Conservation and Functional Element Discovery in 20 Angiosperm Plant Genomes

Abstract

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.

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

“…Here we report the first genome-wide high-resolution atlas of noncoding regions under selection in crucifers. Because the detection of CNSs is based on the comparison of a large number of closely related species, the sensitivity of this map is higher than that in previous studies based on pairs or sets of more distant species 20,65 or on intragenomic comparisons 22 , resulting in an eight to tenfold increase in the number of constrained regions identified.…”

“…These CNSs are thought to be involved in diverse regulatory functions, including transcription initiation and transcript processing (for example, splicing or mRNA localization), as well as being implicated in complex patterning, such as embryonic development [9][10][11][12][13] . Plant CNSs have previously been identified on a genome-wide scale on the basis of the comparison of few or distant genomes (for example, maize versus rice [14][15][16] , Brachypodium distachyon versus rice 17 , A. thaliana versus Brassica oleracea 18,19 and sets of diverse angiosperms 20 ). This approach limits either the specificity provided by large divergence times or the sensitivity provided by the comparison of more closely related species 10,11,21 .…”

Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis

“…To further validate our set of CNSs, we compared our results with three other CNS data sets from published genomewide phylogenetic footprinting approaches (Figure 2) (Baxter et al, 2012;Haudry et al, 2013;Hupalo and Kern, 2013). Apart from evaluating the sensitivity of the different studies, which relates to finding true positive AtProbe results, we also assessed the specificity, which relates to identifying negative results.…”

“…These methods have shown greater power in the detection of functional elements and lineage-specific conservation than detection methods based on comparing more distantly related genomes in vertebrates, insects, worms, and yeast (Siepel et al, 2005). However, these approaches require aligned genomes and the fraction of the genome that can be aligned drops drastically (<40%) when comparing species from different genera in flowering plants (Hupalo and Kern, 2013). This is due to large-scale genome rearrangements and high sequence divergence.…”

“…Conservation in the aligned regions was determined using PhyloP (Pollard et al, 2010), yielding a set of 95,142 Arabidopsis CNSs. Similarly, Hupalo and Kern (2013) created a whole-genome alignment between 20 closely and distantly related angiosperm genomes by making use of the LASTZ tool and used PhastCons (Siepel et al, 2005) to identify sequence constraint.…”