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
The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.
Feature NameUnique NameType
CF836115CF836115EST
CF836114CF836114EST
CF836113CF836113EST
CF836112CF836112EST
CF836111CF836111EST
CF836110CF836110EST
CF836109CF836109EST
CF836108CF836108EST
CF836107CF836107EST
CF836106CF836106EST
CF836105CF836105EST
CF836104CF836104EST
CF836103CF836103EST
CF836102CF836102EST
CF836101CF836101EST
CF836100CF836100EST
CF836099CF836099EST
CF836098CF836098EST
CF836097CF836097EST
CF836096CF836096EST
CF836095CF836095EST
CF836094CF836094EST
CF836093CF836093EST
CF836092CF836092EST
CF836091CF836091EST

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