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.
SNP Chip Base
Array NameWashington Navel Orange Shoot Meristem cDNA Library
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Features
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Feature NameUnique NameType
CF838821CF838821EST
CF838820CF838820EST
CF838819CF838819EST
CF838818CF838818EST
CF838817CF838817EST
CF838816CF838816EST
CF838815CF838815EST
CF838814CF838814EST
CF838813CF838813EST
CF838812CF838812EST
CF838811CF838811EST
CF838810CF838810EST
CF838809CF838809EST
CF838808CF838808EST
CF838807CF838807EST
CF838806CF838806EST
CF838805CF838805EST
CF838804CF838804EST
CF838803CF838803EST
CF838802CF838802EST
CF838801CF838801EST
CF838800CF838800EST
CF838799CF838799EST
CF838798CF838798EST
CF838797CF838797EST

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