Документ взят из кэша поисковой машины. Адрес оригинального документа : http://mccmb.belozersky.msu.ru/2013/abstracts/abstracts/170.pdf Дата изменения: Wed May 29 22:31:44 2013 Дата индексирования: Thu Feb 27 21:03:45 2014 Кодировка:

DE NOVO SEQUENCING, ASSEMBLY AND CHARACTERIZATION OF GENOME IN TETRAPLOID PLANT CAPSELLA BURSA-PASTORIS

Kasianov A.S.1*, Logacheva M.D.2, Makeev V.J.1, Penin A.A. 1. Vavilov Institute of General Genetics, RAS Moscow, Russia 2. Lomonosov Moscow State University, Moscow, Russia * Corresponding author

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Key words: plants, polyploidy, genome, sequence assembly, Capsella bursa-pastoris

Motivation and Aim Genome sequencing data are a basic part of modern genetics, genomics and evolutionary biology. Evolution of sequencing technologies gives us capabilities for characterization of genomes in many non-model species. However, de novo assembly of genomes of flowering plants is still a very difficult task, because many of them are polyploids. As a result their similar multiple paralogs presents in their genomes and it complicates the assembly. Subject of our study was Capsella bursa-pastoris. It is a tetraploid plant with uncertain origin. C. bursa-pastoris may be a recent allotetraploid or more ancient autotetraploid. It is a perfect model for the studies of gene and genome evolution after duplication events due to the fact that C. bursa-pastoris has a close relationship with a model plant Arabidopsis thaliana (Capsella belongs to the same family). Methods and Algorithms We have sequenced DNA from Capsella bursa-pastoris using Illumina sequencing platform. Nearly 300 million paired-end reads were generated, . Coverage of genome was 150x. Insert lengths of paired-end libraries were 150bp and 450bp. We tried to assembly obtained data set by different programs ( Velvet, CLC Genomics workbench, SOAPdenovo), but none of them demonstrated the capacity to assemble paralogous genome regions separately because of their high similarity. To get over this problems, the new algorithm for partition of reads


into subsets conforming to each of the paralogous genome regions, with using information of genome assembly of Capsella rubella(closely-related to Capsella bursa-pastoris plant) was developed. Generated subsets were used to obtain paralogous genome regions. Constructed sequences were annotated with using additonal sequenced data of Capsella bursa-pastoris transcriptome. Results and conclusion Genome of C. bursa-pastoris was sequenced and assembled using newly developed algorithm for separation of reads into subsets corresponding to the paralogous genome regions. Patterns of molecular evolution in paralogous genes were inferred.