Wang ◽  
Ordy Gnewou ◽  
Charles Modlin ◽  
Leticia C. Beltran ◽  
Chunfu Xu ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Synthetic Peptide ◽  
Quaternary Structure ◽  
De Novo ◽  
Rational Approach ◽  
Lateral Interactions ◽  
Protein Assemblies ◽  
Self Assembling ◽  
Arginine Residues ◽  
Insight Into

AbstractThe exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.

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