1. Shin-Han Shiu Department of Plant Biology
Evolution of Plant Stress Responsiveness: Genome-wide and Gene Family Level Analysis
Shin-Han Shiu
Department of Plant Biology

2. Outline Major interests and why
Gene families and stress responsiveness:
The interplay between gene family expansion, duplication mechanism, and the elusive selection pressure
The Receptor Kinase family as an example
One of the biggest plant gene families and their involvement in plant biotic interactions
If there is enough time, the short story on plant pseudogenes
When can you can a gene pseudogene?

3. Major interests
Source of selection pressure: abiotic and biotic stress conditions
Target of selection: duplicate genes
Molecular
evolutionary
patterns
Genetic basis
of adaptation

4. Where does all these duplicates come from
Whole genome duplication
Tandem duplication
Segmental duplication
Replicative transposition +

5. Measuring Lineage-specific Gain
Orthologous group and lineage-specific gain
Reconcile species and gene trees

6. Expansion at the orthologous group level
Most successful RLK: LRR type
But Arabidopsis may not be representative of land plants
log(freq)
Enrichment:
log(OG size)

7. Two major patterns in OG expansion
Convergent expansion
Single lineage expansion
Most successful RLK: LRR type
But Arabidopsis may not be representative of land plants
Enrichment:

8. Expansion patterns and duplication mechanisms
Comparison of ratios between tandem and non-tandem genes
e.g. for A-M orthology
Convergent
Single-lineage
Tandem
756
848
Non-tandem
4500
2918
Ratio
0.17
0.30
Most successful RLK: LRR type
But Arabidopsis may not be representative of land plants

9. Summary I Duplicate gene turn over
But even though some of them are retained for millions of years, the majority of them will be lost over hundreds MY time scale.
The degree of lineage-specific expansion is similar at the family level but with substantial variation
Expansion patterns fall into two major categories
Convergent expansion
Single lineage expansion
Orthologous group with single lineage expansion
Tend to be enriched in tandemly repeated genes
Most successful RLK: LRR type
But Arabidopsis may not be representative of land plants

10. Expansion of responsive genes and conditions
Genes in expanded OGs tends be enriched in stress responsive genes
+: significant at
the 5% level
Most successful RLK: LRR type
But Arabidopsis may not be representative of land plants

11. Stress responsiveness and duplication mechanisms
Enrichment of tandemly over non-tandemly expanded genes under biotic conditions
Most successful RLK: LRR type
But Arabidopsis may not be representative of land plants
Significant at the 5% level
T: tandem >> non-tandem
N: non-tandem >> tandem

12. Summary II Over the course of plant evolution, retention rate:
Stress response genes >> genome average
True for genes up-regulated in both biotic and abiotic stress conditions
Influence of duplication mechanism, particularly for biotic stress conditions, retention rate:
Tandem >> non-tandem
However, genes responsive to biotic stimuli are not necessarily tandem
Depend on their location in the signaling network
e.g. Plant receptor kinase: biotic -> tandem
e.g. Transcription factors -> non-tandem, presumably WGD
Most successful RLK: LRR type
But Arabidopsis may not be representative of land plants

13. Functional evolution of duplicate genes
Question: What is the fate of duplicate gene?
Address this question in the context of stress responsiveness.
Most successful RLK: LRR type
But Arabidopsis may not be representative of land plants

14. Step1:construct the phylogeny of genes Step2: map current functions
Reconstruction of ancestral functions
Step1:construct the phylogeny of genes
Step2: map current functions
Step3:reconstruct the function of ancestral genes

15. Branch-based analysis
Ancestral state determined by BayesTraits
An MCMC/ML combination to estimate the trait values at ancestral nodes
Definition 1,-1,o }}

16. Relative abundance of functional evolution classes
Retention > loss >> gain >> switch
0->0
Big one one col
Lost gain

17. Evolution of stress responsiveness over Ks
What ks

18. Relative abundance of functional evolution classes
N Maintenance
NLoss
Nswitch
N = NM+NL+NS
Abiotic stress
Biotic stress
Number of Nm N total number Ks Ks

19. Relative abundance of functional evolution classes
N Maintenance
NGain
N = total
Nswitch
Abiotic stress
Biotic stress Ks Ks

20. What is the nature of functional switch?
Switch: e.g. 1 to -1
Up regulation in the ancestral state
But down regulated in the current state
Does switch involve a one-step or a 2-step process:
Seem to be the second case since:
Loss rate >> gain rate >> switch rate
Function switch

21. Summary III Branch-based analysis
Maintenance > loss > gain > switch
Retention of stress responsiveness
Ks< 0.8, continued loss
Ks> 0.8, nearly constant
Responsiveness gain has a similar trajectory
Loss > gain > switch
Suggest a two-step evolutionary process of functional swtich.
Most successful RLK: LRR type
But Arabidopsis may not be representative of land plants

22. Functional evolution in the context of duplicate pairs
Functional partition

23. Relative abundance of functional evolution classes
Looking at each gene pair under each condition
Partition is the most abundant class
Retention
Partition
Neo-F
PL RET PAR NEO
Parallel loss

24. Functional partition of gene pairs
Partition tend to be extremely asymmetric
Condition - refers to condition and time?
How many

25. Statistical significance of asymmetry
Partition tend to be extremely asymmetric, why?
Gene 2 conditions
Gene 1 conditions
Condition - refers to condition and time?
How many

26. Stress responsiveness of genes over multiple conditions
Over-representation of broadly responsive genes
ABIOTIC CONDITIONS
BIOTIC CONDITIONS
Add explain

27. Enrichment of cis elements under each condition
Some cis-elements are in genes that are broadly responsive
Up-regulated
Down-regulated
Both
Neither
Add explain
Cis-elements
Stress conditions

28. Enrichment of cis elements under each condition
Some cis-elements are in genes that are broadly responsive
Add explain

29. Breadth in responsiveness vs. cis-element complexity
Positive correlation between these two factors
Spearman rank: ρ = 0.51, p < 2.2e-16
Add explain
Number of cis-element types
Number of responsive conditions

30. Expression and cis-element asymmetries
Some cis-elements are in genes that are broadly responsive
Spearman rank: ρ = 0.62, p < 2.2e-16
Add explain
Asymmetry (cis-element)
Asymmetry (up-regulation)

31. Summary IV Sub- vs. neofunctionalization
Sub > retention > neo > parallel loss
Subfunctionalization asymmetry
Significant asymmetry
Explanation
Some genes are controlled by multi-responsive elemenents
Differential loss/gain of cis-elements
Add explain

32. Acknowledgement Lab members Melissa Lehti-Shiu Gaurav Moghe Cheng Zou
Past member
Kosuke Hanada, RIKEN
Collaborators
Jeff Conner
Gregg Howe, PRL
Rong Jin, CSE
Doug Schemske
Mike Thomashow, PRL
Funding: