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A model of genome length estimation based on k-mers detection

Garbulowski M., Polański A.

Studia Informatica

2015

Vol. 36, nr 4

5--16

The genome length estimation at raw sequencing data level gives a practical knowledge about size of the DNA sequence at early stage of analysis. In our research, we created a model based on random sampling of k-mer (very short DNA fragments), that we used to predict genome size. Furthermore, we made the comparison of model results with empirical whole-genome sequencing data.

Oszacowanie rozmiaru genomu na podstawie surowych danych pochodzących z sekwencjonowania dostarcza wiedzy na temat długości DNA na wczesnym etapie analizy. W naszej pracy stworzony został model szacujący długość genomu oparty na losowym doborze krótkich fragmentów DNA zwanych k-mer. Wyniki powstałe przy użyciu modelu zostały odniesione do danych pochodzących z eksperymentów sekwencjonowania całych genomów.

Does genome size explain rarity in beetles? The case from Coccinelidae and Chrysomelidae families

Zalewski M., Ciurzycki W.

Polish Journal of Ecology

2010

Vol. 58, nr 3

585-591

Accumulation of selfish DNA in cells has fundamental consequences for organism metabolism. Detrimental effects of large genome size have been demonstrated for several aspects of performance in plant and animal species. Here we check if a large genome affects occupancy among Coccinelidae and Chrysomelidae occurring in Poland. It was possible to match literature data on distribution and genome-size data for 19 species of chrysomelids and 10 species of coccinelids of different rarity (occurrence expressed as % of Poland area) and body size. There was a marginally significant (P = 0.04) and expected excess of species with large genomes among rare species (<0.73% of area), as well as an excess of species with small genomes among common species (>0.89% of area) However overall correlation was not significant (P = 0.13). Body size was not related to rarity in these species. The detection of this weak signal provides a clue to the important idea that large-scale patterns may stem from differences observed at the cellular level.