Here we have proposed the functional space hypothesis, positing that mutational target size scales with genome size, impacting the number, source, and genomic location of beneficial mutations that contribute to adaptation. Though motivated by preliminary evidence, mostly from Arabidopsis and maize, more data are needed before any rigorous assessment of the hypothesis can be made. If correct, the functional space hypothesis suggests that we should expect plants with large genomes to exhibit more functional mutations outside of genes, more regulatory variation, and likely less signal of strong selective sweeps reducing diversity. These differences have implications for how we study the evolution and development of plant genomes, from where we should look for signals of adaptation to what patterns we expect adaptation to leave in genetic diversity or gene expression data. While flowering plant genomes vary across more than three orders of magnitude in size, most studies of both functional and evolutionary genomics have focused on species at the extreme small edge of this scale. Our hypothesis predicts that methods and results from these small genomes may not replicate well as we begin to explore large plant genomes. Finally, while we have focused here on evidence from plant genomes, we see no a priori reason why similar arguments might not hold in other taxa as well.
Botany krishna series 2nd semester Only Mcq type questions
Adaptation in plant genomes: bigger is different
1. Jeffrey Ross-Ibarra
@jrossibarra • www.rilab.org
Plant Sciences • Center for Population Biology • Genome Center
University of California Davis
Bigger is different: the role of plant genome
size in adaptation
5. Lloyd et al. 2017 bioRxiv
A .thaliana functional prediction
6. Lloyd et al. 2017 bioRxiv
A .thaliana functional prediction
7. Lloyd et al. 2017 bioRxiv
A .thaliana functional prediction
Rodgers-Melnick et al. 2016 PNAS
b Ames Diversity Panel
Intergenic Open
Chromatin (33%)
Coding
(41%)
UTR, proximal
% VA explained in maize
(height, flowering, etc.)
8. ● ●
●
●
0
5
10
15
20
25
200 400 600 800 1000
Genome Size (Mb)
OpenChromatinSize(Mb)
Genome_feature
●
Exon
Intergenic
Proximal
Total_open_chromatin
A
75%
80%
85%
90%
95%
%Non−exonicOpenChromatin
B
Maher et al. 2017 bioRxiv
Mei et al. 2017 bioRxiv
Rodgers-Melnick et al. 2016 PNAS
b Ames Diversity Panel
Intergenic Open
Chromatin (33%)
Coding
(41%)
UTR, proximal
% VA explained in maize
(height, flowering, etc.)
11. Doebley 2004, Studer et al. 2011
tb1
Hopscotch
ZmCCT
CACTA
Yang et al. 2013
plant architecture flowering time
12. Pyhäjärvi et al. 2013 GBEFigure S4 LD in chromosome 9 among mexicana populations based on SNPs with minor
allele frequency >0.1.
Inv9d
Inv9e
13. Inv4n
macrohairs,
anthocyanin
Hufford et al. 2013 PLoS Genetics
Pyhäjärvi et al. 2013 GBEFigure S4 LD in chromosome 9 among mexicana populations based on SNPs with minor
allele frequency >0.1.
Inv9d
Inv9e
Pyhäjärvi et al. 2013 GBE
14. 4% of B73 absent
~8% absent
30% of the low copy sequence
absent from reference genome
%readsunmappedreads
Gore et al. 2009 Science
Chia et al 2012 Nat Gen
✓⇡
n 1X
i=1
1
i
= S
θπ ~ 8% pairwise diff
1-S% pan-genome in ref
23. Beissinger et al. 2016 Nature Plants
nucleotidediversity
distance to nearest substitution (cM)
prediction: bigger genomes have few hard sweeps
24. Beissinger et al. 2016 Nature Plants
nucleotidediversity
distance to nearest substitution (cM)
prediction: bigger genomes have few hard sweeps
25. Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
Beissinger et al. 2016 Nature Plants
L = 2,500 Mbp
26. Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
Beissinger et al. 2016 Nature Plants
L = 2,500 Mbp
diversity
L = 220 Mbp
27. Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
Beissinger et al. 2016 Nature Plants
L = 2,500 Mbp
distance from substitution
L = 3,100 Mbp
L = 130 Mbp
diversity
L = 220 Mbp
28. M T G P H R L
GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
29. M T G P H R L
GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
M T N P H R L
GGTCGAC ATG ACT GAT CCA CAT CGA CTG TAG
structural
change to protein
30. M T G P H R L
GGTAAAC ATG ACT GGT CCA CAT CGA CTG TAG
GG—-AC ATG ACT GGT CCA CAT CGA CTG TAG
regulatory change to
expression
31. Hufford et al. 2012 Nat. Gen.
Chia et al. 2012 Nat. Gen
maizeteosinte
prediction: bigger genomes have more intergenic (regulatory?) adaptation
32. Hufford et al. 2012 Nat. Gen.
Chia et al. 2012 Nat. Gen
maizeteosinte
prediction: bigger genomes have more intergenic (regulatory?) adaptation
33. Hufford et al. 2012 Nat. Gen.
Chia et al. 2012 Nat. Gen
maizeteosinte
prediction: bigger genomes have more intergenic (regulatory?) adaptation
5-10% selected regions
do not include genes
42. Acknowledgements
UC Davis
Graham Coop
Wenbin Mei
Dan Gates
Markus Stetter
Michelle Stitzer
Plant Genome
Research Program
HiLo
Lab Alumni
Matt Hufford (Iowa State)
Tanja Pyhäjärvi (Oulu)
Shohei Takuno (Sokendai)