Washington Navel Orange Shoot Meristem cDNA Library

Overview
Library NameWashington Navel Orange Shoot Meristem cDNA Library
Unique NameWashington Navel Orange Shoot Meristem cDNA Library
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Vector: Lambda Uni-ZAP XR, excised phagemid; Site_1: EcoRI; Site_2: XhoI; Parent Washington Navel Orange trees on Troyer rootstock (UCR 16K) were the source of tissue. Trees, at UC Riverside Agricultural Operations, were planted October 12, 1992. In each of 17 reps one tree on Troyer rootstock was initially treated with Enzone, one with Alliette and Nemacure, and one was left untreated. These treatments were discontinued in 1998. At the time of sampling, there were differences in the apparent health and size of the trees on Troyer rootstock. Fall-flush shoots were sampled in early November 2002 to minimize the number of floral shoot meristems. Federici and Mu (Roose lab) harvested meristems only from trees that appeared to be healthy and had a large number of young shoot tips on the day of collection. The average weight of a meristem was about 2 mg. Federici noted that there were quite a few insects and signs of insect damage to the shoot tips. Mealy bugs, thrips and aphids were observed, plus a few very tiny fast moving insects that may have been mites or crawler stage of scale (although Federici did not see any mature scale). It was not difficult to avoid collecting most of these because they were easy to see with the dissecting microscope. It was harder to exclude the frass. Some frass was definitely retained in the samples. Tissues were snap frozen and then stored at -80C until further processing. Fenton (Close lab) purified RNA by the phenol method described in J. Japanese Soc. Hort. Sci. 1996. 64 (4): 809-814, 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 the Arizona Genomics Institute, University of Arizona (Kim, Kudrna, Wing, Yu). 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 deposited to GenBank.
Features
The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.
Feature NameUnique NameType
CF835730CF835730EST
CF835731CF835731EST
CF835732CF835732EST
CF835733CF835733EST
CF835734CF835734EST
CF835735CF835735EST
CF835736CF835736EST
CF835737CF835737EST
CF835738CF835738EST
CF835739CF835739EST
CF835740CF835740EST
CF835741CF835741EST
CF835742CF835742EST
CF835743CF835743EST
CF835744CF835744EST
CF835745CF835745EST
CF835746CF835746EST
CF835747CF835747EST
CF835748CF835748EST
CF835749CF835749EST
CF835750CF835750EST
CF835752CF835752EST
CF835753CF835753EST
CF835754CF835754EST
CF835755CF835755EST

Pages

Properties
Property NameValue
Genbank library cultivarParent Washington Navel
Genbank library dev stage10 year old trees
Genbank library noteVector: Lambda Uni-ZAP XR, excised phagemid; Site_1: EcoRI; Site_2: XhoI; Parent Washington Navel Orange trees on Troyer rootstock (UCR 16K) were the source of tissue. Trees, at UC Riverside Agricultural Operations, were planted October 12, 1992. In each of 17 reps one tree on Troyer rootstock was initially treated with Enzone, one with Alliette and Nemacure, and one was left untreated. These treatments were discontinued in 1998. At the time of sampling, there were differences in the apparent health and size of the trees on Troyer rootstock. Fall-flush shoots were sampled in early November 2002 to minimize the number of floral shoot meristems. Federici and Mu (Roose lab) harvested meristems only from trees that appeared to be healthy and had a large number of young shoot tips on the day of collection. The average weight of a meristem was about 2 mg. Federici noted that there were quite a few insects and signs of insect damage to the shoot tips. Mealy bugs, thrips and aphids were observed, plus a few very tiny fast moving insects that may have been mites or crawler stage of scale (although Federici did not see any mature scale). It was not difficult to avoid collecting most of these because they were easy to see with the dissecting microscope. It was harder to exclude the frass. Some frass was definitely retained in the samples. Tissues were snap frozen and then stored at -80C until further processing. Fenton (Close lab) purified RNA by the phenol method described in J. Japanese Soc. Hort. Sci. 1996. 64 (4): 809-814, 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 the Arizona Genomics Institute, University of Arizona (Kim, Kudrna, Wing, Yu). 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 deposited to GenBank.
Genbank library tissue typeShoot meristem
Shoot meristemtissue type