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
CF838042CF838042EST
CF838043CF838043EST
CF838044CF838044EST
CF838045CF838045EST
CF838046CF838046EST
CF838047CF838047EST
CF838048CF838048EST
CF838049CF838049EST
CF838050CF838050EST
CF838051CF838051EST
CF838052CF838052EST
CF838053CF838053EST
CF838054CF838054EST
CF838055CF838055EST
CF838056CF838056EST
CF838057CF838057EST
CF838058CF838058EST
CF838059CF838059EST
CF838060CF838060EST
CF838061CF838061EST
CF838062CF838062EST
CF838063CF838063EST
CF838065CF838065EST
CF838066CF838066EST
CF838067CF838067EST

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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