De novo assembly of Trifolium pratense genome.
| Autoři | |
|---|---|
| Rok publikování | 2012 |
| Druh | Článek ve sborníku |
| Konference | Biotechnology in Legume Breeding |
| Fakulta / Pracoviště MU | |
| Citace | |
| Obor | Šlechtění rostlin |
| Klíčová slova | de novo assembly; new generation sequencing; red clover; Trifolium pratense |
| Popis | Recent progress of new generation sequencing (NGS) platforms has provided many researchers novel opportunity to use diversity in plant genetic resources. Red clover (Trifolium pratense) is very important forage crop from the leguminous family. It is an allogamous diploid with a 418 Mb genome. NGS platform Illumina was used to the whole genome sequencing of T. pratense cv. Tatra to study intraspecific variability. Testing datasets of chromosome 2 from Medicago truncatula with different error rates were firstly used for assessment of several frequently used de novo assembling programmes in terms of contiguity and accuracy. Afterwards, the best performing assemblers were used in the de novo assembly of the real datasets from T. pratense. On the testing data with very low frequency of errors (0.1%), the best performing assemblers were Celera wgs assembler, Edena and Abyss. The best results were achieved by Abyss, Gossamer and Velvet with more frequent error rate (1%). The best performing tested read error correction software were Echo and Quake. The red clover genome set generated here provides a resource for development of high-throughput DNA marker typing systéme and for comparative analyses. |
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