EST Sequencing in Spruce
Summary
We produced 25 different cDNA libraries, and sequenced random clones in spruce (nearly 50 K) and poplar (14 K). Sequences have been analyzed and released; a sequence database has been developed and implemented.
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cDNA Spruce Libraries (Arborea Phase 2 - 2006-2009)
| Library code | Name | Quality sequences * | Data release | |
|---|---|---|---|---|
Quality reads | Average length | |||
Cambium / phloem scrappings (Normalized library) | 11227 | 727 | ||
Xylem scrapings - AT NITE | 5623 | 730 | ||
Xylem planings - daytime and seasonal | In progress |
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Xylem Scrapings (Normalized library) |
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Shoot tip (Normalized library) |
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Terminal leader (Normalized library) |
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cDNA Spruce Libraries (Arborea Phase I - 2002-2006)
| Library code | Name | Quality sequences * | Data release | |
|---|---|---|---|---|
Quality reads | Average length | |||
Male strobili developmental sequence | 2589 | |||
Female cones developmental sequence | 2324 | 500 | ||
Vegetative buds developmental sequence | 1062 | 560 | ||
Non-lignified secondary xylem from mature trees | 7735 | 600 | ||
Cambium and phloem from mature tree | 6705 | 635 | ||
Secondary xylem of girdled saplings | 1053 | 556 | ||
Cambium, phloem and bark of girdled saplings | 937 | 577 | ||
Elongating ROOTS tips - saplings | 1053 | 395 | ||
Primary, sec. SHOOT - N fertil. Treatments | 3031 | 736 | ||
Immature somatic EMBRYOS | 2220 | 692 | ||
Clean ROOTS systems - N treatments | 858 | 659 | ||
Clean ROOTS systems - P treatments | 3776 | 705 | ||
Clean ROOTS systems - Diurnal cycle | 8601 | 757 | ||
ROOT XYLEM - mature trees | 1532 | 598 | ||
Annual flush SHOOTS diurnal cycle - trees | 5164 | 658 | ||
GQ026 | NEEDLES - N fertilization treatments | 461 | 686 | October 2004 |
Mature Somatic EMBRYOS | 281 | 490 | ||
| TOTAL QUALITY READS - SPRUCE | 49102 |
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* Quality sequences contain 100 nucleotides or more of Phred 20 quality, after vector sequence is removed.
Sequencing results in SPRUCE
A total of 57 193 processed EST sequences containing a minimum of 100bp meeting a quality score of phred 20 or higher have been obtained in Arborea Phase I (2002-2006) from libraries GQ001, GQ002, GQ003, GQ004, GQ006, GQ007, GQ008, GQ013, GQ016 to GQ020, GQ022, GQ025, GQ026, GQ027.
Sequences, sequence assemblies and blast reports may be visualized and searched in Biodata web pages hosted at the Center for Computational Genomics and Bioinformatics :
- http://biodata.ccgb.umn.edu/spruce
Order cDNA clones
You can order cDNA clones from our project.
Requests are filled free of charge or on cost recovery basis, depending on volume of the request, the type of institution (for-profit or non-for-profit) and the origin of the request (Canada or outside Canada).
For more information, click here : Order cDNA clones
