Comparative Genomics of Rice and Arabidopsis. Analysis of 727 Cytochrome P450 Genes and Pseudogenes from a Monocot and a Dicot  

Abstract

Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice (Oryza sativa) genome using sequence information available from both the indica and japonica strains. Because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. Comparison of these rice genes with the 246 P450 genes and 26 pseudogenes in the Arabidopsis genome has indicated that most of the known plant P450 families existed before the monocot-dicot divergence that occurred approximately 200 million years ago. Comparative analysis of P450s in the Pinus expressed sequence tag collections has identified P450 families that predated the separation of gymnosperms and flowering plants. Complete mapping of all available plant P450s onto the Deep Green consensus plant phylogeny highlights certain lineage-specific families maintained (CYP80 in Ranunculales) and lineage-specific families lost (CYP92 in Arabidopsis) in the course of evolution.

Identification and bioinformatics analysis of pseudogenes from whole genome sequence of Phaeodactylum tricornutum

“…There were less numbers of "true" processed pseudogenes than there were "putative"; there was only one "disruptive" processed pseudogenes, indicating that there were no insertions of repeated sequences in most of the ORFs of the processed pseudogenes. These results are very different from what has been reported for other species (such as human and rice [14,19]) in which "disruptive" pseudogenes are commonly found.…”

“…The identification of pseudogenes in genomes is important for the accurate identification and annotation of the functional genes, for the evolutionary analysis of genomes and functional genes [7], and for the determination of the function of the pseudogenes [8][9][10]. Pseudogenes are commonly found in the genomes of a great variety of species, having been found in E. coli [11], yeast [12], Arabidopsis [13,14], rice [15], nematodes [16], Drosophila [17], mice [18], and humans [19,20]. It has been predicted that the human genome encodes from 22000 to 75000 genes, about 22% of which are pseudogenes [21,22].…”

Plant MicroRNAs Display Differential 3' Truncation and Tailing Modifications That Are ARGONAUTE1 Dependent and Conserved Across Species

“…These patterns vary among miRNAs, yet are often similar for the same miRNA between monocots and dicots, which diverged ;200 million years ago (Nelson et al, 2004). The cross-species conservation of 39 modifications of miRNAs suggests that it is the sequence of the mature miRNA that is the primary determinant of these modifications, both in the wild type and the hen1 mutants.…”

Plant P450s as versatile drivers for evolution of species-specific chemical diversity

“…Based on the available sequences, land plant P450s can be grouped in 11 phylogenetically distinct clans [4,5]. However, it is to be expected that new clans will emerge as older plant lineages are sequenced, as seen when the genome of the green algae Chlamydomonas was released.…”

“…However, it is to be expected that new clans will emerge as older plant lineages are sequenced, as seen when the genome of the green algae Chlamydomonas was released. Plant clans are named according to the lowest-numbered family member [5]. Originally, the view on plant P450s was more simplified and they were grouped as either A-type or non-A-type [6,7].…”