The reverse genetics approach is a powerful tool for detemining gene functions. Recently, many loss-of-function mutant lines have been generated using transposons or T-DNA and gain-of-function mutant lines have been generated using transformation, and then resulting phenotypes have been observed by several research institutes. This database allows for a transparent search of the genomic information and phenotypes of the mutant lines.
Recently, the resources described below were collected, organized, and made publicly accessible via the Internet.
RIKEN Arabidopsis Ds transposon mutant lines (RATM) constitute a series of mutant lines that have a Ds transposon in the genome of the Arabidopsis thaliana Nössen ecotype (background by Fedoroff and Smith). This section provides information on the mutants produced in our laboratory. Each mutant line is assigned by stipulating line codes (ex. 13-4480-1). We determined the flanking sequences of the Ds insertion for each independent line.
The transposon insertion sites of mutants were estimated by a BLASTN homology search against the genome sequence database of Arabidopsis thaliana Columbia ecotype. The closest genes (predicted by AGI) to the transposon insertion sites were picked up.
Structure of the transposon. The constructs used here have been described by Fedoroff and Smith. The amount of the Ac element in each Ds construct is represented by the filled portions at the beginning, middle and end of the transposon and the exact number of the base pairs is indicated above the diagram. Ds11, Ds51 and Ds52 contain only the first of the Ac element's four transcription start sites, whereas the other constructs contain all of the start sites with Ds13 and Ds16 part or without the Ds12, Ds15, Ds53 and Ds54 part of the element's untranslated leader. Ds constructs 15, 16, 52 and 53 contain the 35S core sequence upstream from the GUS gene, whereas Ds constructs 11-13, 51 and 54 do not. Abbreviations: GUS: ß-glucuronidase; 19S: promoters of the CaMV and 19S transcripts; hygro: bacterial aph4 gene, which confers hygromycin resistance.
Ds-transposon primer sequences [PDF: 43.4KB]
Cold Spring Harbor Laboratory genetrap mutant lines (TRAPPER) constitute a collection of transposon insertions and their flanking sequences from the Martienssen laboratory at Cold Spring Harbor Laboratory. Most of the lines carry a unique insertion of a genetrap (GT) or enhancer trap (ET) transposable Ds element somewhere in the Arabidopsis genome. These elements simultaneously disrupt gene function and monitor gene expression (Sundaresan et al., 1995; Martienssen, 1998).
Insertion sites were amplified by TAIL PCR (Liu et al., 1995; Tsukegi et al., 1996) and sequenced in the McCombie lab (CSHWU Sequencing Consortium, 2000). These sequence tags were validated and annotated according to the sequence of the Arabidopsis genome. Many of the lines have been stained and approximately 20% of them have reporter gene expression. Photographs of positive lines have been included as links with each entry.
Cited from Arabidopsis Genetrap Website at Cold Spring Harbor Laboratory
RIKEN Arabidopsis full-length cDNA overexpressed Arabidopsis lines (AtFOX) constitute a collection of transgenic Arabidopsis lines generated using the FOX hunting system (Full-length cDNA Over-eXpressing gene hunting system) (Ichikawa et al., 2006) for Arabidopsis full-length cDNAs (Seki et al., 2002).
Normalized Arabidopsis full-length cDNAs were introduced into Arabidopsis by in planta transformation, and were expressed independently under the CaMV 35S promoter in Arabidopsis. Each transgenic line contained, on an average, 2.6 cDNA clones. The morphological phenotypes observed in the T1 and T2 generations were recorded by text and photos.
RIKEN rice full-length cDNA overexpressed Arabidopsis lines (OsFOX)constitute a collection of transgenic Arabidopsis lines generated using the FOX hunting system for rice full-length cDNAs (Kikuchi et al., 2003).
The scheme is similar to that of AtFOX, except for the use of rice full-length cDNAs . Each transgenic line contained, on an average, 1.11 cDNA clones.