TY  - JOUR
A1  - Hill, Natascha
A1  - Leow, Alexander
A1  - Bleidorn, Christoph
A1  - Groth, Detlef
A1  - Tiedemann, Ralph
A1  - Selbig, Joachim
A1  - Hartmann, Stefanie
T1  - Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information
JF  - Theory in biosciences
N2  - Many deep evolutionary divergences still remain unresolved, such as those among major taxa of the Lophotrochozoa. As alternative phylogenetic markers, the intron-exon structure of eukaryotic genomes and the patterns of absence and presence of spliceosomal introns appear to be promising. However, given the potential homoplasy of intron presence, the phylogenetic analysis of this data using standard evolutionary approaches has remained a challenge. Here, we used Mutual Information (MI) to estimate the phylogeny of Protostomia using gene structure data, and we compared these results with those obtained with Dollo Parsimony. Using full genome sequences from nine Metazoa, we identified 447 groups of orthologous sequences with 21,732 introns in 4,870 unique intron positions. We determined the shared absence and presence of introns in the corresponding sequence alignments and have made this data available in "IntronBase", a web-accessible and downloadable SQLite database. Our results obtained using Dollo Parsimony are obviously misled through systematic errors that arise from multiple intron loss events, but extensive filtering of data improved the quality of the estimated phylogenies. Mutual Information, in contrast, performs better with larger datasets, but at the same time it requires a complete data set, which is difficult to obtain for orthologs from a large number of taxa. Nevertheless, Mutual Information-based distances proved to be useful in analyzing this kind of data, also because the estimation of MI-based distances is independent of evolutionary models and therefore no pre-definitions of ancestral and derived character states are necessary.
KW  - Mutual Information
KW  - Evolution
KW  - Gene structure
Y1  - 2013
U6  - https://doi.org/10.1007/s12064-012-0173-0
SN  - 1431-7613
VL  - 132
IS  - 2
SP  - 93
EP  - 104
PB  - Springer
CY  - New York
ER  - 
TY  - JOUR
A1  - Vi, Son Lang
A1  - Trost, Gerda
A1  - Lange, Peggy
A1  - Czesnick, Hjördis
A1  - Rao, Nishta
A1  - Lieber, Diana
A1  - Laux, Thomas
A1  - Gray, William M.
A1  - Manley, James L.
A1  - Groth, Detlef
A1  - Kappel, Christian
A1  - Lenhard, Michael
T1  - Target specificity among canonical nuclear poly(A) polymerases in plants
 modulates organ growth and pathogen response
JF  - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
 AMERICA
N2  - Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability, and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are coexpressed in different tissues. However, in neither case is it known whether the isoforms fulfill different functions or polyadenylate distinct subsets of pre-mRNAs. Here we show that the three canonical nuclear PAPS isoforms in Arabidopsis are functionally specialized owing to their evolutionarily divergent C-terminal domains. A strong loss-of-function mutation in PAPS1 causes a male gametophytic defect, whereas a weak allele leads to reduced leaf growth that results in part from a constitutive pathogen response. By contrast, plants lacking both PAPS2 and PAPS4 function are viable with wild-type leaf growth. Polyadenylation of SMALL AUXIN UP RNA (SAUR) mRNAs depends specifically on PAPS1 function. The resulting reduction in SAUR activity in paps1 mutants contributes to their reduced leaf growth, providing a causal link between polyadenylation of specific pre-mRNAs by a particular PAPS isoform and plant growth. This suggests the existence of an additional layer of regulation in plant and possibly vertebrate gene expression, whereby the relative activities of canonical nuclear PAPS isoforms control de novo synthesized poly(A) tail length and hence expression of specific subsets of mRNAs.
Y1  - 2013
U6  - https://doi.org/10.1073/pnas.1303967110
SN  - 0027-8424
VL  - 110
IS  - 34
SP  - 13994
EP  - 13999
PB  - NATL ACAD SCIENCES
CY  - WASHINGTON
ER  -