A tree constructed from Arabidopsis, rice, and maize sequences had indicated that Group B is " Arabidopsis only" [ 90].
The tree we obtained showed that the maize BX2-5 sequences had orthologs distributed in four branches, boxed in Figure 2 as BX2 -Bx5 clades.
The use of rice, sorghum, maize, and Brachypodium genome sequences have been extremely useful for synteny based applications and identification of shared genes and traits [ 31].
The dicot and moncot intron sequences have diverged completely and the maize introns are generally larger - from start to stop codons the maize LKR/SDH gene spans 9515 bp while the Arabidopsis gene spans 5590 bp.
ESTs of helitron sequences have been detected in certain maize tissues [ 15].
CNS (within introns or upstream regulatory sequences), have been recently surveyed in cereals (maize vs rice) and mammals (human vs mouse) [ 45, 46].
It is highly implausible that these newly created sequences have not played a role in the evolution of maize genes and of maize.
A complete, annotated maize genome sequence is not yet available, but a large number of sequences have been collected in the GSS (Genome Survey Sequence) database, which contains gene-enriched maize DNA sequences derived by methylation filtration [ 13, 26], High-Cot enrichment and other methods that reduce repetitive sequences [ 44].
The maize genome sequence has been completed, and filtered protein and cds sequences have also become available [ 21].
A total of 3082 nifH sequences have been reported from soils used for cultivation of maize, whereas 854 have been reported from soils used for cultivation of rice.
So far, conserved miRNAs in maize have been identified by sequence homology analyses [ 18- 20], and new miRNA sequences have been identified by traditional [ 21- 23] or high-throughput [ 17, 24- 30] sequencing methods.
