Compositional Gradients in Gramineae Genes

Compositional gradients in Gramineae genes.

In this study, we describe a property of Gramineae genes, and perhaps all monocot genes, that is not observed in eudicot genes. Along the direction of transcription, beginning at the junction of the 5'-UTR and the coding region, there are gradients in GC content, codon usage, and amino-acid usage. The magnitudes of these gradients are large enough to hinder the annotation of the rice genome and...

The distribution of genes in the genomes of Gramineae (chromosomesyisochoresyplants)

Recent investigations showed that most maize genes are present in compositional fractions of nuclear DNA that cover only a 1–2% GC (molar fraction of guanosine plus cytosine in DNA) range and represent only 10–20% of the genome. These fractions, which correspond to compositional genome compartments that are distributed on all chromosomes, were collectively called the ‘‘gene space.’’ Outside the...

Isoenzymatic Variation in Zea (Gramineae)

An average of 14(7-34) plants each for 61 different collections of Zea (maize and its wild relatives, the teosintes) were studied for 12 enzyme systems coded for by 21 loci. Principal component and cluster analyses based on allele frequencies showed Zea can be divided into two major groups: 1) sect. Luxuriantes, including Z. perennis, Z. diploperennis, and Z. luxurians; and 2) sect. Zea (in par...

Transcription-Associated Compositional Skews in Drosophila Genes

In many organisms, local deviations from Chargaff's second parity rule are observed around replication and transcription start sites and within intron sequences. Here, we use expression data as well as a whole-genome data set of nearly 200 haplotypes to investigate such compositional skews in Drosophila melanogaster genes. We find a positive correlation between compositional skew and gene expre...

Structural and compositional gradients : basic idea, preparation, applications