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Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes

Y Lokko, JV Anderson, S Rudd, A Raji, D Horvath, MA Mikel, R Kim, L Liu, A Hernandez, AGO Dixon, et al. (2007) PLANT CELL REPORTS. 26(9). p.1605-1618
abstract
Cassava (Manihot esculenta Crantz) is a staple food for over 600 million people in the tropics and subtropics and is increasingly used as an industrial crop for starch production. Cassava has a high growth rate under optimal conditions but also performs well in drought-prone areas and on marginal soils. To increase the tools for understanding and manipulating drought tolerance in cassava, we generated expressed sequence tags (ESTs) from normalized cDNA libraries prepared from dehydration-stressed and control well-watered tissues. Analysis of a total of 18,166 ESTs resulted in the identification of 8,577 unique gene clusters (5,383 singletons and 3,194 clusters). Functional categories could be assigned to 63% of the unigenes, while another similar to 11% were homologous to hypothetical genes with unclear functions. The remaining similar to 26% were not significantly homologous to sequences in public databases suggesting that some may be novel and putatively specific to cassava. The dehydration-stressed library uncovered numerous ESTs with recognized roles in drought-responses, including those that encode late-embryogenesis-abundant proteins thought to confer osmoprotective functions during water stress, transcription factors, heat-shock proteins as well as proteins involved in signal transduction and oxidative stress. The unigene clusters were screened for short tandem repeats for further development as microsatellite markers. A total of 592 clusters contained 646 repeats, representing 3.3% of the ESTs queried. The ESTs presented here are the first dehydration stress transcriptome of cassava and can be utilized for the development of microarrays and gene-derived molecular markers to further dissect the molecular basis of drought tolerance in cassava.
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author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
ABSCISIC-ACID ACCUMULATION, EXPRESSED SEQUENCE TAGS, LIPID-TRANSFER PROTEIN, HORDEUM-VULGARE L., ARABIDOPSIS-THALIANA, WATER-DEFICIT, STRESSED SEEDLINGS, OSMOTIC ADJUSTMENT, DEHYDRATION STRESS, CDNA LIBRARIES
journal title
PLANT CELL REPORTS
Plant Cell Reports
volume
26
issue
9
pages
1605 - 1618
Web of Science type
Article
Web of Science id
000248856700019
JCR category
PLANT SCIENCES
JCR impact factor
1.974 (2007)
JCR rank
41/149 (2007)
JCR quartile
2 (2007)
ISSN
0721-7714
DOI
10.1007/s00299-007-0378-8.
language
English
UGent publication?
no
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1982377
handle
http://hdl.handle.net/1854/LU-1982377
date created
2012-01-10 20:11:52
date last changed
2016-12-19 15:45:28
@article{1982377,
  abstract     = {Cassava (Manihot esculenta Crantz) is a staple food for over 600 million people in the tropics and subtropics and is increasingly used as an industrial crop for starch production. Cassava has a high growth rate under optimal conditions but also performs well in drought-prone areas and on marginal soils. To increase the tools for understanding and manipulating drought tolerance in cassava, we generated expressed sequence tags (ESTs) from normalized cDNA libraries prepared from dehydration-stressed and control well-watered tissues. Analysis of a total of 18,166 ESTs resulted in the identification of 8,577 unique gene clusters (5,383 singletons and 3,194 clusters). Functional categories could be assigned to 63\% of the unigenes, while another similar to 11\% were homologous to hypothetical genes with unclear functions. The remaining similar to 26\% were not significantly homologous to sequences in public databases suggesting that some may be novel and putatively specific to cassava. The dehydration-stressed library uncovered numerous ESTs with recognized roles in drought-responses, including those that encode late-embryogenesis-abundant proteins thought to confer osmoprotective functions during water stress, transcription factors, heat-shock proteins as well as proteins involved in signal transduction and oxidative stress. The unigene clusters were screened for short tandem repeats for further development as microsatellite markers. A total of 592 clusters contained 646 repeats, representing 3.3\% of the ESTs queried. The ESTs presented here are the first dehydration stress transcriptome of cassava and can be utilized for the development of microarrays and gene-derived molecular markers to further dissect the molecular basis of drought tolerance in cassava.},
  author       = {Lokko, Y and Anderson, JV and Rudd, S and Raji, A and Horvath, D and Mikel, MA and Kim, R and Liu, L and Hernandez, A and Dixon, AGO and Ingelbrecht, Ivan},
  issn         = {0721-7714},
  journal      = {PLANT CELL REPORTS},
  keyword      = {ABSCISIC-ACID ACCUMULATION,EXPRESSED SEQUENCE TAGS,LIPID-TRANSFER PROTEIN,HORDEUM-VULGARE L.,ARABIDOPSIS-THALIANA,WATER-DEFICIT,STRESSED SEEDLINGS,OSMOTIC ADJUSTMENT,DEHYDRATION STRESS,CDNA LIBRARIES},
  language     = {eng},
  number       = {9},
  pages        = {1605--1618},
  title        = {Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes},
  url          = {http://dx.doi.org/10.1007/s00299-007-0378-8.},
  volume       = {26},
  year         = {2007},
}

Chicago
Lokko, Y, JV Anderson, S Rudd, A Raji, D Horvath, MA Mikel, R Kim, et al. 2007. “Characterization of an 18,166 EST Dataset for Cassava (Manihot Esculenta Crantz) Enriched for Drought-responsive Genes.” Plant Cell Reports 26 (9): 1605–1618.
APA
Lokko, Y., Anderson, J., Rudd, S., Raji, A., Horvath, D., Mikel, M., Kim, R., et al. (2007). Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. PLANT CELL REPORTS, 26(9), 1605–1618.
Vancouver
1.
Lokko Y, Anderson J, Rudd S, Raji A, Horvath D, Mikel M, et al. Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. PLANT CELL REPORTS. 2007;26(9):1605–18.
MLA
Lokko, Y, JV Anderson, S Rudd, et al. “Characterization of an 18,166 EST Dataset for Cassava (Manihot Esculenta Crantz) Enriched for Drought-responsive Genes.” PLANT CELL REPORTS 26.9 (2007): 1605–1618. Print.