BioMed Central
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BMC Genomics
Open AccessResearch article
Synteny conservation between the Prunus genome and both the
present and ancestral Arabidopsis genomes
Sook Jung*1, Dorrie Main2, Margaret Staton1, Ilhyung Cho3,
Tatyana Zhebentyayeva1, Pere Arús4 and Albert Abbott1
Address: 1Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA, 2Department of Horticulture and Landscape
Architecture, Washington State University, Pullman, WA 99164, USA, 3Department of Computer Science, Saginaw Valley State University,
University Center, MI 48710, USA and 4Departament de Gentica Vegetal, Laboratori de Gentica Molecular Vegetal. CSIC-IRTA,08348 Cabrils,
Spain
Email: Sook Jung* - sook@genome.clemson.edu; Dorrie Main - dorrie@wsu.edu; Margaret Staton - meg@genome.clemson.edu;
Ilhyung Cho - icho@svsu.edu; Tatyana Zhebentyayeva - tzhebe@clemson.edu; Pere Arús - pere.arus@irta.es;
Albert Abbott - aalbert@clemson.edu
* Corresponding author
Abstract
Background: Due to the lack of availability of large genomic sequences for peach or other Prunus species, the
degree of synteny conservation between the Prunus species and Arabidopsis has not been systematically assessed.
Using the recently available peach EST sequences that are anchored to Prunus genetic maps and to peach physical
map, we analyzed the extent of conserved synteny between the Prunus and the Arabidopsis genomes. The
reconstructed pseudo-ancestral Arabidopsis genome, existed prior to the proposed recent polyploidy event, was
also utilized in our analysis to further elucidate the evolutionary relationship.
Results: We analyzed the synteny conservation between the Prunus and the Arabidopsis genomes by comparing
475 peach ESTs that are anchored to Prunus genetic maps and their Arabidopsis homologs detected by sequence
similarity. Microsyntenic regions were detected between all five Arabidopsis chromosomes and seven of the eight
linkage groups of the Prunus reference map. An additional 1097 peach ESTs that are anchored to 431 BAC contigs
of the peach physical map and their Arabidopsis homologs were also analyzed. Microsyntenic regions were
detected in 77 BAC contigs. The syntenic regions from both data sets were short and contained only a couple of
conserved gene pairs. The synteny between peach and Arabidopsis was fragmentary; all the Prunus linkage groups
containing syntenic regions matched to more than two different Arabidopsis chromosomes, and most BAC contigs
with multiple conserved syntenic regions corresponded to multiple Arabidopsis chromosomes. Using the same
peach EST datasets and their Arabidopsis homologs, we also detected conserved syntenic regions in the pseudo-
ancestral Arabidopsis genome. In many cases, the gene order and content of peach regions was more conserved
in the ancestral genome than in the present Arabidopsis region. Statistical significance of each syntenic group was
calculated using simulated Arabidopsis genome.
Conclusion: We report here the result of the first extensive analysis of the conserved microsynteny using DNA
sequences across the Prunus genome and their Arabidopsis homologs. Our study also illustrates that both the
ancestral and present Arabidopsis genomes can provide a useful resource for marker saturation and candidate gene
search, as well as elucidating evolutionary relationships between species.
Published: 14 April 2006
BMC Genomics 2006, 7:81 doi:10.1186/1471-2164-7-81
Received: 13 December 2005
Accepted: 14 April 2006
This article is available from: http://www.biomedcentral.com/1471-2164/7/81
 2006 Jung et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Background
The eukaryote genome size is vastly diverse and is not
dependent on the genetic and organismal complexity.
Most of the DNA in large genomes, however, is non-cod-
ing and the gene content is relatively constant [1,2]. Ara-
bidopsis thaliana (estimated haploid size of 115 Mb)
contains more than 25,000 genes [3], and the Human
genome (estimated haploid size of 3200 Mb) contains
20,000­25,000 genes [4]. In addition to the gene content,
the conservation in the synteny (the presence of two or
more genes in the same chromosome) and gene order has
been observed among many plant species. One of the ear-
liest observations of conserved macrosynteny was
between potato and tomato in Solanaceae, where cDNA
markers along the 12 chromosomes were largely collinear
[5].
Significant conservation in the marker and gene order has
been observed among grass species, despite the diverse
genome size and chromosome numbers [6-8]. Similar
conserved macrosynteny has also been observed in
Rosaceae. Comparisons of anchor markers of the Prunus
reference map with those of 13 maps constructed with
other Prunus populations showed that the genomes of
seven Prunus diploid species are essentially collinear [9].
Large collinear blocks were also detected among different
genera in Rosaceae, such as Prunus and Malus [9].
On the other hand, genome sequence comparisons have
revealed that plant genome evolution involved various
small chromosomal rearrangements, such as insertions,
deletions, inversions and translocations [10]. For exam-
ple, Kilian and coworkers have shown that a barley gene
in regions of high microsynteny with rice is in fact trans-
posed to a position that is no longer syntenous with rice
[11]. In addition to small chromosomal rearrangements,
large segmental duplications and polyploidy is prevalent
in plant genome evolution [12-14]. Genome duplication
was well observed in Brassicaceae; The Brassica genome is
extensively triplicated [15] and the Arabidopsis genome
contains numerous large duplicated chromosomal seg-
ments [3,16]. Comparative physical mapping between
Brassica species and Arabidopsis showed high conservation
in the gene order but not the gene content, possibly result-
ing from random gene loss after extensive genome dupli-
cation in both genomes [14].
The degree of synteny conservation has also been exam-
ined between Arabidopsis and less closely related species.
Rosid I and rosid II comparisons (Figure 1) have been
made by sequence homology between soybean marker
sequences and Arabidopsis sequences [17]. Shared linkages
were identified along with signs of extensive genome
duplication and reorganization. A few microsyntenic
regions were also identified by comparative physical map-
ping between Arabidopsis and soybean [18]. A gene-con-
taining BAC sequence of tomato (asteroid I) had
conserved synteny with four different segments of Arabi-
dopsis chromosomes 2­5 [19].
Synteny between Arabidopsis and four dicotyledonous spe-
cies from three major families, caryophyllids, rosids and
asteroids, has also been explored by constructing genetic
maps based on ESTs that are homologous to Arabidopsis
genes [20]. Some syntenic blocks were conserved in all
five maps, Arabidopsis, sugar beet, potato, sunflower and
Prunus, suggesting their evolutionary significance. The
syntenic blocks usually contained only several loci, how-
ever, and each linkage group of the crop genetic maps
matched to multiple Arabidopsis genome regions. Com-
A dendrogram depicting the phylogenetic relationship of peach, Arabidopsis and many other crop speciesFigure 1
A dendrogram depicting the phylogenetic relationship of peach, Arabidopsis and many other crop species. The probable posi-
tion of the recent polyploidization event identified from Blanc and corworkers (22) is marked by an arrow. Figure is based on
Figure 1 in reference 19 and Figure 5 in reference 22.
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plex syntenic relationships, suggestive of chromosome
rearrangement, selective gene loss and genome duplica-
tion, were also observed [20]. Synteny between rice and
Arabidopsis genomes, after 200 million years of divergence
[21], were also observed, but the syntenic regions were
scarce and separated by intervening proteins as previously
suggested [20]. Also, most of the rice syntenic regions map
to more than one Arabidopsis chromosome [21], support-
ing the theme of large scale genome duplication and selec-
tive gene loss in plant genome evolution.
A recent study has systematically analyzed the timing and
number of segmental duplications in the Arabidopsis
genome and suggested a recent polyploidy superimposed
on older large-scale duplication [22]. The recent poly-
ploidy appeared to have occurred during the early emer-
gence of the Brassicaceae family and the older set of
duplicated blocks between rosid I and rosid II groups.
One of the interesting outcomes from this study is the
reconstruction of the approximate gene order of the
ancestral genome that existed prior to the recent poly-
ploidy event. The reconstruction was done by merging
genes in both sister regions duplicated at the time of poly-
ploidy.
Rosaceae contains numerous important fruit crops such as
peach, apple, cherry, pear, raspberry, blackberry and
strawberry [23]. Due to the lack of availability of large
genomic sequences for peach or other Rosaceae species,
little information has been available to study the degree of
synteny conservation between the Rosaceae species and
Arabidopsis. A recent study has detected fragmentary mac-
rosynteny between the Prunus general map and Arabidop-
sis, from comparisons of the genetic marker sequences
Table 1: Number of conserved syntenic regions between Arabidopsis and Prunus genetic maps.
Map Name No. anchored ESTs No. Syntenic regions
(No. three or more gene pairs)
1TxE (almond × peach) 306 68 (12)
2PxF (peach × peach × P. ferganensis) 188 9 (1)
3JxF (peach) 78 7 (1)
4GxN (almond × peach) 82 1 (0)
5FxT (almond) 171 45 (6)
6FxB (almond) 119 9 (0)
All Maps 475 139 (20)
1Dirlewanger et al. 2004 (9); 2Dettori et al. 2001 (33); 3Dirlewanger et al. 1999 (34); 4Jáuregui et al. 2001 (35); 5Joobeur et al. 2004 (36); 6Ballester
et al. 2001 (37)
Number of syntenic groups in each TxE linkage group that match to each Arabidopsis chromosomeFigure 2
Number of syntenic groups in each TxE linkage group that match to each Arabidopsis chromosome.
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Table 2: Conserved syntenic regions with three or more gene pairs between the Arabidopsis genome and Prunus genetic maps.
Peach
Group # Pairs Arabidopsis Putative Function EST Name Linkage Group
gp15 3 AT1G02460 glycoside hydrolase family 28 protein PP_LEa0030E14f FxT-G3F
AT1G02130 Ras-related protein (ARA-5) PP_LEa0010O05f
AT1G03000 AAA-type ATPase family protein PP_LEa0001O24f
gp21 3 AT1G53750 26S proteasome AAA-ATPase subunit (RPT1a) PP_LEa0010K05f PxF-G6
AT1G54080 oligouridylate-binding protein PP_LEa0012K19f
AT1G54110 cation exchanger, putative (CAX10) Ca2+ PP_LEa0007O07f
gp33 3 AT1G66540 cytochrome P450 PP_LEa0013L12f TxE-G5
AT1G66250 glycosyl hydrolase family 17 protein PP_LEa0012I12f
AT1G66680 S locus-linked protein PP_LEa0003H24f
gp42 3 AT2G35330 zinc finger (C3HC4-type RING finger) protein PP_LEa0017P13f JxF-G7
AT2G35930 U-box domain-containing protein PP_LEa0004C12f
AT2G36530 enolase PP_LEa0003M24f
gp54 3 AT2G36530 enolase PP_LEa0003M24f TxE-G7
AT2G35930 U-box domain-containing protein PP_LEa0004C12f
AT2G35330 zinc finger (C3HC4-type RING finger) protein-related PP_LEa0017P13f
gp74 3 AT3G60340 palmitoyl protein thioesterase family protein PP_LEa0012C18f TxE-G5
AT3G60510 enoyl-CoA hydratase/isomerase family protein PP_LEa0009I06f
AT3G60030 squamosa promoter-binding protein-like 12 (SPL12) PP_LEa0002J03f
gp75 3 AT3G07160 glycosyl transferase family 48 protein PP_LEa0004K19f TxE-G5
AT3G06650 ATP-citrate synthase, ATP-citrate (pro-S-)-lyase PP_LEa0005D13f
AT3G06880 transducin family protein PP_LEa0009A14f
gp76 3 AT3G02770 dimethylmenaquinone methyltransferase PP_LEa0030G03f TxE-G5
AT3G01930 nodulin family protein similar to nodulin-like protein PP_LEa0012O21f
AT3G02420 expressed protein PP_LEa0037N22f
gp80 3 AT3G08560 vacuolar ATP synthase subunit E PP_LEa0009M17f TxE-G6
AT3G08710 thioredoxin family protein PP_LEa0016G12f
AT3G08770 lipid transfer protein 6 (LTP6) PP_LEa0029C22f
gp85 3 AT4G17720 RNA recognition motif (RRM)-containing protein PP_LEa0027L14f FxT-G2F
AT4G16900 disease resistance protein (TIR-NBS-LRR class) PP_LEa0003A21f
AT4G17483 palmitoyl protein thioesterase family protein PP_LEa0012C18f
gp98 3 AT4G17483 palmitoyl protein thioesterase family protein PP_LEa0012C18f TxE-G5
AT4G17486 expressed protein PP_LEa0005J05f
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AT4G17615 calcineurin B-like protein 1 (CBL1) PP_LEa0009N08f
gp101 3 AT4G32450 pentatricopeptide (PPR) repeat-containing protein PP_LEa0009C16f TxE-G5
AT4G31970 cytochrome P450 family protein PP_LEa0013L12f
AT4G31810 enoyl-CoA hydratase/isomerase family protein PP_LEa0009I06f
gp106 3 AT5G61790 calnexin 1 (CNX1) PP_LEa0006I23f FxT-G1F
AT5G62310 incomplete root hair elongation (IRE)/protein kinase PP_LEa0009I05f
AT5G62090 expressed protein PP_LEa0030I08f
gp109 3 AT5G47350 palmitoyl protein thioesterase family protein PP_LEa0012C18f FxT-G2F
AT5G47710 C2 domain-containing protein contains PP_LEa0011F23f
AT5G46870 RNA recognition motif (RRM)-containing protein PP_LEa0027L14f
gp114 3 AT5G03520 Ras-related GTP-binding protein PP_LEa0010O05f FxT-G3F
AT5G03340 cell division cycle protein 48, putative/CDC48 PP_LEa0001O24f
AT5G03650 1,4-alpha-glucan branching enzyme PP_LEa0009P15f
gp115 3 AT5G07990 flavonoid 3'-monooxygenase PP_LEa0007M11f FxT-G3F
AT5G07340 calnexin PP_LEa0006I23f
AT5G08470 peroxisome biogenesis protein (PEX1) PP_LEa0001O24f
gp126 3 AT5G08390 transducin family protein PP_LEa0010I06f TxE-G1
AT5G07990 flavonoid 3'-monooxygenase PP_LEa0007M11f
AT5G07340 calnexin PP_LEa0006I23f
gp128 4 AT5G47350 palmitoyl protein thioesterase family protein PP_LEa0012C18f TxE-G2
AT5G46870 RNA recognition motif (RRM)-containing protein PP_LEa0027L14f
AT5G47810 phosphofructokinase family protein PP_LEa0001K06f
AT5G47710 C2 domain-containing protein PP_LEa0011F23f
gp132 3 AT5G47100 calcineurin B-like protein 9 (CBL9) PP_LEa0009N08f TxE-G5
AT5G47350 palmitoyl protein thioesterase family protein PP_LEa0012C18f
AT5G47310 expressed protein PP_LEa0005J05f
gp133 3 AT5G10840 endomembrane protein 70, putative TM4 family PP_LEa0015M20f TxE-G5
AT5G11110 sucrose-phosphate synthase PP_LEa0003F22f
AT5G10430 arabinogalactan-protein (AGP4) PP_LEa0008B15f
Table 2: Conserved syntenic regions with three or more gene pairs between the Arabidopsis genome and Prunus genetic maps.
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and their Arabidopsis homologs [9]. When sequences of
three peach genomic regions were used, only short (two or
three genes) blocks that are collinear with the Arabidopsis
genome were found [24]. With the international effort to
make peach the reference species for the Rosaceae family,
peach physical mapping is underway and peach ESTs are
being anchored to both the genetic and physical map
[25].
The objective of this study was to assess the degree of con-
served synteny between Prunus and Arabidopsis using these
extensive EST sequences anchored to the genetic and
physical maps. We also used the reconstructed ancestral
Arabidopsis genome to see if we coulc find additional syn-
tenic regions. This study demonstrates that comparative
genome analyses between the reconstructed Arabidopsis
genome and other plant species can further facilitate the
utilization of the genetic resources of both species and
help us to understand the evolutionary relationship
between these species.
Results
Conserved synteny between Prunus and Arabidopsis
We searched for conserved syntenic regions between the
Prunus maps and the Arabidopsis genome using 475 peach
ESTs anchored to the Prunus maps and their Arabidopsis
homologs detected by a FASTX sequence similarity search
(E value less than 10 -5). The syntenic groups were selected
when the distance between the two adjacent matches were
less than 250 kb in the Arabidopsis genome and less than
10 cM in the Prunus maps. We detected 139 conserved
syntenic regions, and 20 of them had three or more gene
pairs. The number of syntenic regions between Arabidopsis
and each of the Prunus maps are shown in Table 1.
Microsyntenic regions were detected between all five Ara-
bidopsis chromosomes and seven of the eight linkage
groups of the Prunus TxE reference map. All of the TxE
linkage groups which contained syntenic regions matched
to more than two different Arabidopsis chromosomes (Fig-
ure 2). The gene pairs in the syntenic regions showed sig-
nificant sequence similarity; 78% had E values less than
10 -15, and 88% had E values less than 10 -10.
There were 20 conserved syntenic regions with three or
more gene pairs between the Prunus TxE map and the Ara-
bidopsis genome (Figure 3). Table 2 lists these syntenic
regions with the putative functions of the Arabidopsis
genes. The largest block (group gp128) had four gene
pairs, and covered 20 cM in G2 of the TxE Prunus map and
342 Kb in chromosome 5 of Arabidopsis (Figure 3). Among
20 regions with three or more gene pairs, five groups
showed conserved gene order. In two groups, the colline-
arity could not be assessed because two different peach
ESTs were anchored to the same BAC, probably by hybrid-
izing to different gene sequences in the same BAC. In the
rest of the syntenic groups, the gene order was not con-
served, suggesting many chromosomal rearrangement
events.
Reflecting the synteny conservation among Prunus maps,
we detected many Arabidopsis regions matching to more
than one Prunus map region. In groups gp42 and gp54,
the Arabidopsis genes matched to the ESTs that were
anchored to the same markers present in the linkage
group G7 of both the TxE Prunus map and the JxF peach
map (Table 2). In groups gp85 and gp98, the Arabidopsis
genes within 350 kb matched to ESTs anchored to G2F of
the FxT almond map and G5 of the TxE Prunus map (Table
2).
Most of the peach ESTs showed strong similarity to more
than one Arabidopsis genes, and we were able to detect Pru-
nus blocks that map to more than one site in the Arabidop-
sis genome. Interestingly, some of these putative
duplicated Arabidopsis regions were located in the Arabi-
Conserved syntenic regions with three or more gene pairsbetween Arabidopsis genome and Prunus genomeFigure 3
Conserved syntenic regions with three or more gene pairs
between Arabidopsis genome and Prunus genome. Bolded
blocks are the ones with conserved gene order.
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dopsis paralogous blocks ­ duplicated blocks in a genome
­ reported in the previous study [21]. Figure 4 shows
those Prunus blocks, syntenic to two different Arabidopsis
regions, juxtaposed to the plot of the paralogous blocks of
Arabidopsis. All three paralogons were the ones that were
generated by a recent polyploidy event that occurred dur-
ing the early emergence of the Brassicaceae. Arabidopsis
blocks with conserved synteny to a region in FxT-G1F and
JxF-G1 belong to the paralogons in chromosome 1 and 4,
and those with conserved synteny to a region in FxT-G2T
belong to the paralogons in two different arms of chromo-
some 5 (Figure 4). Three distinct regions in TxE ­ linkage
groups G2, G4 and G5 ­ showed conserved synteny to
three overlapping blocks in each paralogon on chromo-
some 4 and 5 (Figure 4). These TxE map regions may rep-
resent triplicated Prunus regions that subsequently went
through selective gene loss.
Synteny between Prunus and the pseudo ancestral
Arabidopsis genome
To further analyze the evolutionary relationship between
the Arabidopsis and Prunus genomes, we searched for con-
served syntenic regions between Prunus maps and the
ancestral Arabidopsis genome [22]. The pseudo ancestral
genome contained 20187 genes, which is about 69% of
the genes in the present genome, arranged in a linear
array. We used the same 475 peach ESTs and their Arabi-
dopsis homologs detected by FASTX sequence similarity
searching (E value less than 10 -5) in our search for the
conserved syntenic regions. The syntenic groups were
selected when the number of genes between the two adja-
Prunus genomic blocks that map to two distinct Arabidopsis regionsFigure 4
Prunus genomic blocks that map to two distinct Arabidopsis regions. Shown are the Prunus blocks that identified Arabidopsis sis-
ter regions generated by the proposed polyploidy event. The Prunus blocks with the same color (red or green) are homologous
regions that share more than two anchored ESTs.
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cent matches is less than 61 in the Arabidopsis genome and
the distance less than 10 cM of the Prunus maps. The esti-
mated number of genes in 250 kb was used as the maxi-
mum distance between two matches in the Arabidopsis
genome, since only the gene order, instead of the kb, was
available as a position along the ancestral genome (see
Methods).
We detected 101 conserved syntenic regions, and 12 of
them had three or more gene pairs. The details, including
the putative functions of the syntenic blocks with three or
more gene pairs, are shown in Table 3. Fewer syntenic
blocks were detected in the ancestral genome using these
criteria, but much fewer blocks matched to the duplicated
Arabidopsis genome. In the present Arabidopsis genome, 20
syntenic blocks, with three conserved genes, matched to
14 distinct Prunus regions, but, in the ancestral genome,
12 syntenic blocks matched to 10 distinct Prunus regions.
Some groups contained the same Arabidopsis gene and
peach EST pairs as in the syntenic groups detected from
the Prunus-present Arabidopsis genome analysis. Several
new Prunus regions were found to have conserved synteny
with the ancestral Arabidopsis genome. The Arabidopsis
genes in these syntenic blocks were apparently relocated
in distinct regions after the putative Arabidopsis genome
duplication event. For example, group ga54 in ancestral
genome is composed of two genes in chromosome 5 and
one from chromosome 3, and they were paired with ESTs
that were anchored to the linkage group G1 of TxE map.
Group ga28 and ga79 represent regions where three genes
were closely located in the ancestral genome but they were
rearranged into two different regions of the present Arabi-
dopsis chromosome 5.
We also found examples where the gene content in the
Prunus genome is more conserved in the ancestral genome
than the present Arabidopsis genome. For example, group
ga81 in ancestral genome contains four gene pairs that
match to the linkage group G5 of the TxE map (Figure 5).
Group gp48 and gp101 in the present genome match to
the same region in TxE-G5, but contain only part of the
gene pairs. Figure 5 illustrates the proposed evolutionary
steps that may have occurred in these regions: large scale
genome duplication and subsequent selective gene loss
and gene duplication. The genomic regions in chromo-
some 2 and 4 were part of the previously reported dupli-
cated regions with 68 gene pairs [22], supporting our
proposed evolutionary steps.
Synteny analysis between the peach physical
transcriptome map and the Arabidopsis genome
We also used peach EST sequences that are anchored to
the developing peach physical map to search for con-
served syntenic regions between peach and Arabidopsis.
Our data were composed of 1097 peach ESTs that are
anchored to 431 BAC contigs, and their Arabidopsis
homologs detected by FASTX sequence similarity search-
ing (E value less than 10 -5). The sequence similarity
search results produced 4448 peach-Arabidopsis sequence
pairs that consist of 904 distinct ESTs and 3747 distinct
Arabidopsis proteins. These sequence pairs were used to
detect syntenic regions between peach and Arabidopsis.
The syntenic groups were selected when the distance
between the two adjacent matches was less than 250 kb in
the Arabidopsis genome and anchored to the same BAC
contig.
Our analysis identified 287 Arabidopsis genes and 204
peach ESTs found in 140 syntenic blocks with at least two
gene pairs. The syntenic blocks were found in all of the
five Arabidopsis chromosomes. In peach, the syntenic
blocks were found in a total of 77 BAC contigs. The syn-
teny conservation was fragmentary; 16 out of the 18 BAC
contigs with multiple syntenic regions matched to more
than one Arabidopsis chromosome.
The number of gene pairs in the syntenic blocks was
small: two blocks with four gene pairs, 14 blocks with
three gene pairs and 124 blocks with two gene pairs. The
syntenic blocks with three or more gene pairs are shown
in Table 4 and Figure 6. Only two of the 16 blocks were
collinear. It is possible that the content in the block is con-
served but the gene order has differentially evolved in the
two genomes. On the other hand, the order of the peach
ESTs was estimated by the positions of the EST-hybridiz-
ing BACs in a BAC contig which may not represent the
actual order of the ESTs in the genome. The average size of
the syntenic blocks in Arabidopsis genome was 97 kb with
a maximum 360 kb (group pp96: Arabidopsis chromo-
some 4 and ctg2264) and minimum 2.7 kb. Groups
pp129 and pp130 were close enough to be combined into
one syntenic region containing five gene pairs, and they
covered 451 kb in the Arabidopsis genome (Figure 6).
Ctg2264 is the BAC contig that has the most anchored
ESTs. It is composed of only five BACs but has 70
anchored ESTs, suggesting it represents a gene-rich region.
Ctg2264 and the Arabidopsis genome had a number of syn-
tenic regions including nine with three gene pairs and 22
with two gene pairs. In eight cases, the same peach EST
sets in ctg2264 matched to two distinct Arabidopsis
regions. It is notable that a relatively small contig, com-
posed of only five overlapping BACs, had numerous
microsyntenic regions found in all five Arabidopsis chro-
mosomes. Ctg1502 has the second most anchored ESTs,
and all the 48 anchored ESTs are limited to three BACs of
the total 14 BACs composing the contig. Despite the many
anchored ESTs in ctg1502, only three syntenic regions
with two gene pairs were found. Only 11 of the 48
anchored ESTs had Arabidopsis homologs, suggesting that
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Table 3: Conserved syntenic regions with three or more gene pairs between the pseudo-ancestral Arabidopsis genome and Prunus
genetic maps.
Peach
Group # Pairs Arabidopsis Putative Function EST Name BAC Contig
ga18 3 AT5G47350 palmitoyl protein thioesterase family protein PP_LEa0012C18f FxT-G2F
AT4G17720 RNA recognition motif (RRM)-containing
protein
PP_LEa0027L14f
AT5G47710 C2 domain-containing protein contains PP_LEa0011F23f
ga28 3 AT5G07340 calnexin, putative PP_LEa0006I23f FxT-G3F
AT5G07990 flavonoid 3'-monooxygenase PP_LEa0007M11f
AT5G61580 phosphofructokinase family protein PP_LEa0001K06f
ga29 3 AT5G14650 polygalacturonase, putative/pectinase, putative PP_LEa0030E14f FxT-G3F
AT3G01610 AAA-type ATPase family protein PP_LEa0001O24f
AT5G14370 expressed protein PP_LEa0011N22f
ga54 3 AT5G59180 DNA-directed RNA polymerase II PP_LEa0026O17f TxE-G1
AT5G59840 Ras-related GTP-binding family protein epsin N-
terminal homology (ENTH) domain-containing
PP_LEa0036D15f
AT3G46540 PP_LEa0003I01f
ga60 4 AT2G24640 ubiquitin carboxyl-terminal hydrolase family
protein
PP_LEa0006J17f TxE-G1
AT4G32400 mitochondrial substrate carrier family protein PP_LEa0009H16f
AT2G25420 transducin family protein PP_LEa0009H21f
AT2G25160 cytochrome P450 PP_LEa0013L12f
ga66 3 AT4G17720 RNA recognition motif (RRM)-containing
protein
PP_LEa0027L14f TxE-G2
AT5G47350 palmitoyl protein thioesterase family protein PP_LEa0012C18f
AT5G47710 C2 domain-containing protein PP_LEa0011F23f
ga77 3 AT4G17486 expressed protein PP_LEa0005J05f TxE-G5
AT5G47350 palmitoyl protein thioesterase family protein PP_LEa0012C18f
AT4G17615 calcineurin B-like protein 1 (CBL1) PP_LEa0009N08f
ga79 3 AT5G25170 expressed protein PP_LEa0005J05f TxE-G5
AT5G11110 sucrose-phosphate synthase PP_LEa0003F22f
AT5G10840 endomembrane protein 70, putative TM4 family; PP_LEa0015M20f
ga81 4 AT4G31940 cytochrome P450 PP_LEa0013L12f TxE-G5
AT2G25190 expressed protein PP_LEa0005J05f
AT2G25160 cytochrome P450 PP_LEa0013L12f
AT4G31810 enoyl-CoA hydratase/isomerase family protein PP_LEa0009I06f
ga83 3 AT1G66540 cytochrome P450 PP_LEa0013L12f TxE-G5
AT1G66250 glycosyl hydrolase family 17 protein PP_LEa0012I12f
AT1G66680 S locus-linked protein PP_LEa0003H24f
ga94 3 AT5G58160 formin homology 2 domain-containing protein PP_LEa0035A24f TxE-G6
AT5G57990 ubiquitin-specific protease 23 PP_LEa0006J17f
AT5G58590 Ran-binding protein 1, putative/RanBP1, putative PP_LEa0003G19f
ga95 3 AT5G01870 lipid transfer protein, putative PP_LEa0029C22f TxE-G6
AT3G08560 vacuolar ATP synthase subunit E PP_LEa0009M17f
AT3G08710 thioredoxin family protein PP_LEa0016G12f
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the rest of the ESTs may represent genes that do not exist
in the Arabidopsis gene repertoire. However, it is also pos-
sible that we will detect more Arabidopsis homologs, hence
more microsyntenic regions, when the entire gene
sequences are available instead of short EST sequences.
In addition to the blocks in ctg2264, we found many
other peach blocks corresponding to more than one syn-
tenic region in Arabidopsis, reflecting the fact that the Ara-
bidopsis genome contains numerous large duplicated
segments [21]. In our data set, there were 21 peach seg-
ments that each corresponds to more than one distinct
Arabidopsis segment. As expected, the Arabidopsis genes
that matched to the same peach ESTs in these duplicated
regions had similar putative function or belong to the
same protein family. Some of the syntenic blocks, espe-
cially those duplicated in the Arabidopsis genome, were
composed of genes with related function, suggesting that
related genes that tend to cluster in Arabidopsis also do in
peach. For example, all four Arabidopsis genes in groups
pp77 and pp110 were FAD-binding domain-containing
protein, similar to reticuline oxidase precursor. Similar
observation has been reported in the analysis between
Arabidopsis and rice [25]. We also observed two Arabidopsis
segments that each corresponds to more than one distinct
peach segment. Groups pp113 and pp132 involve an Ara-
bidopsis region with three genes in chromosome 5 match-
ing three peach ESTs in two different contigs (ctg1505 and
ctg2269) and groups pp114 and pp123 involve an Arabi-
dopsis region that matches to two different peach contigs
(ctg1565 and ctg2287).
Synteny analysis between the peach physical
transcriptome map and the reconstructed Arabidopsis
ancestral genome
The evolutionary relationship between Arabidopsis and
peach was further analyzed by searching for conserved
syntenic regions between the ancestral Arabidopsis genome
and the peach physical transcriptome map. The syntenic
groups were selected when the number of genes between
the two adjacent matches was less than 61 in the Arabidop-
sis genome and anchored to the same BAC contig. This
analysis identified 231 Arabidopsis proteins and 179 peach
ESTs found in 111 conserved gene blocks. The average
block size in the Arabidopsis genome was 27.6 genes with
a maximum of 97 genes and a minimum of two genes.
The estimated size of the syntenic blocks, using the aver-
age size of the Arabidopsis genome containing one gene per
4.1 kb (see Methods), is on average 113.2 kb with a max-
imum 397.7 kb and a minimum of 8.2 kb. The syntenic
blocks were distributed quite evenly across the ancestral
genome. In peach, the syntenic blocks were found in a
Proposed evolutionary steps involving some syntenic blocks between Arabidopsis and the Prunus genomesFigure 5
Proposed evolutionary steps involving some syntenic blocks between Arabidopsis and the Prunus genomes. Blocks in the puta-
tive ancestral Arabidopsis genome and Arabidopsis chromosome 2 and 4 that match to the same block in Prunus TxE map are
illustrated. Red and green colors were used to help track the genes. Dashed lines were used to indicate the relationship with
less stronger homology when the same EST was homologous to more than one Arabidopsis genes.
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Table 4: Conserved syntenic regions with three or more gene pairs between the Arabidopsis genome and EST-anchored peach BAC
contigs.
Peach
Group # Pairs Arabidopsis Putative Function EST Name BAC Contig
pp23 3 AT1G19570 dehydroascorbate reductase PP_LEa0036C16f ctg2264
AT1G20010 tubulin beta-5 chain (TUB5) PP_LEa0035B10f
AT1G20450 dehydrin (ERD10) PP_LEa0035C17f
pp48 3 AT2G18470 protein kinase family protein PP_LEa0036C20f ctg2264
AT2G18840 integral membrane Yip1 family protein PP_LEa0034N14f
AT2G18280 tubby-like protein 2 (TULP2) PP_LEa0034J18f
pp52 4 AT2G40280 Putative methyltransferase PP_LEa0017H06f ctg58
AT2G39750 Putative methyltransferase PP_LEa0017H06f
AT2G39770 GDP-mannose pyrophosphorylase (GMP1) PP_LEa0005L09f
AT2G40060 expressed protein PP_LEa0017F24f
pp54 3 AT2G19740 60S ribosomal protein L31 (RPL31A) PP_LEa0008A18f ctg9
AT2G19680 mitochondrial ATP synthase g subunit PP_LEa0025C15f
AT2G19730 60S ribosomal protein L28 (RPL28A) PP_LEa0001M19f
pp69 3 AT3G02200 proteasome family protein PP_LEa0025D12f ctg2264
AT3G02310 developmental protein SEPALLATA2 PP_LEa0035H10f
AT3G01520 universal stress protein (USP) family PP_LEa0025L13f
pp94 3 AT4G27880 seven in absentia (SINA) family protein PP_LEa0035M04f ctg2264
AT4G27560 glycosyltransferase family protein PP_LEa0036D18f
AT4G27740 Yippee putative zinc-binding protein PP_LEa0035H22f
pp96 3 AT4G10710 transcriptional regulator-related PP_LEa0034P24f ctg2264
AT4G11450 expressed protein PP_LEa0035H16f
AT4G11030 long-chain-fatty-acid ­ CoA ligase PP_LEa0034M07f
pp113 3 AT5G66460 PP_LEa0003M21f ctg1505
AT5G66140 20S proteasome alpha subunit D2 PP_LEa0027M15f
AT5G66510 bacterial transferase PP_LEa0009C17f
pp114 4 AT5G08400 expressed protein PP_LEa0011C13f ctg1565
AT5G08380 alpha-galactosidase PP_LEa0009B18f
AT5G08540 expressed protein PP_LEa0027N06f
AT5G08410 ferredoxin-thioredoxin reductase PP_LEa0009N05f
pp119 3 AT5G47040 Lon protease homolog 1 PP_LEa0001P13f ctg190
AT5G47020 glycine-rich protein PP_LEa0012O09f
AT5G47010 RNA helicase PP_LEa0010E19f
pp126 3 AT5G54010 glycosyltransferase family protein PP_LEa0036D18f ctg2264
AT5G53940 Yippee putative zinc-binding protein PP_LEa0035H22f
AT5G53770 nucleotidyltransferase family protein PP_LEa0025D10f
pp127 3 AT5G51050 mitochondrial substrate carrier family protein PP_LEa0034P07f ctg2264
AT5G50550 WD-40 repeat family protein/St12p protein PP_LEa0036H23f
AT5G51180 expressed protein similar to auxin down-
regulated protein
PP_LEa0035K24f
pp128 3 AT5G43830 ARG10 PP_LEa0034K23f ctg2264
AT5G44340 tubulin beta-4 chain (TUB4) PP_LEa0035B10f
AT5G44090 calcium-binding EF hand family protein PP_LEa0035H07f
pp130 3 AT5G15160 bHLH family protein PP_LEa0035P14f ctg2264
AT5G14680 universal stress protein (USP) family protein PP_LEa0025L13f
AT5G14590 isocitrate dehydrogenase PP_LEa0034O16f
pp132 3 AT5G66460 PP_LEa0003M21f ctg2269
AT5G66510 bacterial transferase PP_LEa0009C17f
AT5G66140 20S proteasome alpha subunit PP_LEa0027M15f
pp137 3 AT5G53280 expressed protein PP_LEa0027O13f ctg378
AT5G53310 myosin heavy chain-related PP_LEa0013H04f
AT5G53340 galactosyltransferase family protein PP_LEa0003L02f
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total of 69 contigs. Among the 111 syntenic blocks, two
blocks had four gene pairs, 12 blocks had three gene pairs
and the rest had two gene pairs. The details of the 12
blocks with three or more gene pairs are shown in Table
5. Four of the 12 blocks with three or more gene pairs were
collinear. Five groups contained the same Arabidopsis gene
and peach EST pairs as those in the syntenic groups
detected from the peach-present Arabidopsis genome anal-
ysis. Four groups involved the same regions to the ones
observed in the peach-present Arabidopsis genome analy-
sis, except that one or two peach ESTs were paired with
Arabidopsis proteins from other duplicated regions. The
rest of the blocks disclose peach regions that have con-
served synteny with the ancestral Arabidopsis genome but
not with the present one. In group pa3, AT5G60910 and
the other two genes are closer in the ancestral genome,
with only four genes in between, than in the present
genome where they are 21 Mbp apart from each other.
Groups pa5 and pa35 shows a similar situation in which
three genes are far apart in the same chromosome of the
present genome, but they are much closer in the ancestral
genome.
Ctg2264, containing the most anchored ESTs, had one
with four unordered gene pairs, four with three unordered
gene pairs and 18 with two gene pairs. Upon close exam-
ination, the syntenic block with the five unordered genes
observed in the present Arabidopsis genome (Figure 6) was
also detected in the ancestral genome (Figure 7). The
block was not detected from our original analysis because
some of the gaps between the genes were larger than the
limit set by the search parameters. The comparison
revealed a syntenic block with six gene pairs in the ances-
tral genome and two blocks containing rearranged gene
pairs in chromosome 3 and 5 of the present Arabidopsis
genome (Figure 7). Figure 7 illustrates the proposed evo-
lutionary steps that may have occurred in these regions:
large scale genome duplication and subsequent selective
gene loss in chromosome 3 and inversion in chromosome
5. Since the reconstructed ancestral Arabidopsis genome
has been reported to contain a considerable amount of
duplicated regions [22], we searched for peach EST seg-
ments that paired with more than one distinct Arabidopsis
region. In this data set, there were eleven peach segments
that each corresponds to two distinct Arabidopsis seg-
Conserved syntenic regions with three or more gene pairs between Arabidopsis genome and EST-anchored peach BAC contigsFigure 6
Conserved syntenic regions with three or more gene pairs between Arabidopsis genome and EST-anchored peach BAC contigs.
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ments. It is notable, however, that twice as many dupli-
cated blocks were identified by the peach EST segments in
the present genome than the ancestral genome. We also
observed three Arabidopsis segments that each corre-
sponded to more than one distinct peach segment. Two
Arabidopsis segments identified the same duplicated peach
segments, detected from the analysis with the present Ara-
bidopsis genome. Another Arabidopsis region identified
duplicated peach regions in ctg1112 and ctg2175.
Simulation study
To determine whether the syntenic groups we report were
detected by chance, we tested the statistical significance
for each group. Both the current and putative ancestral
Arabidopsis genomes were randomized by leaving the loca-
tions the same but permuting the gene names. We ana-
lyzed 1000 simulated Arabidopsis genomes for the
occurrence of the each conserved syntenic group and cal-
culated the probability of the match occurring by chance.
The probability of the association by chance was less than
1% for all the syntenic groups with more than three gene
pairs. The numbers of syntenic groups at various signifi-
cance thresholds are shown in Table 6.
Discussion
We surveyed the degree of synteny conservation between
the Prunus and the Arabidopsis genomes using extensive
EST sequences anchored to several Prunus genetic maps
and the developing peach physical map. Our study is the
first to systematically examine the conserved microsyn-
teny using DNA sequences across the Prunus genome and
their Arabidopsis homologs. We could detect considerable
conserved microsytenic regions even with our stringent
parameters. Among the 475 genetically anchored ESTs,
142 distinct ESTs belong to the syntenic groups that were
conserved with either the present or ancestral Arabidopsis
genomes. However, the syntenic blocks were rather small
in size and contained only a few gene pairs. In addition,
most of the BAC contigs with more than two conserved
syntenic regions matched to more than one Arabidopsis
chromosome. Our finding is in accordance with the previ-
ous study of peach BAC sequences that the segments with
a gene order congruent with Arabidopsis were short in any
peach region studied and the corresponding segments
were found in diverse locations in the Arabidopsis genome
[24]. From the analysis with the genetically anchored
ESTs, the largest block we detected had four gene pairs,
and covered 20 cM in G2 of the TxE Prunus map and 342
Kb in chromosome 5 of Arabidopsis. From the analysis
with the physical map-anchored ESTs, the largest block we
detected contained five gene pairs and spanned 451 kb in
the Arabidopsis genome. We may be able to find more syn-
tenic blocks with over three gene pairs when more ESTs
are hybridized to map-anchored BACs and longer BAC
contigs are available. We may also find more syntenic
blocks when the entire gene sequences are available. The
results from the BAC contig rich in anchored ESTs, how-
ever, suggest that the syntenic regions between Arabidopsis
and peach are typically small and contain several gene
pairs at most. For example, ctg2264, with five BACs and
70 anchored ESTs, have numerous microsyntenic regions
in all five Arabidopsis chromosomes instead of having rel-
atively large syntenic regions.
We also detected conserved syntenic regions in the pseudo
ancestral Arabidopsis genome that existed prior to the
Proposed evolutionary steps involving some syntenic blocks between Arabidopsis and Peach genomesFigure 7
Proposed evolutionary steps involving some syntenic blocks between Arabidopsis and Peach genomes. Blocks in the putative
ancestral Arabidopsis genome and Arabidopsis chromosome 3 and 5 that match to the same peach BAC contig are illustrated.
Red colors were used to help track the genes. The order of the ESTs in the BAC contig was not shown because the ESTs were
anchored to overlapping BACs.
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Table 5: Conserved syntenic regions with three or more gene pairs between the pseudo-ancestral Arabidopsis genome and EST-
anchored peach BAC contigs.
Peach
Group # Pairs Arabidopsis Putative Function EST Name BAC Contig
pa3 3 AT5G07990 flavonoid 3'-monooxygenase PP_LEa0010I09f ctg1172
AT5G08100 L-asparaginase/L-asparagine amidohydrolase PP_LEa0007L05f
AT5G60910 agamous-like MADS box protein AGL8 PP_LEa0002N13f
pa4 3 AT2G45560 cytochrome P450 family protein PP_LEa0010I09f ctg1172
AT3G61040 cytochrome P450 family protein PP_LEa0010I09f
AT2G45650 MADS-box protein (AGL6) PP_LEa0002N13f
pa5 3 AT1G68020 glycosyl transferase family 20 protein PP_LEa0001F16f ctg1172
AT1G23870 glycosyl transferase family 20 protein PP_LEa0001F16f
AT1G24260 MADS-box protein (AGL9) PP_LEa0002N13f
pa23 3 AT5G66510 contains bacterial transferase hexapeptide
repea
PP_LEa0009C17f ctg1505
AT5G66140 20S proteasome alpha subunit D2 PP_LEa0027M15f
AT5G66460 PP_LEa0003M21f
pa26 4 AT5G08380 alpha-galactosidase/melibiase PP_LEa0009B18f ctg1565
AT5G08540 expressed protein PP_LEa0027N06f
AT5G08400 expressed protein predicted proteins PP_LEa0011C13f
AT5G23440 ferredoxin-thioredoxin reductase PP_LEa0009N05f
pa35 3 AT5G26030 ferrochelatase I PP_LEa0004A06f ctg1823
AT5G11710 epsin N-terminal homology domain-
containing protein
PP_LEa0003I01f
AT5G11770 NADH-ubiquinone oxidoreductase 20 kDa
subunit
PP_LEa0001H16f
pa37 3 AT5G47010 RNA helicase PP_LEa0010E19f ctg190
AT5G47040 Lon protease homolog 1, mitochondrial
(LON)
PP_LEa0001P13f
AT5G47020 glycine-rich protein PP_LEa0012O09f
pa59 3 AT4G27740 yippee family protein PP_LEa0035H22f ctg2264
AT4G27880 seven in absentia (SINA) family protein PP_LEa0035M04f
AT4G27560 glycosyltransferase family protein PP_LEa0036D18f
pa61 3 AT5G51050 mitochondrial substrate carrier family
protein
PP_LEa0034P07f ctg2264
AT5G51180 expressed protein PP_LEa0035K24f
AT5G50550 WD-40 repeat family protein/St12p protein PP_LEa0036H23f
pa64 3 AT4G14960 tubulin alpha-6 chain (TUA6) PP_LEa0035B10f ctg2264
AT3G22170 far-red impaired responsive protein PP_LEa0036G03f
AT3G22850 similar to auxin down-regulated protein
ARG10
PP_LEa0034K23f
pa71 3 AT2G18280 tubby-like protein 2 (TULP2) PP_LEa0034J18f ctg2264
AT4G30260 integral membrane Yip1 family protein PP_LEa0034N14f
AT2G18470 protein kinase family protein PP_LEa0036C20f
pa82 3 AT5G66510 contains bacterial transferase hexapeptide
repea
PP_LEa0009C17f ctg2269
AT5G66460 PP_LEa0003M21f
AT5G66140 20S proteasome alpha subunit D2 PP_LEa0027M15f
pa103 4 AT3G56080 dehydration-responsive protein-related PP_LEa0017H06f ctg58
AT2G40060 expressed protein PP_LEa0017F24f
AT2G39750 dehydration-responsive family protein PP_LEa0017H06f
AT3G55590 GDP-mannose pyrophosphorylase PP_LEa0005L09f
pa108 3 AT4G29410 60S ribosomal protein L28 (RPL28C) PP_LEa0001M19f ctg9
AT4G29480 mitochondrial ATP synthase g subunit family
protein
PP_LEa0025C15f
AT2G19740 60S ribosomal protein L31 (RPL31A) PP_LEa0008A18f
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recent polyploidy event. We did not find markedly differ-
ent results in the conserved synteny with the ancestral
genome compared to the present genome, which was to
be expected given that the polyploidization event that dif-
ferentiated the present and the ancestral Arabidopsis
genome occurred 24­40 million years ago, which is rela-
tively recent compared to the peach-Arabidopsis diver-
gence, 90 million years ago. We did find, however, a
number of syntenic regions in the ancestral genome that
do not exist in the present genome. We also found some
examples where gene content and the gene order is more
conserved in the ancestral genome than in the present
genome. Our study illustrates that comparative genome
analysis of both the ancestral and present Arabidopsis
genomes with other plant species can provide a useful
resource for marker saturation in a specific region and
candidate gene searches, as well as elucidating evolution-
ary relationships between species.
Conclusion
We report the results of the systematic examination of
conserved microsynteny between the Prunus and Arabidop-
sis. Our study is the first to systematically examine the
conserved microsynteny using extensive DNA sequences
across the Prunus genome and their Arabidopsis homologs.
More importantly, this study utilized the pseudo-ancestral
Arabidopsis genome, as well as the present Arabidopsis
genome, in the comparison of the Arabidopsis with other
plant genomes. This method helped us to find more con-
served microsyntenic regions between the ancestral Arabi-
dopsis and Prunus genomes and also to delineate the
putative evolutionary steps in the microsyntenic regions.
We believe that this report will give a new insight in the
study of evolutionary relationships among plants and
provide new way to more efficient utilization of the
resources of the model genome.
Methods
Data description
For the synteny analysis between the Prunus and Arabidop-
sis genomes, we used peach EST sequences anchored to
the Prunus genetic maps [25]. Among the 475 genetically
anchored peach ESTs used in this analysis, 306 ESTs were
hybridized to BACs that have been hybridized to genetic
markers, and the rest were hybridized to BACs belonging
to a contig containing other BACs hybridized to genetic
markers. The positions (cM) of the genetic markers were
used as the positions for the genetically anchored ESTs.
For the synteny analysis between the peach physical tran-
scriptome map and Arabidopsis, we used peach EST
sequences that are anchored the developing peach physi-
cal map. The data set is composed of 1097 sequences that
are anchored to 431 BAC contigs containing at least two
anchored ESTs. The position of the individual BACs in the
BAC contigs were used as the positions of the physical
map anchored ESTs. For the ESTs that are anchored to
multiple overlapping ESTs in a BAC contig, the innermost
left and right positions were assigned. All the sequences
and positions of the peach ESTs were obtained from the
Genome Database for Rosaceae (GDR) [27,28].
The sequence data (ATH1_pep_cm_20040228) and the
chromosome coordinate data (sv_gene.data) of the 29161
Arabidopsis translated proteins were downloaded from the
Arabidopsis Information Resources (TAIR) database
[29,30] in March 2005. The ordered list of 20187 gene
names in the reconstructed ancestral Arabidopsis genome
was downloaded from the Paralogons in Arabidopsis thal-
iana web site [22,31].
Detection of the conserved syntenic regions
Mapped peach ESTs that are homologous to the Arabidop-
sis proteins were determined using the FASTX 3.4 algo-
rithm [27]. Matches with E values less than 10 -5 were
selected for further analysis. For the comparison between
the Arabidopsis genome and the Prunus maps, the syntenic
groups were selected when the distance between the two
adjacent matches were less than 250 kb in the Arabidopsis
genome and less than 10 cM for the Prunus maps. For the
comparison between the Arabidopsis genome and the
peach physical map, the syntenic groups were selected
when the matches were located within 250 kb in the cur-
rent Arabidopsis genome and belong to the same BAC con-
tigs. In the analysis of the conserved synteny between the
ancestral Arabidopsis genome and the peach physical map
Table 6: Number of syntenic groups between Prunus/Peach and Arabidopsis that are detectecd at various significance thresholds.
Significance threshold
Syntenic Group 99.90% 99% 95% 90% 80% Total
gp 21 (17) 27 (20) 56 81 108 139 (20)
ga 11 (8) 22 (12) 39 64 86 101 (12)
pp 18 (11) 36 (16) 65 85 102 140 (16)
pa 13 (10) 25 (14) 50 70 93 111 (14)
Numbers in parenthesis stands for the syntenic groups with more than three gene pairs.
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or the Prunus genetic maps, we used the estimated number
of genes in 250 kb (61 genes) as the maximum distance
between the two adjacent matches in the Arabidopsis
genome. The estimation was done by dividing 250 kb by
the average size per gene (4.1 kb) in Arabidopsis, which is
derived by the division of the total length in kb by the
number of genes in the Arabidopsis genome.
We used a program called DAGchainer [32] to detect col-
linear chromosomal segment conserved in the peach/Pru-
nus and Arabidopsis genomes. DAGchainer was run with
parameters set to detect any collinear blocks with two or
more gene pairs and with the maximum distance between
the two adjacent matches specified above. Since the
DAGchainer program detects only the regions with con-
served order, we developed scripts to detect both collinear
and non-collinear regions from the output.
Evaluation of the conserved syntenic regions
To determine whether the syntenic groups we report were
detected by chance, we tested the statistical significance
for each group. Both of the current and putative ancestral
Arabidopsis genomes were randomized by leaving the loca-
tions the same but permuting the gene names. We ana-
lyzed 1000 simulated Arabidopsis genomes for the
occurrence of each conserved syntenic group and calcu-
lated the probability of the match occurring by chance.
Authors' contributions
SJ designed the protocol for synteny analysis and the sta-
tistical analysis, designed and developed scripts, per-
formed the research, analyzed the data and wrote the
paper. DM conceived of the study and participated in its
design and coordination, and critically revised the manu-
script. MS performed the sequence similarity search and
wrote the scripts for statistical analysis. IC wrote the
scripts for detecting non-linear syntenic regions and
duplicate syntenic regions and parting the DAGchainer
outputs. TZ provided the EST data hybridized to peach
BAC contigs. PA critically revised the manuscript. AA con-
ceived of the study and critically revised the manuscript.
All authors read and approved the final manuscript.
Acknowledgements
This work was supported by an award (#0320544) from the National Sci-
ence Foundation.
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