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.
SNP Chip Base
Array NameMadame Vinous Sweet Orange Multiple Pathogen-Infected cDNA Library UCRCS10
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Features
The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.
Feature NameUnique NameType
CX673836CX673836EST
CX673837CX673837EST
CX673838CX673838EST
CX673839CX673839EST
CX673840CX673840EST
CX673841CX673841EST
CX673842CX673842EST
CX673843CX673843EST
CX673844CX673844EST
CX673845CX673845EST
CX673846CX673846EST
CX673847CX673847EST
CX673848CX673848EST
CX673849CX673849EST
CX673850CX673850EST
CX673851CX673851EST
CX673852CX673852EST
CX673853CX673853EST
CX673854CX673854EST
CX673855CX673855EST
CX673856CX673856EST
CX673857CX673857EST
CX673858CX673858EST
CX673859CX673859EST
CX673860CX673860EST

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