The document discusses gene family size changes in fungi. It notes that gene duplications are important for new gene and function evolution. It analyzed gene family sizes across 37 fungal genomes using computational methods to identify lineage-specific expansions. The analysis used probabilistic models to evaluate gene family size changes along phylogenetic branches and identify families with unusually large size increases or decreases in specific lineages.
Organisms are classified into a hierarchical classification that groups closely related individuals.
The species is the basic biological unit around which classifications are based.
This PPT explores the different attributes related to numerical taxonomy or Taxi- metrics in the domain of plant taxonomy along with different fundamental principles.
Organisms are classified into a hierarchical classification that groups closely related individuals.
The species is the basic biological unit around which classifications are based.
This PPT explores the different attributes related to numerical taxonomy or Taxi- metrics in the domain of plant taxonomy along with different fundamental principles.
The SPECIAL - GIANT CHROMOSOMES which are very transcriptionally active DNA, where loops of DNA emerging from an apparently continuous chromosomal axis are coated with RNA polymerase.
Comparatively much larger than polytene chromosomes.
Highly significant for scientific analysis especially regarding gene amplification.
The process by which a new species develops from the existing species is known as speciation.
Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book On the Origin of Species. He also identified sexual selection as a likely mechanism, but found it problematic.
A species can be defined as one or more populations of interbreeding organisms that are reproductively isolated in nature from all other organisms.
When populations no longer interbreed, they are thought to be separate species.
There are four geographic modes of speciation in nature, based on the extent to which speciating populations are isolated from one another: allopatric, peripatric, Parapatric, and sympatric.
Speciation may also be induced artificially, through animal husbandry, agriculture, or laboratory experiments.
Allopatric speciation: It is regarded as the most common type of speciation. It involves the physical separation of a species into two groups. This may occur due to climatic changes, movement of tectonic plates leading to the fragmentation of a mass of land, or eruption of a land mass, formation of waterways, or due to the presence of an impassable mountain range.
Parapatric mode of speciation: It occurs due to partial spatial isolation of populations, and is characterized by a small overlap in their ranges as well as significant gene flow amongst the populations. However, the gene flow reduces due to changes in the local conditions, and the two populations become reproductively isolated.
Sympatric mode of speciation: It involves the formation of new species due to a genetic divergence among a few members of the species inhabiting a single geographic area. Unlike the other modes of speciation, here genetic divergence does not arise due to increase in geographic distance, but occurs within the same niche.
Peripatric speciation was Proposed by Ernst Mayr. In this type of speciation, a small group of members inhabiting a peripheral region of the range undergo reproductive isolation to form a new species. Many a time, it is considered to be a variation of allopatric speciation.
To determine the variation and the limitation between species, many concepts have been proposed.
When a taxonomist study a particular taxa, he/she must adopted a species concept and provide a species limitation to define this taxa.
Plant kingdom as other living kingdoms has a hierarchy structure ends mostly with species rank.
Species are one of the basic units to compare in almost all fields of biology.
A species is defined as the largest group of organisms in which two individuals are capable of reproducing fertile offspring, typically using sexual reproduction.
Definition of a species as a group of interbreeding individuals cannot be easily applied to organisms that reproduce only or mainly asexually.
If two lineages of oak look quite different, but occasionally form hybrids with each other, should we count them as different species?
Idea of a species is something that we humans invented for our own convenience.
‘‘No matter what variations occur in the individuals or the species, if they spring from the seed of one and the same plant, they are accidental variations and not such as distinguish a species permanently; one species never springs from the seed of another nor vice versa” - JOHN RAY.
Used a sexual system ‘‘natural system” for defining species - LINNAEUS.
‘‘A species is a collection of all the individuals which resemble each other more than they resemble anything else, which can by natural fecundation produce fertile individuals, and which reproduce themselves by generation, in such a manner that we may from analogy suppose them all to have sprung from one single individual” - DE CANDOLLE.
Taxonomy is the methodology and principles of systematic botany and zoology and sets up arrangements of the kinds of plants and animals in hierarchies of superior and subordinate groups
Basics of Undergraduate/university fellows
Nucleosome model of chromosome is proposed by ROGER KORNBERG (son of Arthur
Kornberg) in 1974.
It was confirmed and crystalised by P. Oudet et al., (1975).
Nucleosome is the lowest level of Chromosome organization in eukaryotic cells.
Nucleosome model is a scientific model which explains the organization of DNA and
associated proteins in the chromosomes.
Nucleosome model also explains the exact mechanism of the folding of DNA in
thenucleus.
It is the most accepted model of chromatin organization.
Iczn(The International Commission on Zoological Nomenclature )Al Nahian Avro
The International Commission on Zoological Nomenclature (ICZN) acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature - a set of rules for the naming of animals and the resolution of nomenclatural problems.
Fixed Action Pattern (FAP) is a series or sequence of acts that occur behaviorally in animals. it is also known as instinctive behaviour as it is determined by gene of an organism and exhibited automatically without having any prior experience.
Parental care is any behavior pattern in which a parent invests time or energy in feeding and protecting its offspring.
Parental care is a form of altruism since this type of behaviour involves increasing the fitness of the offspring at the expense of the parents.
The evolution of parental care is beneficial as it facilitates offspring performance traits that are ultimately tied to offspring fitness.
Parental care is evolved in those organism which produce limited no. of eggs to ensure the continuity of their race.
It is the fundamental law of population genetics and provides the basis for studying Mendelian populations ( Mendelian population: A group of sexually inbreeding organisms living within a circumscribed area). It describes populations that are not evolving.
An Empirical Evaluation of VoIP Playout Buffer Dimensioning in Skype, Google ...Academia Sinica
VoIP playout buffer dimensioning has long been a challeng- ing optimization problem, as the buffer size must maintain a balance between conversational interactivity and speech quality. The conversational quality may be affected by a number of factors, some of which may change over time. Although a great deal of research effort has been expended in trying to solve the problem, how the research results are applied in practice is unclear.
In this paper, we investigate the playout buffer dimension- ing algorithms applied in three popular VoIP applications, namely, Skype, Google Talk, and MSN Messenger. We conduct experiments to assess how the applications adjust their playout buffer sizes. Using an objective QoE (Quality of Experience) metric, we show that Google Talk and MSN Messenger do not adjust their respective buffer sizes appropriately, while Skype does not adjust its buffer at all. In other words, they could provide better QoE to users by improving their buffer dimensioning algorithms. Moreover, none of the applications adapts its buffer size to the network loss rate, which should also be considered to ensure optimal QoE provisioning.
The SPECIAL - GIANT CHROMOSOMES which are very transcriptionally active DNA, where loops of DNA emerging from an apparently continuous chromosomal axis are coated with RNA polymerase.
Comparatively much larger than polytene chromosomes.
Highly significant for scientific analysis especially regarding gene amplification.
The process by which a new species develops from the existing species is known as speciation.
Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book On the Origin of Species. He also identified sexual selection as a likely mechanism, but found it problematic.
A species can be defined as one or more populations of interbreeding organisms that are reproductively isolated in nature from all other organisms.
When populations no longer interbreed, they are thought to be separate species.
There are four geographic modes of speciation in nature, based on the extent to which speciating populations are isolated from one another: allopatric, peripatric, Parapatric, and sympatric.
Speciation may also be induced artificially, through animal husbandry, agriculture, or laboratory experiments.
Allopatric speciation: It is regarded as the most common type of speciation. It involves the physical separation of a species into two groups. This may occur due to climatic changes, movement of tectonic plates leading to the fragmentation of a mass of land, or eruption of a land mass, formation of waterways, or due to the presence of an impassable mountain range.
Parapatric mode of speciation: It occurs due to partial spatial isolation of populations, and is characterized by a small overlap in their ranges as well as significant gene flow amongst the populations. However, the gene flow reduces due to changes in the local conditions, and the two populations become reproductively isolated.
Sympatric mode of speciation: It involves the formation of new species due to a genetic divergence among a few members of the species inhabiting a single geographic area. Unlike the other modes of speciation, here genetic divergence does not arise due to increase in geographic distance, but occurs within the same niche.
Peripatric speciation was Proposed by Ernst Mayr. In this type of speciation, a small group of members inhabiting a peripheral region of the range undergo reproductive isolation to form a new species. Many a time, it is considered to be a variation of allopatric speciation.
To determine the variation and the limitation between species, many concepts have been proposed.
When a taxonomist study a particular taxa, he/she must adopted a species concept and provide a species limitation to define this taxa.
Plant kingdom as other living kingdoms has a hierarchy structure ends mostly with species rank.
Species are one of the basic units to compare in almost all fields of biology.
A species is defined as the largest group of organisms in which two individuals are capable of reproducing fertile offspring, typically using sexual reproduction.
Definition of a species as a group of interbreeding individuals cannot be easily applied to organisms that reproduce only or mainly asexually.
If two lineages of oak look quite different, but occasionally form hybrids with each other, should we count them as different species?
Idea of a species is something that we humans invented for our own convenience.
‘‘No matter what variations occur in the individuals or the species, if they spring from the seed of one and the same plant, they are accidental variations and not such as distinguish a species permanently; one species never springs from the seed of another nor vice versa” - JOHN RAY.
Used a sexual system ‘‘natural system” for defining species - LINNAEUS.
‘‘A species is a collection of all the individuals which resemble each other more than they resemble anything else, which can by natural fecundation produce fertile individuals, and which reproduce themselves by generation, in such a manner that we may from analogy suppose them all to have sprung from one single individual” - DE CANDOLLE.
Taxonomy is the methodology and principles of systematic botany and zoology and sets up arrangements of the kinds of plants and animals in hierarchies of superior and subordinate groups
Basics of Undergraduate/university fellows
Nucleosome model of chromosome is proposed by ROGER KORNBERG (son of Arthur
Kornberg) in 1974.
It was confirmed and crystalised by P. Oudet et al., (1975).
Nucleosome is the lowest level of Chromosome organization in eukaryotic cells.
Nucleosome model is a scientific model which explains the organization of DNA and
associated proteins in the chromosomes.
Nucleosome model also explains the exact mechanism of the folding of DNA in
thenucleus.
It is the most accepted model of chromatin organization.
Iczn(The International Commission on Zoological Nomenclature )Al Nahian Avro
The International Commission on Zoological Nomenclature (ICZN) acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature - a set of rules for the naming of animals and the resolution of nomenclatural problems.
Fixed Action Pattern (FAP) is a series or sequence of acts that occur behaviorally in animals. it is also known as instinctive behaviour as it is determined by gene of an organism and exhibited automatically without having any prior experience.
Parental care is any behavior pattern in which a parent invests time or energy in feeding and protecting its offspring.
Parental care is a form of altruism since this type of behaviour involves increasing the fitness of the offspring at the expense of the parents.
The evolution of parental care is beneficial as it facilitates offspring performance traits that are ultimately tied to offspring fitness.
Parental care is evolved in those organism which produce limited no. of eggs to ensure the continuity of their race.
It is the fundamental law of population genetics and provides the basis for studying Mendelian populations ( Mendelian population: A group of sexually inbreeding organisms living within a circumscribed area). It describes populations that are not evolving.
An Empirical Evaluation of VoIP Playout Buffer Dimensioning in Skype, Google ...Academia Sinica
VoIP playout buffer dimensioning has long been a challeng- ing optimization problem, as the buffer size must maintain a balance between conversational interactivity and speech quality. The conversational quality may be affected by a number of factors, some of which may change over time. Although a great deal of research effort has been expended in trying to solve the problem, how the research results are applied in practice is unclear.
In this paper, we investigate the playout buffer dimension- ing algorithms applied in three popular VoIP applications, namely, Skype, Google Talk, and MSN Messenger. We conduct experiments to assess how the applications adjust their playout buffer sizes. Using an objective QoE (Quality of Experience) metric, we show that Google Talk and MSN Messenger do not adjust their respective buffer sizes appropriately, while Skype does not adjust its buffer at all. In other words, they could provide better QoE to users by improving their buffer dimensioning algorithms. Moreover, none of the applications adapts its buffer size to the network loss rate, which should also be considered to ensure optimal QoE provisioning.
Jonathan Eisen: Phylogenetic approaches to the analysis of genomes and metage...Jonathan Eisen
Talk by Jonathan Eisen March 7, 2012 at the National Academy of Sciences Institute of Medicine "Forum on Microbial Threats" meeting on the "Social Biology of Microbes"
This was a last minute microtalk given at the Swiss Institute of Bioinformatics SIB 2011 Summer school in Bioinformatics & Population Genomics in Adelboden (http://edu.isb-sib.ch/course/view.php?id=111 ).
The neurobiological nature of free willBjörn Brembs
Our own experience of our free will has been classified as either supernatural or an illusion because it is difficult to reconcile with macroscopic determinism as well as with microscopic quantum randomness. The former constituting a prison in which no freedom can exist, the latter signifying destructive chaos rather than creative action. Lost in this dichotomy is the demonstrated constructive combination of chance and necessity in complex systems, such as evolution. Recent converging evidence from neuroscience, ecology and genetics suggests that nervous systems, including human brains, have evolved neural circuits that harness (potentially quantum) chance events by embedding them in the controlling architecture of neuronal rules, in order to carefully inject them as creative components into ongoing goal-directed behavior. This presentation contains evidence that this form of behavioral variability may constitute a necessary neural mechanism for free will to evolve in humans.
GraphSummit Singapore | The Art of the Possible with Graph - Q2 2024Neo4j
Neha Bajwa, Vice President of Product Marketing, Neo4j
Join us as we explore breakthrough innovations enabled by interconnected data and AI. Discover firsthand how organizations use relationships in data to uncover contextual insights and solve our most pressing challenges – from optimizing supply chains, detecting fraud, and improving customer experiences to accelerating drug discoveries.
Removing Uninteresting Bytes in Software FuzzingAftab Hussain
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.
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
zkStudyClub - Reef: Fast Succinct Non-Interactive Zero-Knowledge Regex ProofsAlex Pruden
This paper presents Reef, a system for generating publicly verifiable succinct non-interactive zero-knowledge proofs that a committed document matches or does not match a regular expression. We describe applications such as proving the strength of passwords, the provenance of email despite redactions, the validity of oblivious DNS queries, and the existence of mutations in DNA. Reef supports the Perl Compatible Regular Expression syntax, including wildcards, alternation, ranges, capture groups, Kleene star, negations, and lookarounds. Reef introduces a new type of automata, Skipping Alternating Finite Automata (SAFA), that skips irrelevant parts of a document when producing proofs without undermining soundness, and instantiates SAFA with a lookup argument. Our experimental evaluation confirms that Reef can generate proofs for documents with 32M characters; the proofs are small and cheap to verify (under a second).
Paper: https://eprint.iacr.org/2023/1886
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.
GraphSummit Singapore | The Future of Agility: Supercharging Digital Transfor...Neo4j
Leonard Jayamohan, Partner & Generative AI Lead, Deloitte
This keynote will reveal how Deloitte leverages Neo4j’s graph power for groundbreaking digital twin solutions, achieving a staggering 100x performance boost. Discover the essential role knowledge graphs play in successful generative AI implementations. Plus, get an exclusive look at an innovative Neo4j + Generative AI solution Deloitte is developing in-house.
UiPath Test Automation using UiPath Test Suite series, part 6DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
Throughout the session, participants will discover how this synergy empowers testers to automate repetitive tasks, enhance testing accuracy, and expedite the software testing life cycle. Topics covered include the seamless integration process, practical use cases, and the benefits of harnessing AI-driven automation for UiPath testing initiatives. By attending this webinar, testers, and automation professionals can gain valuable insights into harnessing the power of AI to optimize their test automation workflows within the UiPath ecosystem, ultimately driving efficiency and quality in software development processes.
What will you get from this session?
1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
Topics covered:
What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
Generative AI Deep Dive: Advancing from Proof of Concept to ProductionAggregage
Join Maher Hanafi, VP of Engineering at Betterworks, in this new session where he'll share a practical framework to transform Gen AI prototypes into impactful products! He'll delve into the complexities of data collection and management, model selection and optimization, and ensuring security, scalability, and responsible use.
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.
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.
UiPath Test Automation using UiPath Test Suite series, part 5DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 5. In this session, we will cover CI/CD with devops.
Topics covered:
CI/CD with in UiPath
End-to-end overview of CI/CD pipeline with Azure devops
Speaker:
Lyndsey Byblow, Test Suite Sales Engineer @ UiPath, Inc.
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.
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...
Evolution of gene family size change in fungi
1. Evolution of gene family
size change in fungi
Jason Stajich
University of California, Berkeley
Gene family evolution
10000
N.crassa
A.gossypii
R.oryzae
A.oryzae
A.terreus
C.cinereus
U.maydis
1000
Frequency of Family size
100
10
1
1 10 100
. The phylogenetic tree. Branch lengths t are given in millions Family size
2. Outline
• Gene family size change - a model
• Cornucopia of fungal genomes
• Methodology for comparing family size
• Lineage specific expansions
3. Gene family evolution
• Gene duplications are the crucible of new
genes and thus new functions
• Many comparative approaches focus only
on identifiable one-to-one orthologs.
• Signature of adaptive evolution can be
confounded in multi-gene families
• How important is lineage-specific
expansion in adaptive changes?
4. Identifying family
expansions
• Previous work only considered pairwise
• Ad hoc comparison of gene family sizes
• C.elegans-C.briggsae - GPCR family
expansions (Stein et al, PLOS Biology 2004)
• A. gambiae-D. melanogaster - Mosquito
specific family expansions related to
symbiotic bacteria (Holt et el, Science 2002).
• Need a null model
5. Gene family sizes follow
power law distribution 10000
N.crassa
single copy genes A.gossypii
R.oryzae
PRP8 (splicing) A.oryzae
CDC48 (cell cycle ATPase) A.terreus
C.cinereus
U.maydis
1000
Frequency of Family size
100
Multicopy genes
Sugar transporters
P450 Enzymes
10
1
1 10 100
Family size
6. Phylogenetic evaluation of
gene family size change
• Previous methods only used ad hoc
statistics
• Explicit model for gene family size change
according to a Birth-Death models
• Apply BD to family size along phylogeny
using probabilistic graph models
• CAFE - Computational Analysis of gene
Family Evolution Hahn et al, Genome Res 2005
De Bie, et al Bioinformatics 2006
Demuth et al, submitted
7. CAFE Gene family evoluti
e phylogenetic
ers an ideal null
•
del inUse a way
this Probabilistic
Graph Model for:
ave undergone
od furthermore
• Ancestral states
ny upon which
• Birth and Death rate
likelihoods can-
(lamda)
milies, because
•
wer likelihoods changes
Per branch
•
bias”). Instead,
P-values
atistics to calcu- Figure 2. The phylogenetic tree. Branch lengths t are given in milli
on one of the of years. The branch numbers used in this study are shown in circles
ional P-value is
Hahn et al, Genome Res 2005
mily (with fixed
To define gene families, we took all of the genes in all f
ihood than the
12. Genome annotation
• Many of the fungal genomes were only
assembled genomic sequence.
• Automated annotation pipeline was built to
generate to get systematic gene prediction.
• Several gene prediction programs were
trained and results were combined with
GLEAN (Liu, Mackey, Roo, et al
unpublished) to produce composite gene
calls.
17. Methods: gene family
identification
• All-vs-All pairwise sequence searches
(FASTP)
• Cluster genes by similarity using Markov
CLustering (MCL) algorithm
• Identify families with unusually large size
changes along phylogeny with CAFE
• Use 37 fungal genomes from 5 major clades
18. FASTA
Family count
all-vs-all
10 1 2
14 18 2
Species
7 1 1
6 1 12
MCL
6 1 8
+ A B C D E
3 1 1
Gene
families
CAFE
18 U. maydis
Family 1 P < 0.001 Branch A 5 C. gattii R265
5 gattii
23 Basidiomycota 5 C. gattii WM276
Family 2 P < 0.001 Branch B 5 Cryptococcus
5 C. neoformans JEC21
5 neoformans
Branch
Family 3 P=0.02 23 Hymenomycota 5 C. neoformans var grubii
C,E
163 P. chrysosporium
136 Homobasidiomycota
Family 4 P=0.03 Branch D 141 C.cinereus
400 300 200 100 0
19. Families with significant expansions
49 significant Vitamin & Cofactor transport Methytransferase
families Lactose & sugar transport Cytochrome P450: CYP64
Amine transport Cytochrome P450: CYP53,57A
Transporters Myo-instol, quinate, and Cytochrome P450
glucose transport
Kinases Oligopeptide transport Kinase
P450
ABC transporter Subtilase family
Oxidation
MFS, drug pump, & sugar NADH flavin oxidoreductase
transport
Transport Aldehyde dehydrogenase
Monocarboxylate & sugar Aldo/kedo reductase
transport
ABC transport Multicopper oxidase
Amino acid permease AMP-binding enzyme
20. Transporters
• Of 45 significant families, 22 were related
to transport
• Vitamin and amino acid transport
• Sugar and sugar-like transporters
• Multidrug and efflux pumps
• ABC transporters (ATP Binding Cassette)
22. Transporter expansions
• Sugar related, Drug pump, and Major
Facilitator Superfamily
• Aspergillus spp, Fusarium spp, S. nodorum
• Euascomycota
Fusarium
• Vitamin transport Aspergillus
• C. neoformans, Fusarium S. nodorum
• A. nidulans (Biotin)
• Saccharomyces expansions independent! C. neoformans
23. Sugar transporter use in
phytopathogens
• Sugar transporters are
used to extract nutrients
from host
• Haustorium:
specialized structure
for plant parasitism Haustorium
• Many sugar
transporters highly and
specifically expressed Robert Bauer http://tolweb.org/
in haustoria
25. P450 CYP64
P450 enzymes involved in synthesis and cleavage of
chemical bonds. Drug metabolism in animals.
CYP64: Step in Aspergillus spp aflatoxin pathway
P. chrysosporium implicated in lignin and hydrocarbon
degradation.
18 U. maydis
5 C. gattii R265
5 gattii
23 Basidiomycota 5 C. gattii WM276
5 Cryptococcus
5 C. neoformans JEC21
5 neoformans
23 Hymenomycota 5 C. neoformans var grubii
163 P. chrysosporium
136 Homobasidiomycota
Million years
141 C.cinereus
ago 400 300 200 100 0
27. Local duplications created
CYP64 expansion
pchr_24
9k 10k 11k 12k 13k 14k 15k 16k 17k 18k 19k 20k 21k 22k 23k 24k
GLEAN models
GLEAN_02414 GLEAN_02415 GLEAN_02416 GLEAN_02417
Probability 1 Probability 0.999937 Probability 0.646357 Probability 0.990598
Pfam domains
p450 p450 p450 p450
Cytochrome P450 evalue:1e-28 Cytochrome P450 evalue:6e-26 Cytochrome P450 evalue:6.3e-23 Cytochrome P450 evalue:9e-07
28. Interpretation of
CYP64 expansion
18 U. maydis
5 C. gattii R265
5 gattii
23 Basidiomycota 5 C. gattii WM276
5 Cryptococcus
5 C. neoformans JEC21
5 neoformans
23 Hymenomycota 5 C. neoformans var grubii
163 P. chrysosporium
136 Homobasidiomycota
141 C.cinereus
Million years 400 300 200 100 0
ago
Angiosperm diversification
29. Hydrophobin Family
P.chr C.cin C.neo U.may
21 33 0 2
• Self assembling proteins involved in fungal
cell wall
• Part of what makes a mushroom
• 8 Cysteine residues critical to function
• Help spores stay airborne resisting water
33. Cryptococcus sugar
1,000.
and internal structures of C. neoformans are shown by means of a modified India ink preparation. Magnification, ca.
transporters
• 3x as many sugar
transporters in C.
neoformans (~50) than
other basidiomycetes
• “sugar coated killer”
2291
• Capsule is a mixture of
glucose, xylose, and
mannose.
• Transporters could be
Zerpa et al, 1996
important in capsule
synthesis
35. Acknowledgments
Sequencing centers
Matthew Hahn (Indiana) Broad Institute
Jeff Demuth Joint Genome Institute
Génolevures
Sang-Gook Han
Stanford University
TIGR
Tijl De Bie Welcome Trust Sanger Centre
Nello Cristianini (NIH and NSF)
Aaron Mackey
Ian Korf
Mario Stanke
Fred Dietrich (Duke)