TY  - JOUR
A1  - Zulawski, Monika
A1  - Schulze, Gunnar
A1  - Braginets, Rostyslav
A1  - Hartmann, Stefanie
A1  - Schulze, Waltraud X.
T1  - The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification
JF  - BMC genomics
N2  - Background: Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication.
 Results: The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases.
 Conclusions: The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.
Y1  - 2014
U6  - https://doi.org/10.1186/1471-2164-15-548
SN  - 1471-2164
VL  - 15
PB  - BioMed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Schedina, Ina-Maria
A1  - Pfautsch, Simone
A1  - Hartmann, Stefanie
A1  - Dolgener, N.
A1  - Polgar, Anika
A1  - Bianco, Pier Giorgio
A1  - Tiedemann, Ralph
A1  - Ketmaier, Valerio
T1  - Isolation and characterization of eight microsatellite loci in the brook lamprey Lampetra planeri (Petromyzontiformes) using 454 sequence data
JF  - Journal of fish biology
N2  - Eight polymorphic microsatellite loci were developed for the brook lamprey Lampetra planeri through 454 sequencing and their usefulness was tested in 45 individuals of both L. planeri and the river lamprey Lampetra fluviatilis. The number of alleles per loci ranged between two and five; the Italian and Irish populations had a mean expected heterozygosity of 0.388 and 0.424 and a mean observed heterozygosity of 0.418 and 0.411, respectively. (C) 2014 The Fisheries Society of the British Isles
KW  - conservation
KW  - population structure
KW  - species pair
Y1  - 2014
U6  - https://doi.org/10.1111/jfb.12470
SN  - 0022-1112
SN  - 1095-8649
VL  - 85
IS  - 3
SP  - 960
EP  - 964
PB  - Wiley-Blackwell
CY  - Hoboken
ER  -