families with >5 genes are more common in plants than in animals
adapted from Lockton S, Gaut BS. 2005. Trends Genet 21: 60-65
0.010.020.030.040.050.060.070.080.090.0
100.0
1 2 3-5 >5
Number of genes per family
Per
cen
tag
e o
f g
enes
Human
Yeast
Fruit fly
Nematode
Rice
Arabidopsis
alternative splicing (AS) is more common in animals than in plants
Boue S, et al. 2003. BioEssays 25: 1031-1034; Iida K, et al. 2004. Nucleic Acids Res 32: 5096-5103; Kikuchi S, et al. 2003. Science 301: 376-379
Arabidopsis and rice AS
duplications occur on any length scale, from individual genes (where tandem refers to a gene and its duplicate being adjacent), to multi-gene segments of the chromosome, to an entire genomee.g. wild wheat is diploid 2n, domestication gave a tetraploid 4n (pasta) and a hexaploid 6n (bread)
synteny is when 2 or more genes are found in the same order/orientation on the chromosomes of related species
polyploidy (whole genome duplication) events among plants
adapted from Blanc G, Wolfe KH. 2004. Plant Cell 16: 1667-1678; Paterson AH, et al. 2004. Proc Natl Acad Sci USA 101: 9903-9908
mon
ocot
dico
t
phylogeny of the favored plantsthere is extensive synteny among Gramineae but between Gramineae and Arabidopsis there is essentially no synteny
sorghum
maize
Arabidopsis
barley
wheat
rice
Gramineae 55~70 Mya
monocot-dicot 170~235 Mya
the duplication history of riceevery cDNA-defined gene is assigned a duplication category
using the methods of Yu J, et al. 2005. PLoS Biol 3: e38
1. analysis relies entirely on 19,079 full length cDNAs; had we used predicted genes instead many of the duplications would have been missed
2. a homolog pair refers to a cDNA and its TblastN match (i.e. comparisons done at amino acid level to genome translation in all 6 reading frames) at an expectation value of 1E-7 and requiring that >50% be aligned; note that the TblastN match is not necessarily expressed itself
3. if a gene has any homologs at all, the mean(median) number of homologs is 40(5)
4. multiple duplications are difficult to analyze; so consider the cDNAs with 1-and-only-1 homolog
ONE whole genome duplication, a recent segmental duplication, and many individual gene duplications
birth
death
whole genome
individual genes
recent segmental
time
18 pairs of duplicated segments covering 65.7% of rice genomehigher order homologs used to backfill established trend lines
RiceChr01Chr02Chr03Chr04Chr05Chr06Chr07Chr08Chr09Chr10Chr11Chr120
10
20
30
40
0 10 20 30Rice Chr02 (Mb)
Rice-Rice Comparison
segmental
ancient whole genome duplication (WGD) in rice
uninterpretable plot if use cDNAs with more than one homolog in rice
mean (median) number of homologs per duplicated gene is 40 (5)
RiceChr01Chr02Chr03Chr04Chr05Chr06Chr07Chr08Chr09Chr10Chr11Chr120
10
20
30
40
0 10 20 30Rice Chr02 (Mb)
Rice-Rice Comparison
unmarked trend along diagonal from tandem gene duplicationsthere were NO segmental duplications within a chromosome
RiceChr01Chr02Chr03Chr04Chr05Chr06Chr07Chr08Chr09Chr10Chr11Chr120
10
20
30
40
0 10 20 30 40Rice Chr01 (Mb)
Rice-Rice Comparison
tandem
background
computing molecular clocks and indicators of evolutionary selection
Ka = non-synonymous changes per available site
Ks = synonymous changes per available site
available site corrects for fact that 76% of substitutions, or 438 of 3364, encode a different amino acid
Ka/Ks < 1 is evidence of purifying selection
Ka/Ks = 1 is evidence of no selection (pseudogene)
Ka/Ks > 1 is evidence of adaptive selection
mean Ka/Ks is 0.20 in primates and 0.14 in rodents
from neutral substitution rate to time since divergence of species
neutral substitution rates vary with genes and evolutionary lineages but on average they are 2.2×10-9 for mammals and 6.5×10-9 for Gramineae
Kumar S, Hedges SB. 1998. Nature 392: 917-920
common ancestor
species1 species2
time since divergence equals species2-species1 divided by (2 × neutral substitution rate)
17 of 18 segments are attributable to a whole genome duplication just before the Gramineae divergence
higher order homologsKs from K-Estimator
0
30
60
90
0 0.5 1 1.5subs per silent site, Ks
Rice-Rice segmental duplicationtwo TblastN hits are allowedKs from K-Estimator
0
100
200
300
400
0 0.2 0.4 0.6subs per silent site, Ks
Rice-Rice tandem duplication
timing of WGD relative to Gramineae divergence is based on observed syntenies and not Ks
background duplications have Ks signature like tandem duplications except that they are more ancient
two TblastN hits are allowedKs from K-Estimator
0
100
200
300
400
0 0.2 0.4 0.6subs per silent site, Ks
Rice-Rice tandem duplicationone and only one homologKs from K-Estimator
0
50
100
150
200
0 1 2 3subs per silent site, Ks
Rice-Rice background duplication
peak at zero Ks and exponential decay thereafter is indicative of ongoing duplication process
duplicated genes undergo periods of relaxed selection and are usually silenced within 4~17 million years
hypothesis introduced by Lynch M, Conery JS. 2000. Science 290: 1151; with details in Lynch M, Conery JS. 2003. J Struct Funct Genomics 3: 35
one copy left alone
one copy to modify
eventual death
novel function
progenitor gene
relaxed selection
reduced expression
post-duplicative ‘transient’ of duration
4~17 million years
rice analysis succeeded only because duplication is not too old
when the duplication is old: an analysis from yeast comparing related genomes with and without the duplicationKellis M, et al. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624
when the duplication is extremely new: an analysis from humanBailey JA, et al. 2002. Recent segmental duplications in the human genome. Science 297: 1003-1007
proof of whole genome duplication in Saccharomyces cerevisiae by
comparison to sequence of Kluyveromyces waltii
duplication
mutation
gene death
interleaving genes from sister segments in comparison to K. waltii
gene and regional correspondences with K. waltii
ancient whole genome duplication in S. cerevisiae
identifying recent segmental duplications in human assembly
whole genome shotgun (WGS) reads from Celera are aligned to map-based genome from IHGSC; recent segmental duplications are detected in similarity and read depth anomalies
patterns of intra-chromosomal and inter-chromosomal duplication
recent segmental duplications of length>10-kb & identity>95%; intra-chromosomal (blue lines) and inter-chromosomal (red bars) duplication; unique regions
surrounded by intra-chromosomal duplications (gold bars) are hot spots for genomic disorders
recent segmental duplications in IHGSC and Celera genomes
proportion of Celera aligned bases falls rapidly as identity exceeds 97% or length exceeds 15-kb, but the total sequence lost is still only 2%~3%
NB: search of the map-based rice genome revealed no segmental duplications of recent origins (Yu J, et al. 2006. Trends Plant Sci 11: 387-391
“Although it is clear that the detailed clone-ordered approach is superior in the resolution of segmental duplications, it would be unrealistic to propose that the sequencing community should abandon whole-genome-shotgun based approaches. These are the most efficient cost-effective means of capturing the bulk of the euchromatic sequence.”
Evan E. Eichler (21 October 2004)
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