Here, we describe the construction of a phylogenetically deep, whole-genome 
alignment of 20 flowering plants, along with an analysis of plant genome 
conservation. Each included angiosperm genome was aligned to a reference genome, 
Arabidopsis thaliana, using the LASTZ/MULTIZ paradigm and tools from the 
University of California-Santa Cruz Genome Browser source code. In addition to 
the multiple alignment, we created a local genome browser displaying multiple 
tracks of newly generated genome annotation, as well as annotation sourced from 
published data of other research groups. An investigation into A. thaliana gene 
features present in the aligned A. lyrata genome revealed better conservation of 
start codons, stop codons, and splice sites within our alignments (51% of 
features from A. thaliana conserved without interruption in A. lyrata) when 
compared with previous publicly available plant pairwise alignments (34% of 
features conserved). The detailed view of conservation across angiosperms 
revealed not only high coding-sequence conservation but also a large set of 
previously uncharacterized intergenic conservation. From this, we annotated the 
collection of conserved features, revealing dozens of putative noncoding RNAs, 
including some with recorded small RNA expression. Comparing conservation 
between kingdoms revealed a faster decay of vertebrate genome features when 
compared with angiosperm genomes. Finally, conserved sequences were searched for 
folding RNA features, including but not limited to noncoding RNA (ncRNA) genes. 
Among these, we highlight a double hairpin in the 5'-untranslated region 
(5'-UTR) of the PRIN2 gene and a putative ncRNA with homology targeting the LAF3 
protein.