1. families with >5 genes are more common in plants than in animals
adapted from Lockton S, Gaut BS Trends Genet 21: 60-65

2. alternative splicing (AS) is more common in animals than in plants
Boue S, et al BioEssays 25: ; Iida K, et al Nucleic Acids Res 32: ; Kikuchi S, et al Science 301:
Arabidopsis and rice AS

3. 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 genome e.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

4. polyploidy (whole genome duplication) events among plants
adapted from Blanc G, Wolfe KH Plant Cell 16: ; Paterson AH, et al Proc Natl Acad Sci USA 101:
monocot
dicot

5. phylogeny of the favored plants there 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

6. the duplication history of rice every cDNA-defined gene is assigned a duplication category using the methods of Yu J, et al PLoS Biol 3: e38
analysis relies entirely on 19,079 full length cDNAs; had we used predicted genes instead many of the duplications would have been missed
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
if a gene has any homologs at all, the mean(median) number of homologs is 40(5)
multiple duplications are difficult to analyze; so consider the cDNAs with 1-and-only-1 homolog

7. ONE whole genome duplication, a recent segmental duplication, and many individual gene duplications
birth
death
whole genome
individual genes
recent segmental
time

8. 18 pairs of duplicated segments covering 65
18 pairs of duplicated segments covering 65.7% of rice genome higher order homologs used to backfill established trend lines
segmental

9. ancient whole genome duplication (WGD) in rice

10. uninterpretable plot if use cDNAs with more than one homolog in rice mean (median) number of homologs per duplicated gene is 40 (5)

11. unmarked trend along diagonal from tandem gene duplications there were NO segmental duplications within a chromosome
tandem
background

12. 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 3364, 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

13. 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 Nature 392:
common ancestor
species1
species2
time since divergence equals species2-species1 divided by (2 × neutral substitution rate)

14. 17 of 18 segments are attributable to a whole genome duplication just before the Gramineae divergence
timing of WGD relative to Gramineae divergence is based on observed syntenies and not Ks

15. background duplications have Ks signature like tandem duplications except that they are more ancient
peak at zero Ks and exponential decay thereafter is indicative of ongoing duplication process

16. post-duplicative ‘transient’ of duration 4~17 million years
duplicated genes undergo periods of relaxed selection and are usually silenced within 4~17 million years
hypothesis introduced by Lynch M, Conery JS Science 290: 1151; with details in Lynch M, Conery JS 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

17. 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 duplication Kellis M, et al Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: when the duplication is extremely new: an analysis from human Bailey JA, et al Recent segmental duplications in the human genome. Science 297:

18. interleaving genes from sister segments in comparison to K. waltii
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

19. gene and regional correspondences with K. waltii

20. ancient whole genome duplication in S. cerevisiae

21. 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

22. 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

23. 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 Trends Plant Sci 11:

24. “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)