First published online December 5, 2002; 10.1104/pp.010207
Plant Physiol, December 2002, Vol. 130, pp. 2118-2128
Cloning and Sequencing of cDNAs for Hypothetical Genes from
Chromosome 2 of Arabidopsis1,[w]
Yong-Li
Xiao,*
Mukesh
Malik,2
Catherine A.
Whitelaw, and
Christopher D.
Town
The Institute for Genomic Research, 9712 Medical Center Drive,
Rockville, Maryland 20850
About 25% of the genes in the fully sequenced and
annotated Arabidopsis genome have structures that are predicted solely
by computer algorithms with no support from either nucleic acid or protein homologs from other species or expressed sequence matches from
Arabidopsis. These are referred to as "hypothetical genes." On
chromosome 2, sequenced by The Institute for Genomic Research, there
are approximately 800 hypothetical genes among a total of approximately
4,100 genes. To test their expression under various growth conditions
and in specific tissues, we used six cDNA populations prepared from
cold-treated, heat-treated, and pathogen (Xanthomonas campestris pv campestris)-infected plants, callus, roots, and young seedlings. To date, 169 hypothetical genes were tested, and 138 of them are found to be expressed in one or more of the six cDNA
populations. By sequencing multiple clones from each 5'- and 3'-rapid
amplification of cDNA ends (RACE) product and assembling the sequences,
we generated full-length sequences for 16 of these genes. For 14 genes,
there was one full-length assembly that precisely supported the
intron-exon boundaries of their gene predictions, adding only 5'- and
3'-untranslated region sequences. However, for three of these genes,
the other assemblies represent additional exons and alternatively
spliced or unspliced introns. For the remaining two genes, the cDNA
sequences reveal major differences with predicted gene structures. In
addition, a total of six genes displayed more than one polyadenylation
site. These data will be used to update gene models in The Institute
for Genomic Research annotation database ATH1.
1
This work was supported by the National Science
Foundation (grant no. DBI-9813586).
2
Present address: Gene Logic Inc., 708 Quince
Orchard Rd., Gaithersburg, MD 20878.
[w]
The online version of this article contains
Web-only data. The supplemental material is available at
www.plantphysiol.org.
*
Corresponding author; e-mail yxiao{at}tigr.org;
fax 301-838-0208.
© 2002 American Society of Plant Biologists
This article has been cited by other articles:
|
|
|
|
 
H. Ner-Gaon, N. Leviatan, E. Rubin, and R. Fluhr
Comparative Cross-Species Alternative Splicing in Plants
Plant Physiology,
July 1, 2007;
144(3):
1632 - 1641.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Bevan and S. Walsh
The Arabidopsis genome: A foundation for plant research
Genome Res.,
December 1, 2005;
15(12):
1632 - 1642.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y.-L. Xiao, S. R. Smith, N. Ishmael, J. C. Redman, N. Kumar, E. L. Monaghan, M. Ayele, B. J. Haas, H. C. Wu, and C. D. Town
Analysis of the cDNAs of Hypothetical Genes on Arabidopsis Chromosome 2 Reveals Numerous Transcript Variants
Plant Physiology,
November 1, 2005;
139(3):
1323 - 1337.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Ayele, B. J. Haas, N. Kumar, H. Wu, Y. Xiao, S. Van Aken, T. R. Utterback, J. R. Wortman, O. R. White, and C. D. Town
Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
Genome Res.,
April 1, 2005;
15(4):
487 - 495.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. JIN and T. BIAN
Nontemplated nucleotide addition prior to polyadenylation: A comparison of Arabidopsis cDNA and genomic sequences
RNA,
November 18, 2004;
10(11):
1695 - 1697.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
B. C. Meyers, D. W. Galbraith, T. Nelson, and V. Agrawal
Methods for Transcriptional Profiling in Plants. Be Fruitful and Replicate
Plant Physiology,
June 1, 2004;
135(2):
637 - 652.
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. Yamada, J. Lim, J. M. Dale, H. Chen, P. Shinn, C. J. Palm, A. M. Southwick, H. C. Wu, C. Kim, M. Nguyen, et al.
Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome
Science,
October 31, 2003;
302(5646):
842 - 846.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
B. J. Haas, A. L. Delcher, S. M. Mount, J. R. Wortman, R. K. Smith Jr, L. I. Hannick, R. Maiti, C. M. Ronning, D. B. Rusch, C. D. Town, et al.
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Nucleic Acids Res.,
October 1, 2003;
31(19):
5654 - 5666.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. R. Wortman, B. J. Haas, L. I. Hannick, R. K. Smith Jr., R. Maiti, C. M. Ronning, A. P. Chan, C. Yu, M. Ayele, C. A. Whitelaw, et al.
Annotation of the Arabidopsis Genome
Plant Physiology,
June 1, 2003;
132(2):
461 - 468.
[Full Text]
[PDF]
|
|
|
|
|
