イベント案内:地域部会 - 北海道地域部会

第12回日本バイオインフォマティクス学会北海道地域部会セミナー

日時:平成23年8月4日(木) 16時30分-18時30分
場所:北海道大学情報科学研究科棟2階A21教室
   http://www.ist.hokudai.ac.jp/facilities/index.php?floor_key=2
参加登録不要、参加費無料
講師:
    Prof. Wojciech Makalowski (University of Münster, Germany)
    Dr. Kazutaka Katoh (CBRC, Japan)

プログラム

16:30-17:30
The Evolution of U12-type Introns
Prof. Wojciech Makalowski (University of Münster, Germany)

Abstracts:
Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) spliceosome removes a small fraction (less than 0.5%) of introns, referred to as U12-type introns.
U12-type introns have distinct sequence elements and usually occur together in genes with U2-type introns.  A phylogenetic distribution of U12-type introns shows that the minor splicing pathway appeared very early in eukaryotic evolution and has been lost repeatedly.  We have investigated the evolution of U12-type introns among eighteen
metazoan genomes by analyzing orthologous U12-type intron clusters. Examination of gain, loss, and type switching shows that intron type is remarkably conserved among vertebrates.  Among 180 intron clusters, only eight show intron loss in any vertebrate species and only five show conversion between the U12 and the U2-type.  Although there are
only nineteen U12-type introns in Drosophila melanogaster, we found one case of U2 to U12-type conversion, apparently mediated by the activation of cryptic U12 splice sites early in the dipteran lineage.
Overall, loss of U12-type introns is more common than conversion to U2-type and the U12 to U2 conversion occurs more frequently among introns of the GT-AG subtype than among introns of the AT-AC subtype.
We also found support for natural U12-type introns with non-canonical terminal dinucleotides (CT-AC, GG-AG, and GA-AG) that have not been previously reported. Although complete loss of the U12-type spliceosome has occurred repeatedly, U12 introns are extremely stable in some taxa, including eutheria.  Loss of U12 introns or the genes
containing them is more common than conversion to the U2-type.  The degeneracy of U12-type terminal dinucleotides among natural U12-type introns is higher than previously thought.


17:30-18:30
Dr. Kazutaka Katoh (CBRC, Japan)
Effect of adding homologs in phylogenetic analysis
Abstracts:

We performed a benchmark of multiple sequence alignment (MSA) and phylogenetic tree inference, focusing on a situation where dozens of sequences are included.  Our benchmark procedure is based on a previous one (Dessimoz & Gil 2010; Genome Biology 11:R37), in which widely accepted phylogenetic relationship is used as a reference.  A set of orthologous sequences are aligned and a tree is inferred using the MSA.  Then, the difference between the inferred tree and the reference tree is evaluated.  If the difference is smaller, the inference is judged to be better.  When inferring a phylogenetic relationship of a few taxa, it is generally believed that additional homologs should be included into the analysis to obtain a stable and reliable inference.  We quantitatively examined the validity of such analysis.  In order to clarify the effects of homologs at the MSA step and at the tree inference step separately, two types of tests, (1) Enriched and (2) Impoverished were performed.  In the (1) Enriched test, the entire MSA, containing additional homologs, was used to infer a tree.  Its result reflects the total effect of homologs on the MSA step and the tree inference step.  In the (2) Impoverished test, the additional homologs were included in the MSA step but excluded
from the tree inference step.  Its result is expected to reflect the effect of homologs specifically on the MSA calculation.  In addition, the effect of homologs specifically on the tree inference step was assessed by using (3) the difference between the results of Enriched and Impoverished.  We examined several combinations of different MSA
methods and tree inference methods.  The results suggest that additional homologs do not improve the quality of MSA in general, but improve the resulting tree in most cases.  This benchmark also provides practical guidelines, for example, an appropriate similarity level of homologs to be included into a phylogenetic analysis.