Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs

<p>Abstract</p> <p>Background</p> <p>Alternative splicing is an important mechanism for generating functional and evolutionary diversity of proteins in eukaryotes. Here, we studied the frequency and functionality of recently gained, rodent-specific alternative exons.</p> <p>Results</p> <p>We projected the data about alternative splicing of mouse genes to the rat, human, and dog genomes, and identified exons conserved in the rat genome, but missing in more distant genomes. We estimated the frequency of rodent-specific exons while controlling for possible residual conservation of spurious exons. The frequency of rodent-specific exons is higher among predominantly skipped exons and exons disrupting the reading frame. Separation of all genes by the rate of sequence evolution and by gene families has demonstrated that rodent-specific cassette exons are more frequent in rapidly evolving genes and in rodent-specific paralogs.</p> <p>Conclusion</p> <p>Thus we demonstrated that recently gained exons tend to occur in fast-evolving genes, and their inclusion rate tends to be lower than that of older exons. This agrees with the theory that gain of alternative exons is one of the major mechanisms of gene evolution.</p

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

BACKGROUND: It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined. RESULTS: We analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences. CONCLUSIONS: Our results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone

Spliced alignment and its application in Arabidopsis thaliana

This thesis describes the development and biological applications of GeneSeqer, which is a homology-based gene prediction program by means of spliced alignment. Additionally, a program named MyGV was written in JAVA as a browser to visualize the output of GeneSeqer. In order to test and demonstrate the performance, GeneSeqer was utilized to map 176,915 Arabidopsis EST sequences on the whole genome of Arabidopsis thaliana, which consists of five chromosomes, with about 117 million base pairs in total. All results were parsed and imported into a MySQL database. Information that was inferred from the Arabidopsis spliced alignment results may serve as valuable resource for a number of projects of special scientific interest, such as alternative splicing, non-canonical splice sites, mini-exons, etc. We also built AtGDB (Arabidopsis thaliana Genome DataBase, http://www.plantgdb.org/AtGDB/) to interactively browse EST spliced alignments and GenBank annotations for the Arabidopsis genome. Moreover, as one application of the Arabidopsis EST mapping data, U12-type introns were identified from the transcript-confirmed introns in the Arabidopsis genome, and the characteristics of these minor class introns were further explored