Polyploids and Chromosomes Lecture Japanese Genetics Society Heslop-Harrison ...Pat (JS) Heslop-Harrison
Polyploidy, its occurrence in plants, consequences and evolutionary significance. Lecture to Japanese Genetics Society, Okayama, September 2017. Covering wheat and its evolution
Homo sapiens (human pepsin) NCBI GENBANKShreyaBhatt23
GenBank format and FASTA format as homo sapiens pepsin as an example bioinformatics practical 1st experiment ; sequence retrival from nucleotide sequence from NCBI
SNP discovery in African taurine and Zebu cattle by whole genome sequencing o...ILRI
Poster by Noyes HA, Agaba M, Anderson SI, Archibald AL, Ashelford K, Bradley D, Brass A, Finalyson HA, Hanotte O, Kay S, Kemp SJ, Khodadadi M, Law AS, Lu Z, Smith S, Talbot R, and Hall N. For the BecA Opening, Nairobi, 5 November 2010
Polyploids and Chromosomes Lecture Japanese Genetics Society Heslop-Harrison ...Pat (JS) Heslop-Harrison
Polyploidy, its occurrence in plants, consequences and evolutionary significance. Lecture to Japanese Genetics Society, Okayama, September 2017. Covering wheat and its evolution
Homo sapiens (human pepsin) NCBI GENBANKShreyaBhatt23
GenBank format and FASTA format as homo sapiens pepsin as an example bioinformatics practical 1st experiment ; sequence retrival from nucleotide sequence from NCBI
SNP discovery in African taurine and Zebu cattle by whole genome sequencing o...ILRI
Poster by Noyes HA, Agaba M, Anderson SI, Archibald AL, Ashelford K, Bradley D, Brass A, Finalyson HA, Hanotte O, Kay S, Kemp SJ, Khodadadi M, Law AS, Lu Z, Smith S, Talbot R, and Hall N. For the BecA Opening, Nairobi, 5 November 2010
Genotoxicity of Eleusine indica (Nkim enang: Efik) was investigated in the Wister strain albino rat (Rattus novergicus). Nine (9) male and nine (9) female rats were randomly assigned to three (3) groups, of which two were exposed to the aqueous extract of E.indica – Group A (control-no extract)), Group B (50 mg/kg BW of E. indica) and Group C (100 mg/kg BW of E. indica). This was administered to the rats by oral gavage for 14 days after which the peripheral blood from the tail tips were collected and assayed for the presence of micronuclei, following standard procedures. Proximate analysis and phytochemical screening of the herb extract was carried out. Results obtained showed that E. indica did not cause any significant (P > 0.05) increase in the incidence of micronucleated polychromatic erythrocytes in rat peripheral blood at any of the doses administered. The polychromatic: normochromatic erythrocyte (PCE: NCE) ratio was found to be in the range of 0.50 ± 0.11 to 0.55 ± 0.02. Also, the aqueous herb extract is rich in Carbohydrates (76.17%) and Tannins (21.76%). Mean body weights (MBW) of rats showed normal distribution throughout the duration of the investigation. The results of this study demonstrate that E. indica does not confer any genotoxicity in mammals. Further in-depth study on its efficacy is recommended.
An overview of some work on the DNA, genomes, chromosomes and genes in saffron crocus, Crocus sativus, from our lab, with mention of other work with whole genome assemblies from several countries, and analysis of repetitive DNA components by in situ hybridization.
A plant genome project aims to discover all genes and their function in a particular plant species.
The main objective of genomic research in any species is to sequence the whole genome and functions of all the different coding and non-coding sequences.
These techniques helped in preparation of molecular maps of many plant genomes.
Plant genome projects initially focused on a few model organisms that are characterized by small genomes or their amenability to genetic studies
Since sequencing technologies have moved on, sequencing cost have dropped and bioinformatics tools advanced, the genomes of many plant species including the enormous genome of bread wheat have been assembled
Genome sequencing projects have been carried out on all three plant genomes: the nuclear, chloroplast and mitochondrial genomes
This opened venues for advanced molecular breeding and manipulation of plant species, but also have accelerated phylogenetics studies amongst species
Several excellent curated plant genome databases, besides the general nucleotide data base archives, allow public access of plant genomes
Rapid Impact Assessment of Climatic and Physio-graphic Changes on Flagship G...Arvinder Singh
‘NATIONAL CONFERENCE ON MAN AND ENVIRONMENT’October 15 – 16, 2012
Organized by
Department of Zoology and Environmental Sciences, Punjabi University, Patiala (Pb.) – 147 002, India
Evolution of North American MicruracarusRachel Shoop
My research focuses on the evolution of North American water mites in the genus Arrenurus, Subgenus Micruracarus. In this presentation, I discuss why I chose to study these little known critters, and present some preliminary findings. Please contact me for more info.
Genome Sequencing in Finger Millet
Genome size estimation
SOLiD Sequencing Technology
Illumina Sequencing Technology
Gene prediction and functional annotation of genes
Mining of plant transcription factors and other genes
Reported some species of plant parasitic nematodes from rhizosphere of peanut...Open Access Research Paper
In order to identify of peanut fields plants parasitic nematodes, 130 samples of soil around the roots of peanut plants were collected in province of Guilan, during the summer and fall of 2011. After extraction, killing, fixation and transferring to anhydrous glycerol, the nematodes were mounted on permanent microscopic slides and nematodes species identified by using light microscope, equipped with digital camera, based on morphological and morphometric characters using valid keys. In this study 20 species belonging 17 genera were identified, that are as followes: 1- Aphelenchoides sacchari 2-Aphelenchus avenae 3- Basiria graminophila 4-Coslenchus costatus 5-Ditylenchus myceliophagus 6-Filenchus vulgaris 7-Helicotylenchus digonichus 8-Heterodera cruciferae 9-Meloidogyne incognita 10-Meloidogyne hapla 11-Merlinius bavaricus 12- Mesocriconemarusticum13- Mesocriconema curvatum 14-Paratylenchus nanus 15-Pratylenchus neglectus 16- Psilenchus hilarulus 17-Quinsulcius capitatus 18-Tylenchorhynchus annulatus 19- Tylenchorhynchus mashhoodi 20- Tylenchus davainei. In thisstudy, 20 species belonging 17 genera were identified that before just 6 Species2-5-7-11-15-16were reported from rhizosphere of Peanut in Iran. Other species (14 Species) are going to report from rhizosphere of Peanut in Iran as a first.
Similar to Latest Advances in Coffea Genomics (20)
Forest and agroforesty options for building resilience in refugee situations:...World Agroforestry (ICRAF)
Humanitarian Networks and Partnerships Week (HNPW) 2020
Climate Crisis Inter-Network
"Fit for Purpose? Current Tools and Approaches to Mitigate Climate Risks in Humanitarian Settings"
HLPE 2019. Agroecological and other innovative approaches for sustainable agriculture and food systems that enhance food security and nutrition. A report by the High Level Panel of Experts on Food Security and Nutrition of the Committee on World Food Security, Rome
Vulnerabilities of forests and forest dependent people
Peter Minang, FTA, ICRAF
Social and environmental justice as a trigger of robust ambitious climate action and prosperous future for all
Chilean pavilion, COP 25, Madrid, 7th December 2019
An increasing multitude of insect pests and pathogens is targeting indigenous trees of natural forests, agroforestry systems, and exotic trees in planted forests in Africa. This is raising major concerns for a continent already challenged by adaptations to climate change, as it threatens a vital resource for food security of rural communities, economic growth, and ecosystem conservation. The accidental introduction through trade of non‐native species in particular is accelerating, and it adds to the damage to tree‐based landscapes by native pests and diseases. Old‐time and new invaders heavily impact planted forests of exotic eucalypts, pines, and acacias, and are spreading quickly across African regions. But many non‐native pathogens are recently found affecting important indigenous trees.
Decent work and economic growth: Potential impacts of SDG 8 on forests and fo...World Agroforestry (ICRAF)
This paper assesses the potential impact of Sustainable Development Goal (SDG) 8 on forests and forest-dependent people. The concepts of decent work and economic growth are put in the context of predominant development theories and paradigms (modernization, economic growth, basic needs, sustainable development) which shape the agendas of governments, private sector, civil society, and investors. These stakeholders pursue different goals and interests, with uneven prioritization of SDG 8 targets and mixed impacts on forests and livelihoods.
Forest conservation and socio-economic benefits through community forest conc...World Agroforestry (ICRAF)
With an extension of 2.1 million ha, the Maya Biosphere Reserve (MBR) in Petén, Guatemala is the largest protected area in Central America. To reconcile forest conservation and socio-economic development, community forest concessions were created in its Multiple Use Zone (MUZ) in the late 1990s and early 2000s. Operated by a community forest enterprise (CFE), and with a cycle of 25 years, the concessions grant usufruct rights to local communities on an area of about 400,000 ha. Currently, nine concessions are active, while the contracts of two concessions were cancelled and the management plan of another suspended.
Sustainable land management for improved livelihoods and environmental sustai...World Agroforestry (ICRAF)
A healthy viable multifunctional landscape has the capability of supporting sustainable agricultural productivity, providing agroforestry and forest products (timber, fuel wood, fruits, medicine, fertilizer, gum etc.) for the sustenance of mankind while providing other environmental services. However these products are increasingly becoming unavailable due to declining soil fertility, climatic extremes, and high costs of inputs. Identifying low-cost, sustainable ways to attain food security and sustainable environment for millions of smallholder farmers in Sub Saharan Africa (SSA) remains a major developmental challenge.
Rangelands are more than just grass but rather complex and biodiverse ecosystems. Covering nearly half the world’s land area, they are in need of restoration and sustainable management.
Goodbye Windows 11: Make Way for Nitrux Linux 3.5.0!SOFTTECHHUB
As the digital landscape continually evolves, operating systems play a critical role in shaping user experiences and productivity. The launch of Nitrux Linux 3.5.0 marks a significant milestone, offering a robust alternative to traditional systems such as Windows 11. This article delves into the essence of Nitrux Linux 3.5.0, exploring its unique features, advantages, and how it stands as a compelling choice for both casual users and tech enthusiasts.
Observability Concepts EVERY Developer Should Know -- DeveloperWeek Europe.pdfPaige Cruz
Monitoring and observability aren’t traditionally found in software curriculums and many of us cobble this knowledge together from whatever vendor or ecosystem we were first introduced to and whatever is a part of your current company’s observability stack.
While the dev and ops silo continues to crumble….many organizations still relegate monitoring & observability as the purview of ops, infra and SRE teams. This is a mistake - achieving a highly observable system requires collaboration up and down the stack.
I, a former op, would like to extend an invitation to all application developers to join the observability party will share these foundational concepts to build on:
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
Communications Mining Series - Zero to Hero - Session 1DianaGray10
This session provides introduction to UiPath Communication Mining, importance and platform overview. You will acquire a good understand of the phases in Communication Mining as we go over the platform with you. Topics covered:
• Communication Mining Overview
• Why is it important?
• How can it help today’s business and the benefits
• Phases in Communication Mining
• Demo on Platform overview
• Q/A
Dr. Sean Tan, Head of Data Science, Changi Airport Group
Discover how Changi Airport Group (CAG) leverages graph technologies and generative AI to revolutionize their search capabilities. This session delves into the unique search needs of CAG’s diverse passengers and customers, showcasing how graph data structures enhance the accuracy and relevance of AI-generated search results, mitigating the risk of “hallucinations” and improving the overall customer journey.
In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
We will explore the capabilities of AI in understanding XML markup languages and autonomously creating structured XML content. Additionally, we will examine the capacity of AI to enrich plain text with appropriate XML markup. Practical examples and methodological guidelines will be provided to elucidate how AI can be effectively prompted to interpret and generate accurate XML markup.
Further emphasis will be placed on the role of AI in developing XSLT, or schemas such as XSD and Schematron. We will address the techniques and strategies adopted to create prompts for generating code, explaining code, or refactoring the code, and the results achieved.
The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
The presentation aims to deliver a comprehensive overview of AI usage in XML development, providing attendees with the necessary knowledge to make informed decisions. Whether you’re at the early stages of adopting AI or considering integrating it in advanced XML development, this presentation will cover all levels of expertise.
By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
DevOps and Testing slides at DASA ConnectKari Kakkonen
My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
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.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
Unlocking Productivity: Leveraging the Potential of Copilot in Microsoft 365, a presentation by Christoforos Vlachos, Senior Solutions Manager – Modern Workplace, Uni Systems
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...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.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
Why You Should Replace Windows 11 with Nitrux Linux 3.5.0 for enhanced perfor...SOFTTECHHUB
The choice of an operating system plays a pivotal role in shaping our computing experience. For decades, Microsoft's Windows has dominated the market, offering a familiar and widely adopted platform for personal and professional use. However, as technological advancements continue to push the boundaries of innovation, alternative operating systems have emerged, challenging the status quo and offering users a fresh perspective on computing.
One such alternative that has garnered significant attention and acclaim is Nitrux Linux 3.5.0, a sleek, powerful, and user-friendly Linux distribution that promises to redefine the way we interact with our devices. With its focus on performance, security, and customization, Nitrux Linux presents a compelling case for those seeking to break free from the constraints of proprietary software and embrace the freedom and flexibility of open-source computing.
A tale of scale & speed: How the US Navy is enabling software delivery from l...sonjaschweigert1
Rapid and secure feature delivery is a goal across every application team and every branch of the DoD. The Navy’s DevSecOps platform, Party Barge, has achieved:
- Reduction in onboarding time from 5 weeks to 1 day
- Improved developer experience and productivity through actionable findings and reduction of false positives
- Maintenance of superior security standards and inherent policy enforcement with Authorization to Operate (ATO)
Development teams can ship efficiently and ensure applications are cyber ready for Navy Authorizing Officials (AOs). In this webinar, Sigma Defense and Anchore will give attendees a look behind the scenes and demo secure pipeline automation and security artifacts that speed up application ATO and time to production.
We will cover:
- How to remove silos in DevSecOps
- How to build efficient development pipeline roles and component templates
- How to deliver security artifacts that matter for ATO’s (SBOMs, vulnerability reports, and policy evidence)
- How to streamline operations with automated policy checks on container images
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.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
Enchancing adoption of Open Source Libraries. A case study on Albumentations.AIVladimir Iglovikov, Ph.D.
Presented by Vladimir Iglovikov:
- https://www.linkedin.com/in/iglovikov/
- https://x.com/viglovikov
- https://www.instagram.com/ternaus/
This presentation delves into the journey of Albumentations.ai, a highly successful open-source library for data augmentation.
Created out of a necessity for superior performance in Kaggle competitions, Albumentations has grown to become a widely used tool among data scientists and machine learning practitioners.
This case study covers various aspects, including:
People: The contributors and community that have supported Albumentations.
Metrics: The success indicators such as downloads, daily active users, GitHub stars, and financial contributions.
Challenges: The hurdles in monetizing open-source projects and measuring user engagement.
Development Practices: Best practices for creating, maintaining, and scaling open-source libraries, including code hygiene, CI/CD, and fast iteration.
Community Building: Strategies for making adoption easy, iterating quickly, and fostering a vibrant, engaged community.
Marketing: Both online and offline marketing tactics, focusing on real, impactful interactions and collaborations.
Mental Health: Maintaining balance and not feeling pressured by user demands.
Key insights include the importance of automation, making the adoption process seamless, and leveraging offline interactions for marketing. The presentation also emphasizes the need for continuous small improvements and building a friendly, inclusive community that contributes to the project's growth.
Vladimir Iglovikov brings his extensive experience as a Kaggle Grandmaster, ex-Staff ML Engineer at Lyft, sharing valuable lessons and practical advice for anyone looking to enhance the adoption of their open-source projects.
Explore more about Albumentations and join the community at:
GitHub: https://github.com/albumentations-team/albumentations
Website: https://albumentations.ai/
LinkedIn: https://www.linkedin.com/company/100504475
Twitter: https://x.com/albumentations
2. An
introduc7on
to
the
Coffea
Genus
The
Coffea
genus
belongs
to
the
Rubiaceae
family
Fourth
Angiosperm
family:
650
genera
and
13,000
species
Other
known
genera
in
the
family:
Gardenia
Cinchona
(quinine)
Rubia
Ixora
(madder)
3. An
introduc7on
to
the
Coffea
Genus
The
Coffea
genus
has
been
recently
increased
with
the
addi7on
of
the
former
genus
Psilanthus.
This
“new”
enlarged
genus
contains
124
described
species
origina7ng
from
Africa,
Madagascar
and
other
Indian
Ocean
islands,
Asia
and
Australia.
From
Davis
et
al.
Botanical
Journal
of
the
Linnean
Society,
2011,
167:
357–377.
4. An
introduc7on
to
the
Coffea
Genus
The
Coffea
genus
is
very
diverse,
it
includes
the
previously
called
subgenus
Coffea,
the
Baracoffea
alliance
and
the
former
Psilanthus
genus
which
was
itself
divided
in
2
subgenera.
The
subgenus
Coffea
is
dived
in
3
botanical
sec7ons:
The
Eucoffea,
found
in
West
and
Central
Africa
The
Mozambicoffea,
found
in
East
Africa
The
Mascarocoffea,
found
in
Madagascar
and
some
Indian
Ocean
Islands.
C
w
E
MMozambicoffea
Eucoffea
Mascarocoffea
5. An
introduc7on
to
the
Coffea
Genus
The
Baracoffea
alliance
is
exclusively
encountered
in
western
Madagascar.
The
ex-‐Psilanthus
species
are
more
widely
spread
as
they
are
origina7ng
from
Africa,
Madagascar,
Asia
and
Australia
6. An
introduc7on
to
the
Coffea
Genus
C.
arabica
is
the
sole
tetraploid
(2n=4x=44)
of
the
genus
and
one
of
the
rare
auto
fer7le
species.
All
the
others
are
diploid
(2n=2x=22)
and
almost
all
are
allogamous.
C.
arabica
is
an
allotetraploid
resul7ng
from
a
spontaneous
hybridiza7on
between
C.
canephora
and
a
wild
East
African
species:
C.
eugenioides.
It
is
a
recent
event
<
0.6
Mya
x
C.
canephora
♂
C.
eugenioides
♀
C.
arabica
7. An
introduc7on
to
the
Coffea
Genus
The
Coffea
genus
has
a
large
phenotypic
diversity
C.
macrocarpa
Mas
C.
pterocarpa
Mad
C.
liberica
WA
C.
brevipes
W/CA
C.
congensis
W/CA
C.
eugenioides
EA
C.
millo5i
Mad
C.
racemosa
EA
C.
kapakata
W/S
C.
pseudozanguebariae
EA
C.
arabica
EA
C.
liberica
var
Koto
W/CA
8. Coffee
economical
importance
Out
of
the
124
species,
only
2
are
widely
cul7vated:
C.
arabica
(Arabica)
and
C.
canephora
(Robusta).
65-‐70%
and
35-‐30%
respec7vely.
Second
trade
product
exported
by
Southern
countries
(aber
oil).
400
Billions
of
coffee
cup
drunk
every
year;
12,000
each
second.
Grown
all
over
the
world
in
intertropical
regions
Robusta
Both
Arabica
10. Molecular
markers
Molecular
markers
are
used
for:
Iden7fying
the
gene7c
diversity
of
popula7ons
/
species
Establishing
the
gene7c
structure
of
popula7ons
/
species)
Iden7fying
species
/
individuals
(Finger
prin7ng
–
barcoding)
Establishing
gene7c
maps
The
most
used
markers
nowadays
are:
SSR:
Single
Sequence
Repeats
=
microsatellites
SNP:
Single
Nucleo7de
Polymorphism
Both
have
their
sequence
known,
they
are
numerous
in
any
genome
and
they
are
co-‐
dominant.
11. Molecular
markers
A
large
set
of
molecular
markers
is
established,
SSR
and
SNPs.
These
markers
are
compiled
in
two
public
data
banks:
MoccaDB
and
SGN
Plechakova
et
al.
BMC
Plant
Biology,
2009;
9:
123.*
Mueller
et
al.
Pl.
Physiol.
2005
138:
1310-‐1317
12. Gene7c
maps
A
C.
canephora
saturated
gene7c
map.
SSR,
SNPs
and
BACs
were
used
to
construct
this
map.
The
present
interna7onal
map
contains
≈3000
markers,
mainly
SNPs
No
saturated
C.
arabica
gene7c
maps
are
available
yet.
From:
de
Kochko
et
al.
Advances
in
Botanical
Research;
2010,
53:
23-‐63.
*
13. Genome
size
Coffea
genome
sizes
vary
from
simple
to
double:
From:
Cross
et
al.
Can.
J.
Bot.
73:
14-‐20;
-‐
Noirot
et
al.
Ann
Bot
92:
709-‐714*;
-‐
Razafinarivo
et
al.
TGG
in
press
(December
2012
issue)
*
14. Chromosome
organiza7on
From:
Hamon
et
al.
Chr.
Res.
2009,
17:
291-‐304*
Schema7c
representa7on
of
chromosomes
in
different
Coffea
species.
5SrDNA
are
in
green
18SrDNA
are
in
red
West
and
Central
Africa
species
present
1
satellite
chromosome
as
well
as
Malagasy
ones
while
East
African
species
have
two.
The
genus
presents
a
differen7al
chromosome
structural
organiza7on
15. Genome
size
and
structure
There
is
a
geographical
related
divergence
in
the
genome
size
and
chromosome
organiza7on
DEW
(1.41)
LIB
(1.41)
HUM
(1.76)
EUG
(1.36)
HET
(1.74)
CAN
(1.45)
PSE
(1.13)
RAC
(1.03)
MIL
(1.32)
TET
(1.07)
16. EST
and
RNASeq
Publicly
available
ESTs:
254
474
Sanger
ESTs
in
total
Mainly
origina7ng
from
the
two
cul7vated
species:
174
275
ESTs
for
C.
arabica;
from
different
organs
and
7ssues
and
from
rust
infected
leaves
69
066
ESTs
for
C.
canephora
also
from
different
organs
and
7ssues
10
838
ESTs
for
C.
racemosa,
a
wild
East
African
species
drought
tolerant
295
are
from
different
sources,
hybrid
plants
and
only
18
from
C.
eugenioides
a
puta7ve
parent
of
C.
arabica
Non
publicly
available
and
NGS
cDNA
sequences
are
much
more
numerous,
e.g.
the
C.
canephora
sequencing
consor7um
project
produced
130.106
Illumina
reads.
17. BAC
libraries
For
C.
canephora:
One
BAC
library
from
the
genotype
126,
an
improved
cul7var.
DNA
digested
with
HindIII
Two
libraries
from
the
genotype
HD200-‐94,
a
double
haploid
used
for
genome
sequencing.
DNA
digested
with
HindIII
and
BstYI.
Leroy
et
al.
2005;
TAG.
111:
1032-‐1041
-‐
de
Kochko
et
al.
2010;
Ad.
Bot.
Res.
53:
22-‐63*
For
C.
arabica:
One
library
from
the
variety
IAPAR59,
an
improved
variety.
DNA
digested
with
HindIII
One
library
from
the
Mokka
variety.
DNA
digested
with
HindIII
Noir
et
al.
2004;
Theor.
Appl.
Genet.
109:
225-‐230
–
Jones
et
al.
2005;
21st
ASIC
conference
BAC
libraries
have
exclusively
been
build
for
the
two
cul7vated
species
19. General
structure
of
Class
II
elements
-‐
DNA
transposons
ITR
=
Inverted
Terminal
Repeat
Transposase
ITR
ITR
CAGC...
GTCG...
...GCTG
...CGAC
Transposable
elements
MITE autonomous copy
trans
ORF
20. Class
I
transposable
elements:
Retrotransposons
Structure
of
a
LTR
retrotransposon
gag=
capside
protein
(Group
An7Gene)
Transposable
elements
UTR
gag
pol
pol=
polyprotein
contains
all
the
func7ons
for
the
element
replica7on
(polymerase)
LTR
5'
LTR
3'
UTR=
Untranslated
region
UTR
21. The
other
Class
I
elements:
LINEs
et
SINEs
(Retroposons
or
non-‐LTR
retroelements)
Transposable
elements
SINEs
gag
LINEs
pol
22. Coffea
Transposable
elements
Iden7fica7on
and
use
of
transposable
elements
in
Coffea
has
been
ini7ated
only
recently.
Iden7fica7on
of
TE
casseqes
in
ESTs
and
unigenes.
Lopes
et
al.
2008,
Mol.
Genet.
Geno.
279:
385-‐401
Iden7fica7on
of
a
MITE
inserted
in
an
intron
and
its
use
for
diversity
study.
Guyot
et
al.
2009
,
BMC
Pl.
Biol.
9:22*
–
Dubreuil-‐Tranchant
et
al.
Int.
J.
Evol.
Biol.
2011
ID
358412*
Iden7fica7on
and
use
of
full
length
LTR-‐Retrotransposons
for
diversity
study.
Hamon
et
al.
2011,
Mol.
Genet.
Geno.
285:
447-‐460*
Iden7fica7on
of
full
length
transposable
elements
in
BAC
clones.
Cenci
et
al.
2012,
Pl.
Mol.
Biol.
78:
135-‐145
Iden7fica7on
of
LTR-‐Retrotransposons
in
BAC-‐ends
and
NGS
reads.
Dubreuil-‐Tranchant
et
al.
2012,
2nd
ICTE*
–
Dias
et
al.
2013
21st
PAG*
23. Coffea
Transposable
elements
LTR-‐retrotransposon
REMAP
Microsatellite
repeats
mul?-‐locus
approaches
for
analyzing
transposon
inser?ons
RBIP
Retrotransposon-‐Based
Inser?onal
Polymorphism
REtrotransposon-‐Microsatellite
Amplified
Polymorphism
Sequence-‐Specific
Amplified
Polymorphism
Restric?on
site
S-‐SAP
How
to
use
transposable
elements
for
diversity
studies
24. Coffea
Transposable
elements
Using
a
MITE
for
polymorphism
survey
From:
Guyot
et
al.
2009
BMC
Pl.
Biol.
9:22*
From:
Dubreuil-‐Tranchant
et
al.
Int.
J.
Evol.
Biol.
2011
ID
358412*
Intra
C.
canephora
Alex-‐1
polymorphism
at
the
g3
locus:
25. Coffea
Transposable
elements
Divo
4396
bp
LTR
pair
iden7ty
94.5%
5749
bp
Nana
LTR
pair
iden7ty
90.5%
First
full
length
LTR
Retrotransposons
iden7fied
in
Coffea
Hamon
et
al.
2011,
Mol.
Genet.
Geno.
285:
447-‐460*
26. Coffea
Transposable
elements
resolve
Coffea
species
lineages
reveal
intra
LIB
and
CAN
differen7a7on
Diversity
of
inser7on
paqern
Hamon
et
al.
2011,
Mol.
Genet.
Geno.
285:
447-‐460*
28. Synteny
studies:
at
the
micro
level
From:
Guyot
et
al.
2009
BMC
Pl.
Biol.
9:22*
29. At
the
micro
level:
Both
studies
show
a
good
conserva7on
of
synteny
despite,
and
independently,
of
the
divergence
7me
between
species
From:
Guyot
et
al.
2012
BMC
Genomics
13:103*
Synteny
studies:
at
the
micro
level
From:
Guyot
et
al.
2009
BMC
Pl.
Biol.
9:22*
30. Macrosyntenic
rela7onships
between
each
of
the
11
coffee
Linkage
Groups
and
the
19
grape
Linkage
Groups
based
on
mapped
coffee
COSII
loci.
From:
Guyot
et
al.
2012
BMC
Genomics
13:103*
Thanks
to
a
set
of
867
COSII
markers,
macrosynteny
was
detected
between
coffee,
tomato
and
grapevine.
While
coffee
and
tomato
genomes
share
318
orthologous
markers
and
27
conserved
syntenic
segments,
coffee
and
grapevine
share
299
syntenic
markers
and
29
CSSs.
Synteny
studies:
at
the
macro
level
31. Macrosyntenic
rela7onships
between
each
of
the
11
coffee
Linkage
Group
and
the
12
tomato
Linkage
Groups
based
on
mapped
coffee
COSII
loci.
From:
Guyot
et
al.
2012
BMC
Genomics
13:103*
Synteny
studies:
at
the
macro
level
32. Significant
conserva7on
is
found
between
distantly
related
species
from
the
Asterid
and
Rosid
clades,
at
the
genome
macrostructure
and
microstructure
levels.
Time
alone
doesn’t
explain
the
observed
divergences
Synteny
analyses
are
considerably
useful
for
syntenic
studies
between
supposedly
remote
species
for
the
isola7on
of
important
genes
for
agronomy.
From:
Guyot
et
al.
2009
BMC
Pl.
Biol.
9:22*
-‐
Guyot
et
al.
2012
BMC
Genomics
13:103*
Synteny
studies:
Conclusion
34. Phylogene7c
analyses
of
Coffea
From:
Davis
et
al.
Bot.
J.
Linnean
So.
2011,
167,
357–377.
Combined
plas7d–ITS
Bayesian
majority
rule
consensus
phylogene7c
tree
35. Phylogene7c
analyses
of
Coffea
Combined
plas7d–ITS
maximum
likelihood
phylogene7c
tree
Whatever
the
method
of
analysis,
these
results
do
not
allow
to
conclude
on
Coffea
evolu7on,
the
different
clades
being
not
hierarchized.
AW
Ex-‐PSI
AC
AE
MAS
MAD
36. Phylogene7c
analyses
of
Coffea
20
COS
par7ally
sequenced
(exons
+
intron)
72
Coffea
species
1st
divergence:
ex-‐Psilanthus
2nd
divergence:
3
non
hierarchized
clades:
Baracoffea/
Mascarocoffea/
Africa.
Psilanthus
Baracoffea
Madagascar
Mascarene
Madagascar
and
Comoros
East
Africa
East
Africa
West
and
Central
Africa
37. Psi
Bar
Coffea
Phylogene7c
analyses
of
Coffea
A
hypothesis
on
Coffea
origin
and
evolu7on:
Psi-‐Coffea
common
ancestor
Coffea
Psi
Psi
39. Genome
sequencing
The
sequenced
genotype
belongs
to
the
C.
canephora
species.
C.
canephora
was
chosen
because
it
is
diploid,
contrary
to
C.
arabica
which
is
an
allotetraploid.
The
sequenced
plant
is
a
double
haploid
(mixoploid)
plant
produced
by
IRD
from
haploid
embryo
and
conserved
in
tropical
green
houses
in
Montpellier
(France).
Plant
Material:
40. Genome
sequencing
Sequencing
Strategy:
Two
steps:
to
produce
a
first
assembly
with:
454
reads,
single
and
mate
ended
(8
and
20
kb
span)
Sanger
sequencing
of
Bac
Ends
Correct
the
assembly
with
Illumina
sequencing,
single
and
pair
ended
reads
41. Assembly
results
:
Genome
sequencing
13,345
scaffolds,
largest
scaffold
9.Mb
N50
=
1.2Mb
N80
=65kb
Coverage
reached:
28.8
X
454
69.7
X
Illumina
0.3
X
Sanger
Total
=
98.8
X
Total
length
assembled
568.6
Mb
(80%
of
the
710
Mb
es7mated
size)
Con7gs
Reads
of
different
origin
Consensus
Pair-‐
mate-‐
end
reads
Gaps
=
span
of
pair
or
mate
end
fragments
Scaffolds
42. Number
of
genes
25574
Number
of
genes
without
intron
5004
Size
in
nt.
(mean
:
med.)
3684.33
:
2788
Exon
number
/
gene
(mean
:
med.)
5.10
:
4
CDS
size
in
nt.
(mean
:
med.)
1205.55
:
1002
Coding
coverage
30,830,841
(5.4%)
Intron
number
104,944
Intron
size
in
nt.
(mean
:
med.)
483.20
:
208
%
con7gs
with
at
least
one
gene.
(%
in
bases)
16.6%
(82.3%)
Automa7c
annota7on
results
:
Genome
sequencing
43. Genome
sequencing
Further
steps
:
To
anchor
the
physical
map
(assembly)
to
the
interna7onal
gene7c
map
(≈3000
SNP
markers)
Annotate
manually
some
genes
from
Coffea
par7cular
pathways
(Caffeine…)
Compara7ve
genomics
Many
other
possible
analyses
Publish!
Shulaev
V.
et
al
(2011)
Nature
Genet.
43:
109–116
Coffea
canephora
44. Evodyn
Team
members
Perla
HAMON
Romain
GUYOT
Chris7ne
DUBREUIL-‐TRANCHANT
Valérie
PONCET
Serge
HAMON
Students,
trainees
and
visitors,
among
them:
N.
Razafinarivo,
P.O.
Duroy,
C.
Duret,
A.
Guellim,
M.
de
la
Mare,
S.
Akaffou,
P.
Mafra
Almeida
da
Costa,
C.
Gomez,
Elaine
Dias
…
Collaborators:
Dominique
CROUZILLAT
Michel
RIGOREAU
Emmanuel
COUTURON
Claudia
CARARETO
Spencer
BROWN
Michael
BOURGE
Vincent
LEFORT
Olivier
GASCUEL
Olivier
CORITON
Sonja
SILJAK-‐YAKOVLEV
Odile
ROBIN
Saranya
SRISUWAN
Aaron
DAVIS
Philippe
BARRE
And
many
more
Acknowledgements
The
Interna7onal
Coffee
sequencing
consor7um:
Victor
A.
ALBERT
(USA)
Alan
C.
ANDRADE
(BRE)
Xavier
ARGOUT
(FR)
Benoit
BERTRAND
(FR)
Alexandre
de
KOCHKO
(FR)
Giovanni
GIULIANO
(ITA)
Giorgio
GRAZIOSI
(ITA)
Robert
HENRY
(AUS)
JAYARAMA
(IND)
Philippe
LASHERMES
(FR)
Ray
MING
(USA)
Chifumi
NAGAI
(USA)
Steve
ROUNSLEY
(USA)
David
SANKOFF
(CAN)
Patrick
WINCKER
(FR)