Conservation and functional element discovery in 20 angiosperm plant genomes

Area of Science:

• Genomics
• Comparative Genomics
• Bioinformatics

Background:

• Understanding plant genome evolution and conservation is crucial for deciphering genetic diversity.
• Previous pairwise alignments offered limited insights into conserved genomic regions across multiple species.

Purpose of the Study:

• To construct a deep, whole-genome alignment of 20 flowering plants.
• To analyze angiosperm genome conservation and identify conserved noncoding elements.
• To compare genome conservation patterns between plants and vertebrates.

Main Methods:

• Whole-genome alignment of 20 angiosperm genomes to Arabidopsis thaliana using LASTZ/MULTIZ.
• Development of a local genome browser for visualizing multi-track annotations.
• Analysis of gene feature conservation, including start/stop codons and splice sites.
• Identification and annotation of conserved noncoding RNAs (ncRNAs).

Main Results:

• Achieved higher conservation rates for gene features (51%) in A. lyrata compared to previous pairwise alignments (34%).
• Discovered extensive intergenic conservation and identified dozens of putative ncRNAs, some with small RNA expression.
• Demonstrated faster decay of vertebrate genome features relative to angiosperm genomes.
• Highlighted a double hairpin in the PRIN2 gene's 5'-UTR and a putative ncRNA targeting LAF3 protein.

Conclusions:

• The study provides a valuable resource for plant genomics, revealing deep conservation across angiosperms.
• Identified novel ncRNAs and conserved intergenic regions, expanding our understanding of noncoding genome functions.
• Angiosperm genomes exhibit remarkable evolutionary stability compared to vertebrate genomes.