ABSTRACT
Treating Arabidopsis roots with exogenous auxin results in dramatic changes in cellular processes including de novo induction of lateral roots which later emerge through the overlying cells. Microarray experiments reveal approximately 80 genes that are substantially up-regulated in the root over the first 12 h following auxin treatment. We hypothesize that the observed increase in expression of pectate lyase family genes leads to degradation of the pectin-rich middle lamellae, allowing cells in the parent root to separate cleanly. Differences in the degree of pectin methylation in lateral and parent roots may explain why lateral roots are not degraded themselves.
Subject(s)
Arabidopsis/growth & development , Arabidopsis/genetics , Gene Expression Profiling , Gene Expression Regulation, Plant/genetics , Indoleacetic Acids/pharmacology , Plant Roots/growth & development , Arabidopsis/physiology , Arabidopsis Proteins/analysis , Arabidopsis Proteins/genetics , Arabidopsis Proteins/physiology , Cell Wall/drug effects , Cell Wall/physiology , DNA, Plant/analysis , DNA, Plant/genetics , Gene Expression Regulation, Plant/drug effects , Gene Expression Regulation, Plant/physiology , Genes, Plant/genetics , Genes, Plant/physiology , Methylation , Oligonucleotide Array Sequence Analysis , Phospholipases A/analysis , Phospholipases A/genetics , Phospholipases A/physiology , Plant Roots/chemistry , Plant Roots/drug effects , Polysaccharide-Lyases/analysis , Polysaccharide-Lyases/genetics , Polysaccharide-Lyases/physiologyABSTRACT
We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy by correcting errors before assembly, read merger based on forward-reverse links, and detection of repeat contigs by forward-reverse link inconsistency. To test ARACHNE, we created simulated reads providing approximately 10-fold coverage of the genomes of H. influenzae, S. cerevisiae, and D. melanogaster, as well as human chromosomes 21 and 22. The assemblies of these simulated reads yielded nearly complete coverage of the respective genomes, with a small number of contigs joined into a smaller number of supercontigs (or scaffolds). For example, analysis of the D. melanogaster genome yielded approximately 98% coverage with an N50 contig length of 324 kb and an N50 supercontig length of 5143 kb. The assembly accuracy was high, although not perfect: small errors occurred at a frequency of roughly 1 per 1 Mb (typically, deletion of approximately 1 kb in size), with a very small number of other misassemblies. The assembly was rapid: the Drosophila assembly required only 21 hours on a single 667 MHz processor and used 8.4 Gb of memory.
