Download LETTER The Preferential Retention of Starch Synthesis Genes

LETTER
The Preferential Retention of Starch Synthesis Genes Reveals the Impact of
Whole-Genome Duplication on Grass Evolution
Yufeng Wu,* Zhengge Zhu, Ligeng Ma,à and Mingsheng Chen*
*State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing,
China; College of Biology, Hebei Normal University, Shijiazhuang, Hebei, China; and àNational Institute of Biological Sciences,
Beijing, China
Gene duplication is a major force in evolution. Here, we analyzed the fate of duplicated genes following the ancient
whole-genome duplication (WGD) in rice. Polyploidy-derived duplicated genes were found to be preferentially lost from
one of each pair of duplicated chromosomal segments, suggesting that the asymmetric gene loss may result from
transcriptome dominance of the ancestral allotetraploid genome. Genes involved in synthesis and catabolism of
saccharides were found to be preferentially retained in rice, reflecting different trajectories of duplicated genes formed by
polyploidy between rice and Arabidopsis. Further studies demonstrated all 3 catalyzing steps in the starch biosynthesis
pathway have polyploidy-derived duplicated genes and one copy in each step forms a dominant pathway in the grain
filling–stage rice. The new starch biosynthesis pathway reflects one aspect of the impact of WGD on grass evolution.
Gene duplication is a major force in evolution and can
provide the genetic material necessary for the origin of new
genes with novel functions (Ohno 1970). Polyploidy, which
duplicates all genes in the genome, is an important source of
biological innovation (Wendel 2000). In paleopolyploids,
gene loss is the main fate of duplicated genes formed by
whole-genome duplication (WGD). In Arabidopsis, only
about 32% of duplicated genes have been retained in sister
duplicated regions derived of polyploidy (Blanc et al. 2003).
The loss and retention of polyploidy-derived duplicated
genes are nonrandom and related to function. In Arabidopsis,
genes involved in transcriptional regulation and signal transduction have been preferentially retained and genes involved
in DNA repair have been preferentially lost (Blanc and
Wolfe 2004; Seoighe and Gehring 2004). Paterson et al.
(2006) found that some gene families have convergent
fates in independent WGD events, such as enrichments
of myb-like and protein kinase families in plants. Moreover, genes were removed preferentially from one homeolog after WGD in Arabidopsis (Thomas et al. 2006). The
overretention of transcriptional regulation and signal
transduction–related genes in polyploidy was predicted
by the gene balance hypothesis (Papp et al. 2003; Birchler
and Veitia 2007).
Data suggest a WGD took place approximately 70
MYA, prior to the divergence of grasses from within the
monocotyledonous lineage, providing evidence that all
grasses are paleopolyploids (Paterson et al. 2004; Yu
et al. 2005). However, the evolutionary impact of this
WGD has yet to be elucidated. Here, we analyzed the fate
of duplicated genes following the ancient WGD in rice.
We identified 1,657 polyploidy-derived gene pairs in
the Nipponbare genome (Oryza sativa L. ssp. japonica cv.
Nipponbare) (Supplement 1, Supplementary Material online). On duplicated blocks, only 15.4% genes have been
retained as duplicates. There are 8 duplicated chromosomal
Key words: genome duplication, genome evolution, comparative
genomics.
E-mail: [email protected]
Mol. Biol. Evol. 25(6):1003–1006. 2008
doi:10.1093/molbev/msn052
Advance Access publication February 23, 2008
Ó The Author 2008. Published by Oxford University Press on behalf of
the Society for Molecular Biology and Evolution. All rights reserved.
For permissions, please e-mail: [email protected]
segments encompassing duplicated blocks formed by the
WGD, that is, chr1–5, chr2–4, chr2–6, chr3–7, chr3–10,
chr3–12, chr4–8, and chr8-9, and one duplicated segment
between chromosomes 11 and 12 formed by segmental duplication (fig. 1). We expect the gene number and size of
each pair of duplicated chromosomal segments to be the
same immediately following the WGD and the current gene
number and size to be similar if the gene loss was random
during the diploidization process. Nevertheless, we found
that the gene loss between homeologous chromosomal segments was very different. The homeologous chromosomal
segment of chr1-5 located on chromosome 1, of chr2-6 on
chromosome 6, of chr2-4 on chromosome 4, of chr3-10 on
chromosome 10, of chr3-12 on chromosome 3, and of chr89 on chromosome 9 have retained significantly more genes
than their counterparts (table 1). For larger duplicated
blocks, 58% (50 of 86) showed significant asymmetric gene
loss (Supplement 1, Supplementary Material online). For
example, on chr1-5 that has 469 polyploidy-derived duplicated pairs, the chromosomal segment on chromosome
1 contains 2,065 genes, 631 more than its homeolog on
chromosome 5 (table 1).
In Arabidopsis, genes were removed preferentially
from one duplicated block after WGD (Thomas et al.
2006). But what is the situation on whole chromosome
level? The duplication relationship between chromosomes
in rice looks more ordered than that in Arabidopsis. In
this study, we observed the asymmetric gene loss of homeologous chromosomes. One likely explanation of the asymmetric gene loss is that the transcriptome of one subgenome
can be dominant to the other in an allopolyploid. In plant
and animal hybrids, the rRNA genes from one parental genome are transcribed, whereas many of them inherited
from the other parent are silenced (nucleolar dominance)
(Pikaard 1999). In allotetraploid Arabidopsis, the progenitor-dependent gene regulation occurs on a genome-wide
scale (Wang et al. 2006). The expression patterns of genes
from Arabidopsis arenosa (one progenitor of the allotetraploid Arabidopsis) are dominant, whereas genes from the
other progenitor Arabidopsis thaliana are more often recessive (Wang et al. 2006). The transcriptome dominance
was observed in several other species as well, such as
1004 Wu et al.
FIG. 1.—The distribution of polyploidy-derived duplicated genes in the rice genome. The duplicated gene pairs were linked by gray lines.
Tragopogon miscellus (Tate et al. 2006) and tetraploid cotton (Adams et al. 2004). Therefore, the asymmetric gene
loss may result from transcriptome dominance of the ancestral genome.
We further used Gene Ontology (Ashburner et al.
2000) to classify rice genes into 2,746 functional categories.
In all, 54 functional categories were significantly overrepresented and 11 functional categories were significantly underrepresented (Supplement 2, Supplementary Material
online). In addition to genes involved in expression regulation and signal transduction, genes related to synthesis
and catabolism of saccharides were found to be overrepresented, such as enzymes involved in glycolysis, amylopectin
biosynthesis, and trehalose biosynthesis (Supplement 2, Supplementary Material online).
In higher plants, 3 enzymes have been found to be
directly involved in starch biosynthesis, including ADPTable 1
Asymmetric Gene Loss/Retention of Sister Duplicated
Chromosomal Segments
No. of
Duplicated Retained
Segments Gene Pairs
chr1–5
chr2–4
chr2–6
chr3–7
chr3–10
chr3–12
chr4–8
chr8–9
chr11–12
a
469
261
292
210
152
42
41
190
250
No. of
Single
Genes
Covered Regions
of Duplicated
Segments (Mb)
2,065/1,434
871/1,142
1,039/1,546
823/787
468/663
226/181
200/135
662/960
328/398
18.6/13.6
9.0/10.0
10.0/14.8
7.1/7.0
4.2/6.6
2.4/1.8
1.8/1.4
6.8/7.7
4.1/3.9
P valuea
0
1.88 10
0
0.19153
6.63 10
0.01634
0.00034
2.03 10
0.00668
P value corrected by Benjamini and Hochberg (1995) method.
09
09
13
glucose pyrophosphorylase (EC: 2.7.7.27), starch synthase
(EC: 2.4.1.21), and starch-branching enzyme (EC:
2.4.1.18) (fig. 2B) (Smith et al. 1997; James et al. 2003).
All the 3 enzymes have polyploidy-derived gene pairs in
rice (fig. 2A). To further understand the function of
polyploid-derived duplicated genes involved in starch synthesis, we used the microarray data from 93-11 (Oryza
sativa L. ssp. indica cv. 93-11) to study expression profiles
(Ma et al. 2005). The expression of duplicates OsAGPS1
and OsAGPS2, OsSSIIa and OsSSIIb, and OsBEIIa and OsBEIIb were divergent from one another (fig. 2C). The expression of one copy in each pair was upregulated in grain
filling–stage of rice panicles (OsAGPS2, OsSSIIa, and OsBEIIb). Moreover, OsAGPS2, OsSSIIa, and OsBEIIb are
highly coexpressed, evidenced by the Pearson correlation
coefficient (OsAGPS2–OsSSIIa: 0.893; OsSSIIa–OsBEIIb:
0.921; and OsAGPS2–OsBEIIb: 0.987). The mutant of
OsAGPS2 (sh-2) displayed a reduction in starch synthesis
in the endosperm, represented by shrunken grains (Lee et al.
2007). The variances of OsSSIIa (alk) showed significant
differences in the gelatinization temperature of the rice
grains, which is related to amylopectin structure (Gao
et al. 2003). In contrast, the expression of the other copy
of each duplicated pair has not been specifically upregulated in these tissues (fig. 2C). Accordingly, OsAGPS2–
OsSSIIa–OsBEIIb forms a dominant pathway of starch
biosynthesis in the grain filling–stage of rice panicles and
composes of one copy of each polyploidy-derived gene pair.
We further discovered that the orthologous genes are
conserved in maize (fig. 3). The ZmAGPS2–ZmSSIIa–
ZmBEIIb (orthologs of OsAGPS2–OsSSIIa–OsBEIIb) have
endosperm-specific expression profiles, and their mutants
(brittle-2, mutant of ZmAGPS2; sugary2, mutant of
ZmSSIIa; and amylose-extender1, mutant of ZmBEIIb)
Impact of Whole-Genome Duplication on Grass Evolution 1005
FIG. 2.—The starch biosynthesis pathway in rice. (A) The Neighbor-Joining trees of the polyploidy-derived duplicated genes involved in starch
biosynthesis in rice. (B) The starch biosynthesis pathway in rice. (C) The expression profiles of the polyploidy-derived duplicated genes involved in
starch biosynthesis in rice. The number on the x axis (1–12) represents rice tissues of roots, shoots, grain filling–stage panicles, heading-stage panicles,
seedlings, lodicules, pistils before insemination, pistils 24 h after insemination, lemmas, stamens, glumes, and paleae, respectively. The number on the y
axis indicates the signal intensity.
show significant changes in starch content and properties in
maize kernels, indicating that this pathway is vital in endosperm development (Giroux and Hannah 1994; Fisher et al.
1996; Zhang et al. 2004). In addition, the brittle-2 and amylose-extender1 were under strong selection during maize
domestication and improvement, suggesting that brittle-2
and amylose-extender1 are important for starch production
(Whitt et al. 2002). All the above suggest the formation of
a dominant starch synthesis pathway in endosperm resulted
from a WGD, which have contributed the genetic material
for the evolution of an important agronomic trait of rice and
maize and likely all cereals.
Methods
The data set of the Nipponbare proteome included
49, 472 gene models (ftp://pub/data/Eukaryotic_Projects/
o_sativa/annotation_dbs/pseudomolecules/version_4.0).
We identified polyploidy-derived duplicated genes according to Tian et al. (2005) with some modifications (see Supplement 1, Supplementary Material online). We used the
InterProScan database version 11 to annotate the gene
function of the Nipponbare on the whole-genome scale
(Zdobnov and Apweiler 2001). The statistical methods
for overrepresented and underrepresented functional categories are included in Supplement 2 (Supplementary Material
online). Phylogenetic trees were constructed employing
the Neighbor-Joining method with MEGA version 3.1
(Kumar et al. 2004).
Supplementary Materials
Supplement 1 and 2 are available at Molecular Biology
and Evolution online (http://mbe.oxfordjournals.org/).
Acknowledgments
This work was supported by Chinese Academy of Sciences (grants number KSCX2-YW-N-028 and CXTDS2005-2) and National Natural Science Foundation of
China (grant numbers 30621001 and 30770143). We thank
anonymous reviewers for their constructive and critical
comments on the manuscript.
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Franz Lang, Associate Editor
Accepted February 15, 2008