N E W S

  • new01.gif (1016 bytes)Rob Martienssen's presentation on progress of Arabidopsis genome sequencing  - Nov 5, 1999

Our Research Goal

Status of Individual Clones

Links to our collaborators at

Washington University Genome Sequencing Center

and the WUGSC Arabidopsis fingerprint database

Sequence Quality Report

Sequenced based maps of the Arabidopsis genome

Visit our Maize Genome Analysis Page

  • 814 ESTs submitted since 24 Jul 98
  

Finished sequence submitted to GenBank: 13,651,965 bp from 146 clones!

Mapping and Sequencing: Short Arm of Chromosome IV

We have completed sequencing the top portion of chromosome IV from the telomeric rDNA to beyond the centromere (0-25cM). A graphic representation of YAC and BAC contigs can be found at this link. The centromere lies between GA1 and HY4 (Copenhaver, et al., 1998) and includes a 900kb region of tandemly arranged satellite repeats (RCEN4) that has not been sequenced (Round, et al., 1997). Recently, the complete sequence of the long and short arms of chromosome 4 was published in collaboration with the European Union Arabidopsis sequencing consortium (Mayer et al., 1999). In addition, a description of the sequence of the pericentromeric regions of chromosomes 2 and 4 was published in collaboration with Daphne Preuss (Copenhaver et al., 1999). A description of the heterochromatic sequences found in this region was also published in the February 4 issue of Cell, in collaboration with Paul Fransz (McCombie et al., 2000).

Mapping and Sequencing: Chromosome V

We have completed the sequence of the 3 Mbp region surrounding the centromere of chromosome V from north of KNAT3 to just north of PhyC. This sequence contains two difficult area that are still being explored: one is the true centromere, the other is a block of 5SrDNA.  This region corresponds to part of YAC contigs 7, 8 and 9 (Schmidt, et al., 1997) and from 9 to 12 Mb on the Kazusa map (Kotani, et al., 1997). The centromere lies between nga76 and PHYC (Copenhaver, et al., 1998; Round, et al., 1997).  We have assembled BAC contigs correpsonding to these YACs and sequence analysis of the BACs is described.  In addition to the centromeric areas, we have also completed the sequence of a 1 Mbp region north of NIT4.  This large contig corresponds to the 6.3 to 7.5 Mb region on the Kazusa map.

Clones from Other Regions

We have sequenced a number of BACs and one YAC found to originate from chromosomes I, II and III. These clones were selected by hybridization before fingerprints were complete and thus, may contain repeats also found on chromosomes IV and V. Links to these sequences can be found here.

GeneTrap Database

A link to a database of transposon insertion site sequences created through collaboration with Rob Martienssen's group here at CSHL. 

Blast Search Tool

This link takes you to AtDB's BLAST server. Select the CSHLPrel database which contains the pooled preliminary genomic sequence from CSHL, ABI and Washington University's GSC. This database is updated nightly from the FTP server at CSHL.

AtRepBase: a database of Arabidopsis genomic repeats

We have established a database of sequences repeated in the Arabidopsis genome. A BLAST server is available for searching that database.

Retrieve Sequences Generated by CSHL/ABI and Washington University

All contiguous sequences larger than 1.5 kbp from each BAC are available at the above FTP sites. The sequences are updated nightly.

Genes and Transposons

Follow this link to search annotated sequence by gene name.

Annotation Resources

Available here is a list of the annotation tools we use and a list of individuals who are experts in a given gene family and have agreed to assist in specific areas of annotation.

Hot Links

Links to some useful Arabidopsis and plant genome web sites.

This page was last updated on January 25, 2002

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