Madame Vinous Sweet Orange Multiple Pathogen-Infected cDNA Library UCRCS10

Overview
Library NameMadame Vinous Sweet Orange Multiple Pathogen-Infected cDNA Library UCRCS10
Unique NameMadame Vinous Sweet Orange Multiple Pathogen-Infected cDNA Library UCRCS10
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Vector: Lambda Uni-ZAP XR, excised phagemidV_TYPE: Phagemid pBluescript SK(-); Site_1: EcoRI; Site_2: XhoI; Samples included bark, leaf and petiole from infected trees of Madame Vinous sweet orange. These trees were growing in pots in greenhouses at the USDA Citrus Repository (Nielsen), UC Riverside. The trees were infected with various pathogens. A total of 14 trees were sampled and pooled. Two trees each were infected with a different strain of Citrus psorosis virus, Citrus viroid IIb, Spiroplasma citri, or Citrus Dweet mottle virus, two trees were infected with a seedling yellows strain of Citrus tristeza virus, one tree was co-infected with Citrus concave gum virus plus Citrus exocortis viroid, and two trees were co-infected with Citrus tatter leaf virus and Citrus vein enation virus. Federici (Roose lab) collected the samples, after consulting with Lee, Krueger and Roose. Samples were collected from three or four young branches per tree. The bark had hardened but was still green and the diameter of the twig was less than approximately 5 mm. The tissue was not washed. The two trees infected with Vein enation/Tatterleaf had some mites on the leaves; the infestation was very light. These were wiped off before freezing the tissue, but mite material may have been included in the sample. Twenty young fully expanded leaf blades with the petioles removed were collected from each tree and placed together in one foil packet submerged in liquid nitrogen. The petioles from these leaves and another twenty from the same plant were frozen in another foil pack. Then the bark was pulled off the branches and chopped into pieces no longer than 3 cm and frozen together in a third packet. The bark from each plant was not weighed to equalize it, but the amounts appeared roughly equal. Mandal and Fenton(Close lab) purified RNA by a TRIzol method, pooled an equal quantity of RNA from each of the three samples, purified poly(A) mRNA using a PolyATtrack mRNA Isolation System IV (Promega), produced a primary cDNA library using a lambda ZAP XR cDNA Synthesis Kit (Stratagene), then mass-excised one million pfu from the primary library to produce a phagemid population. Phagemids were plated, plasmid DNA purified, cDNA clones archived, and DNA sequences determined bi-directionally using an ABI3730 at DNA Landmarks (Landry, Hubert, Laforest, Landry, Ligonde). Chromatogram files were downloaded by FTP to UC Riverside (by Close), then processed at UC Riverside (by Wanamaker, Close lab) using the HarvEST pipeline (http://harvest.ucr.edu) to remove vector and cloning oligo sequences and various contaminants, and to trim to a high quality region. Sequences that retained a phred 17 region of at least 100 bases were assembled, then chimeras were removed following manual inspection of assemblies (Close, Roose, Wanamaker). Sequences that survived all removal steps were submitted to GenBank.
Features
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Feature NameUnique NameType
CX671460CX671460EST
CX671461CX671461EST
CX671462CX671462EST
CX671463CX671463EST
CX671464CX671464EST
CX671465CX671465EST
CX671466CX671466EST
CX671467CX671467EST
CX671468CX671468EST
CX671469CX671469EST
CX671470CX671470EST
CX671471CX671471EST
CX671472CX671472EST
CX671473CX671473EST
CX671474CX671474EST
CX671475CX671475EST
CX671476CX671476EST
CX671477CX671477EST
CX671478CX671478EST
CX671479CX671479EST
CX671480CX671480EST
CX671481CX671481EST
CX671482CX671482EST
CX671483CX671483EST
CX671484CX671484EST

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Properties
Property NameValue
Genbank library cultivarMadame Vinous
Genbank library dev stageTrees in pots
Genbank library noteVector: Lambda Uni-ZAP XR, excised phagemidV_TYPE: Phagemid pBluescript SK(-); Site_1: EcoRI; Site_2: XhoI; Samples included bark, leaf and petiole from infected trees of Madame Vinous sweet orange. These trees were growing in pots in greenhouses at the USDA Citrus Repository (Nielsen), UC Riverside. The trees were infected with various pathogens. A total of 14 trees were sampled and pooled. Two trees each were infected with a different strain of Citrus psorosis virus, Citrus viroid IIb, Spiroplasma citri, or Citrus Dweet mottle virus, two trees were infected with a seedling yellows strain of Citrus tristeza virus, one tree was co-infected with Citrus concave gum virus plus Citrus exocortis viroid, and two trees were co-infected with Citrus tatter leaf virus and Citrus vein enation virus. Federici (Roose lab) collected the samples, after consulting with Lee, Krueger and Roose. Samples were collected from three or four young branches per tree. The bark had hardened but was still green and the diameter of the twig was less than approximately 5 mm. The tissue was not washed. The two trees infected with Vein enation/Tatterleaf had some mites on the leaves; the infestation was very light. These were wiped off before freezing the tissue, but mite material may have been included in the sample. Twenty young fully expanded leaf blades with the petioles removed were collected from each tree and placed together in one foil packet submerged in liquid nitrogen. The petioles from these leaves and another twenty from the same plant were frozen in another foil pack. Then the bark was pulled off the branches and chopped into pieces no longer than 3 cm and frozen together in a third packet. The bark from each plant was not weighed to equalize it, but the amounts appeared roughly equal. Mandal and Fenton(Close lab) purified RNA by a TRIzol method, pooled an equal quantity of RNA from each of the three samples, purified poly(A) mRNA using a PolyATtrack mRNA Isolation System IV (Promega), produced a primary cDNA library using a lambda ZAP XR cDNA Synthesis Kit (Stratagene), then mass-excised one million pfu from the primary library to produce a phagemid population. Phagemids were plated, plasmid DNA purified, cDNA clones archived, and DNA sequences determined bi-directionally using an ABI3730 at DNA Landmarks (Landry, Hubert, Laforest, Landry, Ligonde). Chromatogram files were downloaded by FTP to UC Riverside (by Close), then processed at UC Riverside (by Wanamaker, Close lab) using the HarvEST pipeline (http://harvest.ucr.edu) to remove vector and cloning oligo sequences and various contaminants, and to trim to a high quality region. Sequences that retained a phred 17 region of at least 100 bases were assembled, then chimeras were removed following manual inspection of assemblies (Close, Roose, Wanamaker). Sequences that survived all removal steps were submitted to GenBank.
Genbank library tissue typeLeaf, petiole, bark
Leaftissue type