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Vol. 11, Issue 12, 2020-2026, December 2001
LETTER
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ABSTRACT |
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 TOP
 ABSTRACT
 INTRODUCTION
RESULTS
DISCUSSION
METHODS
REFERENCES
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We have investigated possible collinearity between the genomes of rice and Arabidopsis by comparing 126 annotated and mapped rice BAC sequences (~20 Mb of sequence) with the annotated and complete Arabidopsis genome (~115 Mb). Although we were able to identify several regions in which gene order is preserved, they are relatively small, and are interrupted by noncollinear genes. Computer simulation showed that these microscale collinearities are above the expectation for a random process. On the other hand, the order of exons within homologous genes (<2.5 kb) was preserved, as expected.
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INTRODUCTION |
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TOP
ABSTRACT
INTRODUCTION
RESULTS
DISCUSSION
METHODS
REFERENCES
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Comparative genomics can be used to gain knowledge
of gene organization, and is particularly helpful in examining genome
evolution (Keller and Geuillet 2000
). Closely related species have
extensive regions of gene collinearity, a phenomenon also known as
synteny (Passarge et al. 1999), but as the evolutionary distance
between two species increases, the segments of collinearity get
shorter. The recent availability of the complete genomes of several
model systems has sparked renewed interest in the study of collinearity because of the phenomenon's potential for transferring useful information from
well-studied small genomes to larger ones (Rubin et al. 2000).
Arabidopsis thaliana, a member of the mustard
family whose genome was completed in 2000, is a popular model system
for dicots. Several studies have shown genome collinearity
between Arabidopsis and closely related dicots. Acarkan et al.
(2000) identified a collinear segment spanning >10 cM (~10 Mb)
between Arabidopsis and Capsella rubella. Over a
60-kb region, gene order and orientation were completely conserved. A
syntenic segment for a 30-kb region on Arabidopsis Chromosome
4 was found to contain six genes also found in the same order in
Brassica (Sadowski and Quiros 1998). Large segment
duplications were identified in the Arabidopsis genome
sequence, comprising 65.6 Mb or 58% of the genome (The Arabidopsis Genome Initiative 2000; Vision et al. 2000). A
105-kb tomato BAC clone shows conservation of gene content and order with four different segments of Arabidopsis chromosomes (Ku et al. 2000).
Rice (Oryza sativa), a model system for grasses, has also
shown collinearity with other monocots. In a 1.9-cM region of rice, five genes show interrupted collinearity with maize Chromosome 4 (Tarchini et al. 2000). Moreover, three genes in the ~20-kb Sh2-A1 region show complete collinearity with sorghum (Chen
et al. 1997).
Arabidopsis and rice are expected to have great value as
models for dicot and monocot genomic studies, respectively (Gale and
Devos 1998). Comparative analysis of these two species will not only
help in understanding the genomic similarities across the dicot/monocot
divide, but also answer the practical question of whether we can use
Arabidopsis as a reference to understand and annotate the rice
genome (Bevan and Murphy 1999).
Previous studies have investigated collinearity between rice and
Arabidopsis at both the genetic and physical map levels. In
one study (Dodeweerd et al. 1999), rice EST clones totaling ~200-300
kb homologous to Arabidopsis genomic DNA sequence were examined across a 194-kb region in Arabidopsis. Out of 24 homologous pairs in this region, 5 have conserved order, with the
exception of a single inversion. However, a similar study across a 3-cM region of Arabidopsis Chromosome 1 did not identify
conservation of gene order in rice (Devos et al. 1999). The scarcity of
rice genomic sequence and the incomplete nature of the database of rice
ESTs hampered both these studies.
In this study, we look at the nature and extent of Arabidopsis/rice collinearity by systematically analyzing 126 annotated rice bacterial artificial chromosome (BAC) genomic sequences at increasingly fine scales.
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RESULTS |
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TOP
ABSTRACT
INTRODUCTION
RESULTS
DISCUSSION
METHODS
REFERENCES
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We adopted the strategy of identifying rice and Arabidopsis homologs at the protein level and examining the collinearity of the homologous pairs across several length scales, starting at BAC lengths (~150 kb), going down to sub-BAC level. This avoids artifacts arising from repetitive regions, which are heavily distributed in both rice and Arabidopsis genomes, and allows us to identify homologs that have diverged at the nucleotide level.
Our data sets for this study consist of all the annotated rice BAC genomic sequences available in the Rice Genome Project (RGP) database as of July 2001, and the set of Arabidopsis proteins (predicted and observed), retrieved from the MIPS Arabidopsis thaliana database (MATDB; http://www.mips.biochem.mpg.de/proj/thal/db/). As described in Methods, we removed overlapping segments from the rice BACs, yielding a rice data set of 126 BACs with a total length of about 20 Mb and 3011 annotated genes. Of the rice BACs in this data set, 108 are from Chromosome 1. The corresponding Arabidopsis protein data set consisted of 24,570 annotated proteins derived from 1567 Arabidopsis BACs.
Chromosome Distribution of Arabidopsis Homologs for Genes on Rice BACs
We first studied the chromosome distribution of
rice/Arabidopsis homologs to determine whether rice and
Arabidopsis share collinear segments on approximately the same
scale as individual BACs (100-170 kb). For each of the annotated
proteins on the 126 rice BACs, we performed BLASTP
(Altschul et al. 1990) against the Arabidopsis protein data
set, and declared a provisional homologous pair if the P value
of the match was 
10
5. This threshold was chosen with the
knowledge that it would detect both orthologs and some paralogs, and
would, if anything, overestimate the incidence of collinearity. Because
the Arabidopsis genome is highly duplicated, some homologs may
fall into duplicated blocks. To avoid missing syntenic segments because
the high-scoring Arabidopsis homolog was involved in a
segmental duplication, we downloaded the duplicated region of the
Arabidopsis genome from the MIPS redundancy viewer
(http://www.mips.biochem.mpg.de/proj/thal/db/gv/rv/rv_frame.html) and incorporated that information into our analysis. We adopted the
rule that if the homolog hit falls into a duplicated block on different
chromosomes or a different region on the same chromosome, homologs on
the lower-numbered chromosome or earlier-region chromosome were chosen.
This procedure effectively collapses duplicated regions into a single
region in an unbiased fashion, and maximizes the opportunity to detect
synteny. We then used the Arabidopsis physical map to relate
the positions of putative rice/Arabidopsis homologs to the
Arabidopsis chromosomes on which they were found.
For the 126 rice BACs analyzed, putative homologs were found on 728 Arabidopsis BACs. Of the 3011 annotated rice proteins, 58% (1747) had homologs on Arabidopsis, of which 26% (456) were involved in segmental duplications of the Arabidopsis genome. Following our rule, 191 homologs were reassigned to lower-numbered chromosomes and 38 homologs were reassigned to a lower region of the same chromosome. Figure 1 shows the distribution of these homolog pairs on the Arabidopsis genome. Each row represents an individual rice BAC. The number of homologs found on various chromosomes of Arabidopsis are represented by the size of the star. The number after the star on each row is the total number of Arabidopsis protein homologs on the rice BAC. The striking observation is that at the BAC size scale, there is no obvious bias of rice BACs for particular Arabidopsis chromosomes. In all but three cases, the proteins annotated on rice BACs are distributed evenly across three or more chromosomes. The three exceptions are rice BACs that have homologous proteins represented on two Arabidopsis chromosomes. These BACs are very short and contain just 2-3 Arabidopsis homologs. No rice BAC in the entire data set had its protein homologs confined to a single Arabidopsis chromosome.
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If there were collinearities at the scale of a rice BAC, we would expect the homologs from a BAC to be concentrated on one or two Arabidopsis chromosomes. The fact that such clustering of homologs is not observed indicates that any collinear segments must be substantially smaller than a BAC.
Microcollinearity at the Sub-BAC Level
Because we were unable to detect collinearity at the BAC scale, we
next asked whether detectable microcollinearity exists across shorter
lengths. To do this, the same BLASTP search was performed
for each rice gene against the Arabidopsis protein database.
In this analysis, all hits with P values 105
were kept. We then performed an exhaustive search for collinear segments. The hits were organized in pairs (each pair consisting of an
Arabidopsis protein and a homologous rice protein), and the
pairs were grouped according to the Arabidopsis BACs on which they occurred. Within each group we then subgrouped and ordered the
pairs according to the rice BACs on which they occurred. This allowed
us to identify the collinear regions, as well as genes from one of the
genomes that appeared to be duplicated several times on the other genome.
Figure 2 shows the results of this analysis. There are 5957 distinct Arabidopsis and rice BAC pairs that share at least one "hit," where a hit is defined as a single distinct match between homologous proteins on rice and Arabidopsis BACs. To avoid complications arising from a single Arabidopsis protein with multiple rice homologs or vice versa, such cases were counted as a single hit only. In our analysis, there are 1103 Arabidopsis/rice BAC pairs that have a single Arabidopsis protein with multiple rice homologs, and 520 pairs that have a single rice protein with multiple Arabidopsis homologs. Of the total 5957 BAC pairs we analyzed, almost 93.3% (5555) of the BAC pairs are related by a single hit only; 330 of the BAC pairs (5.5%) are related by two hits, 72 pairs (1.2%) are related by three or more hits, and eight (0.1%) by four or more hits. None of the pairs were related by more than six hits.
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We selected the 72 rice/Arabidopsis BAC pairs with three or
more hits for further study of microcollinearity at the sub-BAC level.
Of this set, 50 were collinear on both the rice and
Arabidopsis genomes. (By chance, we would expect roughly
one-third of the triplets, or 20 pairs, to be collinear.) We aligned
the genomic sequences using PipMaker (Schwartz et al.
2000) and examined the results.
Table 1 summarizes this analysis. For each
putative collinear segment, we list the accession numbers and
approximate collinear size for both rice and Arabidopsis BACs,
the number of times the collinear triples were interrupted by
noncollinear gene pairs, and the brief identification of the
Arabidopsis gene as reported in the MATDB database.
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From the perspective of the rice genome, the longest collinear group is 159 kb, and the shortest is 2 kb, with a mean length of 45 kb. For Arabidopsis, the corresponding figures are 61 kb, 6 kb, and 25 kb. However, these figures include regions that are interrupted by noncollinear Arabidopsis/rice homolog pairs. Considering only regions with 2 or fewer interruptions, the longest region of rice collinearity is 63 kb, with a mean length of 25 kb. Among the 10 collinear regions with no interruptions, the corresponding lengths are 26 kb and 16 kb.
It is interesting to note that rice BAC clone AP001551 in group 21 and clone AP003076 in group 47 are both on Chromosome 1; the corresponding conserved segments on Arabidopsis AL035526 and AL021711 are adjacent on Arabidopsis Chromosome 4. When we combine these two groups, as shown in Figure 3, the conserved region has 11 homologs with conserved order in Arabidopsis and spans >130 kb. However, the rice BACs are thought to be more than 100 cM apart on the genetic map. Similar phenomena were observed between groups 7 and 8, groups 16 and 28, groups 23 and 40/46, and groups 49 and 50. In each case, BACs that are adjacent on Arabidopsis contain collinear segments with rice BACs from the same chromosome. However, in all cases, the homolog pairs are not consecutively linked, but are frequently interrupted by noncollinear pairs.
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Groups 15 and 17 contain adjacent Arabidopsis BACs on Chromosome 4 that match to the same rice BAC on Chromosome 1. When we merge these groups, it extends the rice collinear segment to 91 kb and the Arabidopsis segment to 97 kb with 2 interruptions in the rice BAC. For other groups in which the matching Arabidopsis and rice BACs are on the same chromosome pairs, the distance between the BACs is at least 1 Mb on the basis of the physical and/or genetic maps. These microcollinear regions cannot be merged.
Because the Arabidopsis genome is highly duplicated, we noticed that the same rice region may correspond to two collinear regions in Arabidopsis, such as groups 2 and 3, groups 8 and 9, groups 10 and 11, groups 15 and 16, groups 20 and 21, and groups 40 and 41. The same phenomena were twice observed in rice as well. Groups 5 and 6, and groups 38 and 39, each involve an Arabidopsis segment that is collinear with two distinct regions on rice chromosomes.
Another interesting finding is that many of the collinear regions involve protein family clusters in both Arabidopsis and rice. For example, groups 38 and 39 show diverged copies of putative cytochrome P450 in both species, groups 22 and 24 show diverged copies of a putative Arabidopsis lipase and copies of a putative rice lipase, and group 12 contains three diverged copies of a putative Arabidopsis glucosyl transferase and three copies of a putative rice glucosyl transferase. Overall, the members of the cytochrome P450 cluster are >82% identical, the lipases are >87% identical, and the glucosyl transferases are >72% identical at the protein level. This finding indicates that clusters of related proteins in Arabidopsis tend to be similarly clustered in rice.
Search for Missing Homologs
It is possible that some of the BAC pairs containing only a single protein hit contain further regions of homology because of incomplete annotation of the rice and/or Arabidopsis genomes. To check whether we missed such regions, we selected 10 pairs of BACs that contained only one hit and aligned them at the nucleotide level using PipMaker. Of the 10 BAC pairs so aligned, 9 showed only the homolog that had been detected earlier, whereas 1 showed an additional region of alignment with a low similarity level of uncertain significance. From the above studies, we conclude that our protein level analysis has not significantly undercounted the number of collinear regions.
Simulation of Microcollinearity in Rice and Arabidopsis
Although we were able to identify small collinear clusters of putative homologous genes among rice and Arabidopsis, it is possible that this finding is the result of chance rather than the evolutionary conservation of gene order. To address this question, we simulated the probability of finding an Arabidopsis BAC homologous to a rice BAC under the model that genes are distributed at random along the genome and that there is no correlation between the position of a gene on the two genomes. We used a genome size of 115 Mb for Arabidopsis and 20 Mb for the corresponding annotated rice genome and assumed a gene density of 1 gene per 4.8 kb for Arabidopsis and 1 gene per 6.25 kb for rice, and that 58% of rice genes have homologs on Arabidopsis (based on the 126 rice BACs we studied). We used an average BAC size of rice of 150 kb and 75 kb for Arabidopsis.
We ran the simulation 10,000 times and sampled the results at each
iteration. As shown in Table 2, the
simulation predicts that the chance of finding a single
rice/Arabidopsis homolog by random chance on a single rice BAC
is almost 1, a value similar to our observations. However, for
detecting linked clusters of three or more homologs the simulation
predicts values 1-2 orders of magnitude lower than we observed,
implying that the linked clusters that we detected in this study are
the result of the conservation of gene order, and not the result of a
random association.
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Microcollinearity at the Exon Level
To determine the degree of collinearity between Arabidopsis and rice at the scale of an individual gene, we analyzed 989 putative rice/Arabidopsis homolog pairs identified earlier after removing paralog pairs, and compared the order of their exons based on the annotations in RGP and MATDB.
As shown in Table 3, a total of 7723 exons
were examined. Of these, 1809 (23%) were present in both members of
the pair, 2902 (38%) were present only in the rice homolog, and 3012 (39%) were present only in the Arabidopsis homolog. On
examining the 989 rice/Arabidopsis homolog pairs, we found
that 315 (32%) pairs had two or more homologous exons. In all such
cases, the exons showed almost perfect collinearity. The exons in the
two species were very similar in size, with a mean difference of 28 bp.
However, introns tended to be larger in rice than in
Arabidopsis, 449 bp for rice versus 164 bp for
Arabidopsis, a 1.7-fold difference.
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DISCUSSION |
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|
TOP
ABSTRACT
INTRODUCTION
RESULTS
DISCUSSION
METHODS
REFERENCES
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We have systematically searched for microcollinearity in the presently available annotated genomic sequence in rice and Arabidopsis. Our strategy has been to identify putative homologs at the protein level, and then to study the order of those homologs on the genome.
Our findings indicate that genomic collinearity is present at the scale of individual genes and occasionally across short uninterrupted clusters of genes up to ~26 kb in total length. However, longer segments of collinearity can only be found by allowing interruptions from noncollinear homolog pairs. Large-scale collinear regions of BAC size or larger were not found.
There have been extensive studies of duplication in the
Arabidopsis genome (The Arabidopsis Genome Initiative
2000), where it has been shown that many regions are present twice in
the genome. Our analysis of collinear segments at the sub-BAC level
allowed for these duplicated regions. However, in most cases, for the collinear regions we found, the similarity within the
Arabidopsis genome was less than the similarity between rice
and Arabidopsis. Hence the duplicated regions do not affect
our conclusions.
It has been suggested that the organization of the rice and
Arabidopsis genomes are substantially different (Barakat et
al. 1998). In Arabidopsis genes are fairly evenly distributed,
but it is hypothesized that in rice genes are confined to clusters accounting for ~12%-24% of the genome separated by large gene-poor regions. Our studies neither confirm nor contradict this hypothesis, but we have found that the introns in rice are substantially larger than their Arabidopsis homologs. This could explain part of
the difference in size between the two genomes. However, it's worth noting that our assessment of gene structure is based on the third annotation party in RGP for rice and MATDB for Arabidopsis.
These annotations may not be independent.
A limitation in this analysis lies in the fact that it is based on third-party annotations. Some of the rice genes were predicted based on similarity to proteins in other species, Arabidopsis among them. This may introduce correlations between the two genomes for which we have not accounted.
Microcollinearity can be used as a tool for annotating one genome based on annotations in another, as well as for positional cloning and mapping studies. Our studies imply that it is not possible to infer the large-scale gene order in the rice genome on the basis of Arabidopsis. Neither genomic assembly of rice based on the Arabidopsis sequence nor attempts to clone rice genes based on comparative mapping in Arabidopsis are likely to succeed.
On a positive note, we find substantial collinearity between the exons of individual rice genes and their Arabidopsis homologs. This validates the strategy of annotating individual genes in the rice genome using predicted and confirmed genes from Arabidopsis.
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METHODS |
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TOP
ABSTRACT
INTRODUCTION
RESULTS
DISCUSSION
METHODS
REFERENCES
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Data Sets
Arabidopsis Annotated Proteins
Arabidopsis annotated proteins were retrieved from MATDB (MIPS Arabidopsis thaliana database, http://mips.gsf.de/proj/thal/db/) in July 2001. There are a total of 24,570 proteins on 1567 BACs.Rice BAC Sequences
After removing overlapping sequence, 3011 (2543 on Chromosome 1) rice proteins on 126 BAC clones (108 on Chromosome 1) were retrieved based on the annotation of RGP (http://rgp.dna.affrc.go.jp/GenomeSeq.html) in July 2001.Homology Search
Arabidopsis proteins homologous to rice proteins were
identified by BLASTP analysis of rice proteins against
Arabidopsis proteins. The Arabidopsis homolog is
defined as the Blast hit to a rice protein with P value
<105 for random chance match.
BAC Sequence Alignment
BAC sequences were compared using PipMaker (Schwartz
et al. 2000) for identifying conserved segments. For each
Arabidopsis and rice BAC pair, a mask file and an exon
position file for Arabidopsis BAC sequences were provided for
the analysis. Repetitive sequences were identified by
RepeatMasker
(http://ftp.genome.washington.edu/cgibin/RepeatMasker), and exon
positions were retrieved from MATDB. Results were analyzed by percent
identity plot (PIP) and dot plot.
Simulation of the Probability of Finding an Arabidopsis BAC Homolog to a Rice BAC Sequence
An ordered data set numbered from 1 to 24,570 is generated, symbolizing Arabidopsis proteins positioned on the chromosome. A second data set includes 3011 numbers, 1747 (58%) of which were randomly picked up from the Arabidopsis data set (1-24, 570) and the rest (1264) represented by 0. The second data set was randomly positioned in an order symbolizing rice proteins on the chromosome. Sets of 24 consecutive numbers on the first data set (symbolizing a BAC) were compared to their positions on the second data set. Two numbers separated by a distance of 16 or less on the second set were considered to be on the same BAC.
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ACKNOWLEDGMENTS |
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We thank Guanming Wu and Steve Schmidt for technical assistance. We are grateful to Dick McCombie, Manpreet Katari, and Harshawardhan Bal for useful discussions. This work was supported with funds from NSF DBI-9872644.
The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
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FOOTNOTES |
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1 Corresponding author.
E-MAIL lstein{at}cshl.org; FAX (516) 367-8389.
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.194501.
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REFERENCES |
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TOP
ABSTRACT
INTRODUCTION
RESULTS
DISCUSSION
METHODS
REFERENCES
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A web server for aligning two genomic DNA sequences.
Genome Res.
10:
577-586Received April 30 2001; accepted in revised form October 10 2001.
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