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
CX671410CX671410EST
CX671411CX671411EST
CX671412CX671412EST
CX671413CX671413EST
CX671414CX671414EST
CX671415CX671415EST
CX671416CX671416EST
CX671417CX671417EST
CX671418CX671418EST
CX671419CX671419EST
CX671420CX671420EST
CX671421CX671421EST
CX671422CX671422EST
CX671423CX671423EST
CX671424CX671424EST
CX671425CX671425EST
CX671426CX671426EST
CX671427CX671427EST
CX671428CX671428EST
CX671429CX671429EST
CX671430CX671430EST
CX671431CX671431EST
CX671432CX671432EST
CX671433CX671433EST
CX671434CX671434EST

Pages

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