|
Plant Physiol, March 2001, Vol. 125, pp. 1283-1292
Active Retrotransposons Are a Common Feature of Grass
Genomes
Carlos M.
Vicient,
Marko J.
Jääskeläinen,
Ruslan
Kalendar, and
Alan H.
Schulman2*
Plant Genomics Laboratory, Institute of Biotechnology, Viikki
Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 6, FIN-00014 Helsinki, Finland
A large fraction of the genomes of grasses, members of the family
Graminae, is composed of retrotransposons. These elements resemble
animal retroviruses in their structure and possess a life cycle similar
to theirs that includes transcription, translation, and integration of
daughter copies. We have investigated if retrotransposons are generally
transcribed in the grasses and other plants, and whether the various
families of elements are translationally and integrationally active in
multiple grass species. A systematic search of 7.8 × 105 publicly available expressed sequence tags from plants
revealed widespread retrotransposon transcripts at a frequency of one
in 1,000. Monocot retrotransposons found relatively more expressed sequence tags from non-source species than did those of dicots. Antibodies were raised to the capsid protein, GAG, of
BARE-1, a transcribed and translated
copia-like retrotransposon of barley (Hordeum
vulgare). These detected immunoreactive proteins of sizes identical to those of the BARE-1 GAG and polyprotein,
respectively, in other species of the tribe Triticeae as well as in
oats (Avena sativa) and rice (Oryza
sativa). Retrotransposon-based markers showed integrational
polymorphisms for BARE-1 in different subfamilies of the
Graminae. The results suggest that grasses share families of
transcriptionally, translationally, and integrationally active retrotransposons, enabling a comparative and integrative approach to
understanding the life cycle of retrotransposons and their impact on
the genome.
2
This author also is affiliated at the present time with
the Agricultural Research Centre of Finland, FIN-31600 Jokioinen, Finland.
*
Corresponding author; e-mail alan.schulman{at}helsinki.fi; fax
358-9-191-58952.
© 2001 American Society of Plant Physiologists
This article has been cited by other articles:
|
|
|
|
 
H. S. Pereira, A. Barao, A. Caperta, J. Rocha, W. Viegas, and M. Delgado
Rye Bs Disclose Ancestral Sequences in Cereal Genomes with a Potential Role in Gametophyte Chromatid Segregation
Mol. Biol. Evol.,
August 1, 2009;
26(8):
1683 - 1697.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
P. Neumann, H. Yan, and J. Jiang
The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference
Genetics,
June 1, 2007;
176(2):
749 - 761.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. M. Li, D. Rotter, S. A. Bonos, W. A. Meyer, and F. C. Belanger
Identification of a Gene in the Process of Being Lost from the Genus Agrostis
Plant Physiology,
August 1, 2005;
138(4):
2386 - 2395.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J.-Y. Lin, B. H. Jacobus, P. SanMiguel, J. G. Walling, Y. Yuan, R. C. Shoemaker, N. D. Young, and S. A. Jackson
Pericentromeric Regions of Soybean (Glycine max L. Merr.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile
Genetics,
July 1, 2005;
170(3):
1221 - 1230.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. Jiao, P. Jia, X. Wang, N. Su, S. Yu, D. Zhang, L. Ma, Q. Feng, Z. Jin, L. Li, et al.
A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription
PLANT CELL,
June 1, 2005;
17(6):
1641 - 1657.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Brunner, K. Fengler, M. Morgante, S. Tingey, and A. Rafalski
Evolution of DNA Sequence Nonhomologies among Maize Inbreds
PLANT CELL,
February 1, 2005;
17(2):
343 - 360.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Puchta
The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution
J. Exp. Bot.,
January 1, 2005;
56(409):
1 - 14.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
R. Kalendar, C. M. Vicient, O. Peleg, K. Anamthawat-Jonsson, A. Bolshoy, and A. H. Schulman
Large Retrotransposon Derivatives: Abundant, Conserved but Nonautonomous Retroelements of Barley and Related Genomes
Genetics,
March 1, 2004;
166(3):
1437 - 1450.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. C. Kuhl, F. Cheung, Q. Yuan, W. Martin, Y. Zewdie, J. McCallum, A. Catanach, P. Rutherford, K. C. Sink, M. Jenderek, et al.
A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and Genomic Differences between the Monocot Orders Asparagales and Poales
PLANT CELL,
January 1, 2004;
16(1):
114 - 125.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. J. Simons, S. B. Gehlhar, S. S. Maan, and S. F. Kianian
Detailed Mapping of the Species Cytoplasm-Specific (scs) Gene in Durum Wheat
Genetics,
December 1, 2003;
165(4):
2129 - 2136.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. Garcia-Martinez and J. A. Martinez-Izquierdo
Study on the Evolution of the Grande Retrotransposon in the Zea Genus
Mol. Biol. Evol.,
May 1, 2003;
20(5):
831 - 841.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. Vandepoele, Y. Saeys, C. Simillion, J. Raes, and Y. Van de Peer
The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice
Genome Res.,
November 1, 2002;
12(11):
1792 - 1801.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. Baumel, M. Ainouche, R. Kalendar, and A. H. Schulman
Retrotransposons and Genomic Stability in Populations of the Young Allopolyploid Species Spartina anglica C.E. Hubbard (Poaceae)
Mol. Biol. Evol.,
August 1, 2002;
19(8):
1218 - 1227.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
R. Siebert and H. Puchta
Efficient Repair of Genomic Double-Strand Breaks by Homologous Recombination between Directly Repeated Sequences in the Plant Genome
PLANT CELL,
May 1, 2002;
14(5):
1121 - 1131.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. Yu, S. Hu, J. Wang, G. K.-S. Wong, S. Li, B. Liu, Y. Deng, L. Dai, Y. Zhou, X. Zhang, et al.
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)
Science,
April 5, 2002;
296(5565):
79 - 92.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Fu, Z. Zheng, and H. K. Dooner
Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude
PNAS,
January 22, 2002;
99(2):
1082 - 1087.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C. FEUILLET and B. KELLER
Comparative Genomics in the Grass Family: Molecular Characterization of Grass Genome Structure and Evolution
Ann. Bot.,
January 1, 2002;
89(1):
3 - 10.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C. M. Vicient, R. Kalendar, and A. H. Schulman
Envelope-Class Retrovirus-Like Elements Are Widespread, Transcribed and Spliced, and Insertionally Polymorphic in Plants
Genome Res.,
December 1, 2001;
11(12):
2041 - 2049.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. Kimura, Y. Tosa, S. Shimada, R. Sogo, M. Kusaba, T. Sunaga, S. Betsuyaku, Y. Eto, H. Nakayashiki, and S. Mayama
OARE-1, a Ty1-copia Retrotransposon in Oat Activated by Abiotic and Biotic Stresses
Plant Cell Physiol.,
December 1, 2001;
42(12):
1345 - 1354.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Fu, Z. Zheng, and H. K. Dooner
Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude
PNAS,
January 22, 2002;
99(2):
1082 - 1087.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. Fernandes, V. Brendel, X. Gai, S. Lal, V. L. Chandler, R. P. Elumalai, D. W. Galbraith, E. A. Pierson, and V. Walbot
Comparison of RNA Expression Profiles Based on Maize Expressed Sequence Tag Frequency Analysis and Micro-Array Hybridization
Plant Physiology,
March 1, 2002;
128(3):
896 - 910.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
