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The Scarlet Runner Bean (Phaseolus coccineus) EST Project

Beans! We are using the giant embryos of the Scarlet Runner Bean (Phaseolus coccineus) to identify genes that are active in the suspensor and embryo proper of globular-stage embryos shortly after fertilization ( Weterings et al., Plant Cell, 13, 2409-2425, 2001; Le et al., Plant Physiology, 144, 562-574, 2007; Kawashima et al., PNAS, 106, 3627-3632, 2009). Our long-term goal is to understand the region-specific differentiation processes that occur during early embryo development and how genes are activated specifically in the suspensor and embryo proper. Total RNAs isolated from hand-dissected suspensor and embryo proper were used to construct cDNA libraries. The 5' ends of individual cDNA clones from each library were sequenced using the Sanger sequencing method whereas random cDNA fragments were sequenced using the 454 sequencing technology. To date, we have sequenced 305,363 suspensor and 85,776 embryo proper ESTs. These ESTs have been grouped into different functional categories based on BLAST searches and organized into an EST relational database on our lab server. Moreover, all EST sequences can be accessed directly from NCBI (GenBank Accession Series CA896559 to CA916678 and GD289845 to GD660862 ).

Our Scarlet Runner Bean (SRB) globular-stage suspensor and embryo proper EST database is open to the scientific community. You can click the Search button on the top right corner to find ESTs categorized by functional category, or browse with putative identification (e.g. cytochrome P450, protein kinase, etc...).

Summary of Embryo EST Project

This table includes the number of ESTs identified in each functional category from the suspensor and embryo proper library. Functional categories were assigned based on BLAST homologies to other genes. The e-value cut-off to consider if a blast hit was significant is 1e-04.
Abbreviations: EP - Embryo Proper; S - Suspensor
FUNCTION
EP
S
Metabolism
3,451
13,839
Energy
2,658
9,598
Cell Growth/Division
492
1,503
Transcription
1,385
4,254
Post-transcription
1,170
3,126
Protein Synthesis
15,074
31,710
Protein Destination and Storage
3,442
12,324
Transporters
2,027
6,878
Intracellular Traffic
851
3,475
Cell Structure
2,410
7,411
Signal Transduction
1,021
3,611
Disease/Defense
1,591
12,605
Secondary Metabolism
2,092
12,194
Transposons
21
52
Unknown or Unclassified Proteins
5,762
23,202
No Significant Homology to Public Databases
42,329
159,581
Total ESTs
85,776
305,363

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