This document explores whether next generation sequencing approaches can be used for DNA barcoding of plants. It sequenced chloroplast genomes from 9 plant species using Illumina sequencing without a reference genome. Most chloroplast genomes were successfully assembled de novo or by mapping to related references. Variation between individuals and locations was low but varied between families. Chloroplast barcoding regions could be retrieved along with some nuclear regions at low coverage. Whole chloroplast genome sequencing shows potential as a DNA barcoding method for plants.
DNA sequence analysis of a uniform target gene like the mitochondrial cytochrome oxidase subunit I (COI) to enable species identification has been referred to as “DNA Barcoding”, by analogy with the Universal Product Code (UPC) system barcodes used to identify manufactured goods.
DNA barcoding has the potential to be a practical method for identification of the estimated 10 million species of eukaryotic life on earth.
DNA barcoding is a standardized approach to identifying plants and animals by minimal sequences of DNA, called DNA barcodes.
DNA barcode - short gene sequences taken from a standardized portion of the genome that is used to identify species
and this presentation gives much introducing about DNA barcodes developed for Prokaryotes and Eukaryotes.
Various barcoding genes which are evolutionary conserved.
techniques to develop a DNA bar-code and its future perspectives
Current technologies and future technologies of DNA barcoding. Applications regarding environment awareness. it also contains 2-3 case studies
DNA sequence analysis of a uniform target gene like the mitochondrial cytochrome oxidase subunit I (COI) to enable species identification has been referred to as “DNA Barcoding”, by analogy with the Universal Product Code (UPC) system barcodes used to identify manufactured goods.
DNA barcoding has the potential to be a practical method for identification of the estimated 10 million species of eukaryotic life on earth.
DNA barcoding is a standardized approach to identifying plants and animals by minimal sequences of DNA, called DNA barcodes.
DNA barcode - short gene sequences taken from a standardized portion of the genome that is used to identify species
and this presentation gives much introducing about DNA barcodes developed for Prokaryotes and Eukaryotes.
Various barcoding genes which are evolutionary conserved.
techniques to develop a DNA bar-code and its future perspectives
Current technologies and future technologies of DNA barcoding. Applications regarding environment awareness. it also contains 2-3 case studies
olymerase chain reaction (PCR) is a method widely used in molecular biology to make several copies of a specific DNA segment. Using PCR, copies of DNA sequences are exponentially amplified to generate thousands to millions of more copies of that particular DNA segment.
DNA fingerprinting is a method used to identify living things based on samples of their DNA. Instead of looking at the whole sequence of a person’s DNA, these techniques look at the presence or absence of common markers that can be quickly and easily identified.
DNA cloning is a technique for reproducing DNA fragments.
It can be achieved by two different approaches:
▪ cell based
▪ using polymerase chain reaction (PCR).
a vector is required to carry the DNA fragment of interest into the host cell.
olymerase chain reaction (PCR) is a method widely used in molecular biology to make several copies of a specific DNA segment. Using PCR, copies of DNA sequences are exponentially amplified to generate thousands to millions of more copies of that particular DNA segment.
DNA fingerprinting is a method used to identify living things based on samples of their DNA. Instead of looking at the whole sequence of a person’s DNA, these techniques look at the presence or absence of common markers that can be quickly and easily identified.
DNA cloning is a technique for reproducing DNA fragments.
It can be achieved by two different approaches:
▪ cell based
▪ using polymerase chain reaction (PCR).
a vector is required to carry the DNA fragment of interest into the host cell.
Molecular marker analysis of A few Capsicum annum varietiesAnkitha Hirematha
The hybrid variety and parental varieties among the 3 chilly varieties were identified by finding out the genetic polymorphism between them. It helps to identify different plant varieties, disputed plant varieties, genetic polymorphism between intraspecific crosses of plants and also to protect Plant Breeder’s Rights (PBR). Based on banding pattern on gel, identification of KA, KS and HK chilly varieties using SSR & ISSR markers was successfully carried out.
DNA barcoding was first proposed by Paul Herbert in 2003.
Basic Principle
Dna Barcoding is based on premise that a short standardized sequence can distinguish individuals of a specie because genetic variation between specie exceeds that within specie.
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Abrachium, a new genus in the Clathraceae, and Itajahya reassessedRhudson Cruz
Molecular and morphological analyses have elucidated phylogenetic relationships of two remarkable species in the Phallales: Aseroe floriformis and Phallus roseus. Genes from ATPase subunit 6 (atp6), the nuclear large subunit ribossomal DNA (nuc-LSU), and the second largest RNA polymerase II subunit (RPB2) underwent Bayesian and parsimony molecular analyses. Molecular datasets combined with morphological characters, support a new genus (Abrachium for Aseroe floriformis), reassessment Itajahya, and emendation of Clathraceae.
Lee Miller Current PhD research - extension presentationncsufairyring
Presentation to golf course superintendents outlining work on identification of fairy ring pathogens and a preventive fungicide control program for fairy ring control on golf putting greens.
The International Journal of Engineering and Science (IJES)theijes
The International Journal of Engineering & Science is aimed at providing a platform for researchers, engineers, scientists, or educators to publish their original research results, to exchange new ideas, to disseminate information in innovative designs, engineering experiences and technological skills. It is also the Journal's objective to promote engineering and technology education. All papers submitted to the Journal will be blind peer-reviewed. Only original articles will be published.
DNA Fingerprinting for Taxonomy and Phylogeny.pptxsharanabasapppa
Deoxyribonucleic acid, a self-replicating material which is present in all living organisms as the main constituent of chromosomes.
DNA is made up of molecules called nucleotides. Each nucleotide contains a phosphate group, a sugar group and a nitrogen base.
The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C). The order of these bases is what determinesDNA's instructions, or genetic code.
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My slides at Nordic Testing Days 6.6.2024
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The Metaverse is popularized in science fiction, and now it is becoming closer to being a part of our daily lives through the use of social media and shopping companies. How can businesses survive in a world where Artificial Intelligence is becoming the present as well as the future of technology, and how does the Metaverse fit into business strategy when futurist ideas are developing into reality at accelerated rates? How do we do this when our data isn't up to scratch? How can we move towards success with our data so we are set up for the Metaverse when it arrives?
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SAP Sapphire 2024 - ASUG301 building better apps with SAP Fiori.pdfPeter Spielvogel
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Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
Alt. GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using ...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
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Speakers:
Bob Boule
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Gopinath Rebala
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Welcome to the first live UiPath Community Day Dubai! Join us for this unique occasion to meet our local and global UiPath Community and leaders. You will get a full view of the MEA region's automation landscape and the AI Powered automation technology capabilities of UiPath. Also, hosted by our local partners Marc Ellis, you will enjoy a half-day packed with industry insights and automation peers networking.
📕 Curious on our agenda? Wait no more!
10:00 Welcome note - UiPath Community in Dubai
Lovely Sinha, UiPath Community Chapter Leader, UiPath MVPx3, Hyper-automation Consultant, First Abu Dhabi Bank
10:20 A UiPath cross-region MEA overview
Ashraf El Zarka, VP and Managing Director MEA, UiPath
10:35: Customer Success Journey
Deepthi Deepak, Head of Intelligent Automation CoE, First Abu Dhabi Bank
11:15 The UiPath approach to GenAI with our three principles: improve accuracy, supercharge productivity, and automate more
Boris Krumrey, Global VP, Automation Innovation, UiPath
12:15 To discover how Marc Ellis leverages tech-driven solutions in recruitment and managed services.
Brendan Lingam, Director of Sales and Business Development, Marc Ellis
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At WSTS 2024, Alon Stern explored the topic of parametric holdover and explained how recent research findings can be implemented in real-world PNT networks to achieve 100 nanoseconds of accuracy for up to 100 days.
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
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Securing your Kubernetes cluster_ a step-by-step guide to success !
Hannah McPherson - Plants Plenary
1. Do Next Generation Sequencing
approaches provide the answer
for DNA barcoding of plants?
Hannah McPherson Marlien van der Merwe
Paul Rymer Mark Edwards Maurizio Rossetto
2. Landscape-level studies of the
Australian flora
Species and population
dynamics
Historical and current
processes shaping
distributions and
assemblages of native
trees
Using a range of molecular
tools, life history traits and
modelling
Reproduced from Crisp et al. 2004
3. Next generation sequencing
Exploring new molecular tools and
approaches
NGS to assemble whole chloroplast
genomes
Use of whole chloroplast as a barcode?
Reproduced from Crisp et al. 2004
4. Technical approach
Full genome shotgun sequencing
Solexa Illumina platform (7Gb/lane)
• 8 labelled paired-end libraries
multiplexed in one lane
• Sub-sampled data from single lanes
No reference sequence
Reproduced from Crisp et al. 2004
5. Sampling
2 locations
Nightcap N
* 20 rainforest tree
species
4 individuals
Sydney S
* pooled from each
species for each
site
Reproduced from Crisp et al. 2004
6. reality check: sampling from
rainforests
Collecting and identifying samples
Preserving leaf material
DNA extraction
9/20 plants successfully sequenced from
both North and South
Reproduced from Crisp et al. 2004
7. questions
Can we bioinformatically assemble chloroplast
genomes from whole genomic shotgun
sequencing without a reference?
What levels of variation do we find across a
broad range of species/families?
Can we mine the data for non-chloroplast
regions too?
Is whole/partial chloroplast genome
sequencing a viable option for barcoding?
Reproduced from Crisp et al. 2004
8. Angiosperm Phylogeny
Model organism tree Atherospermataceae
Monimiaceae
Lauraceae
Proteaceae
Euphorbiaceae
Urticaeae
Malvaceae
Sapindaceae,
Meliaceae
Pittosporaceae
From Angiosperm Phylogeny Website
http://www.mobot.org/MOBOT/Research/APweb/welcome.html
11. assembling chloroplast genomes
Map trimmed reads to whole cp genome of
closest relative available on Genbank (CLC)
• Consensus of N & S
De Novo assembly (CLC and Velvet)
• N & S separately
• Local BLAST / cpDNA genome database
Assemble contigs to N & S reference
(Geneious Pro)
14. NC_008325 Daucus carota
Pittosporum multiflorum
Toona ciliata
Synoum glandulosum
NC_008334 Citrus sinensis
Diploglottis cunninghamii
Brachychiton acerifolius
NC_008641 Gossypium barbadense
Claoxylon australe
NC_010433 Manihot esculenta
NC_004993 Calycanthus floridus var. glaucus
Cinnamomum oliveri
Wilkiea huegelii Aligned with MAFFT
RAXML tree from
Doryphora sassafras
Cipres Sci Gateway
~40Kbp excluding gaps
15. quantifying variation
Map trimmed reads to newly constructed
references (assembled contigs)
SNP detection (CLC)
SNP verification
• exploring data
• Sanger sequencing
Reproduced from Crisp et al. 2004
16. SNP detection
Synoum glandulosum (~140Kbp)
• SNPs between N and S
• ~1 in 550bp
• SNPs within N and S
• N ~1 in 2800bp
• S ~1 in 4500bp
reference
reference
Synoum N
Synoum N S
Synoum S
18. data mining
Chloroplast barcoding genes
Universal cpSSR markers
Other data BLAST
The question of coverage
Reproduced from Crisp et al. 2004
19. Citrus
Toona
Wilkiea
Daucus
Synoum
Claoxylon
Doryphora
Gossypium
Diploglottis
Pittosporum
Calycanthus
Brachychiton
Cinnamomum
rbcL a-f F
rbcL a-r R
rbcL 1F
rbcL 724R
accD 1 F
accD 2 F
accD 3 R
accD 4 R
matK 2.1 F
matK 2.1a F
matK X F
matK 3.2 R
matK 5 R
390 F
1326 R
matK_1F
matK_1R
matK_2F
matK_2R
rpoB 1 F
rpoB 2 F
rpoB 3 R
rpoB 4 R
rpoC1 1 F
rpoC1 2 F
rpoC1 3 R
rpoC1 4 R
ycf5 1 F
ycf5 2 F
ycf5 3 R
ycf5 4 R
ndhJ 1 F
ndhJ 2 F
ndhJ 3 R
ndhJ 4 R
trnH2 F
psbAF R
trn H (GUG) F
psb A R
choroplast barcoding loci
atpF F
atpH R
psbK R
psbI R
trnL-c F
trnL-d R
trnL-e F
trnL-f R
trnL-g F
Vijayan and Tsou 2010
trnL-h R
21. data mining
26S coverage ~35-300
Rpb2 only returned when sequence
available in same family or sister family
coverage ~3-5
Resistance genes – good return but
coverage ~2-10
Leafy – no returns
Reproduced from Crisp et al. 2004
22. data mining
Matches were good
Seem to be in more conserved bits
Single copy nuclear genes present but
low coverage
Some difficulty retrieving regions
depending on available data for BLAST
Reproduced from Crisp et al. 2004
23. viability for barcoding
Large portion of the chloroplast genome
retrieved and easily assembled even
without a reference
Potential for retrieving other regions with
increased coverage/ carefully designed
multiplexing
Reproduced from Crisp et al. 2004
24. to sum up the story so far
We can assemble large portions of chloroplast
genomes from whole genomic shotgun
sequencing even without a reference
Variation is low and varies from family to
family
Single copy nuclear genes present but low
coverage?
Is whole/partial chloroplast genome
sequencing a viable option for barcoding?
Reproduced from Crisp et al. 2004
25. acknowledgements
Friends of the Botanic Gardens Trust
Southern Cross University – Robert
Henry Nicole Rice Stirling Bowen
Evolutionary Ecology team at the Royal
Botanic Gardens Sydney
Emma McIntosh Alexander Dohms
Juelian Siow Ashlee Wakefield
Reproduced from Crisp et al. 2004