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
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Feature NameUnique NameType
CF835463CF835463EST
CF835464CF835464EST
CF835465CF835465EST
CF835466CF835466EST
CF835467CF835467EST
CF835468CF835468EST
CF835469CF835469EST
CF835470CF835470EST
CF835472CF835472EST
CF835473CF835473EST
CF835474CF835474EST
CF835475CF835475EST
CF835476CF835476EST
CF835477CF835477EST
CF835478CF835478EST
CF835479CF835479EST
CF835480CF835480EST
CF835481CF835481EST
CF835482CF835482EST
CF835483CF835483EST
CF835484CF835484EST
CF835486CF835486EST
CF835489CF835489EST
CF835490CF835490EST
CF835491CF835491EST

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