The presumed novel clusters were annotated using SwissProt, PGSC DM v3.4 superscaffolds and NCBI-nt databases. The resulting two sets of preliminary transcriptomes were then merged using the CD-HIT clustering algorithm (Limin et al., 2012) and merged with existing gene models with BLAST against stNIB-v1. De novo assembly was performed using Trinity (Grabherr et al., 2011). The hybrid approach, combining genome-guided and de novo RNA-Seq assembly, was implemented using the pipeline available from CLC Genomics Workbench 7.0.3 1. The preliminary transcriptomes were assembled using both hybrid and de novo assembly approaches. tuberosum gene groups, which included two genome assemblies and two EST datasets (Ramšak et al., 2014). In house generated raw reads were complemented with data already deposited in the NCBI database and stNIB-v1 S. PW363 leaves was conducted on Illumina NGS platform.
In order to avoid problems, such as discriminating between paralogous genes, divergence and expression bias between the reference genome and potato cultivars, and to identify traits that are not present in initially sequenced genotype, RNA-sequencing for cv. To bypass polyploidy related sequencing problems, Potato Genome Sequencing Consortium (PGSC, 2011) sequenced a double monoploid derived from S. Most potato cultivars are highly heterozygous tetraploids with high genetic variability while being susceptible to pathogens, pests and inbreeding depression. The rapid development of modern life science technologies, such as Next Generation Sequencing (NGS) techniques, allows the generation of biological data with increasing speed and precision. Maja Zagorščak 1 ✉, Marko Petek 1, Mohamed Zouine 2, Kristina Gruden 1ġNational Institute of Biology - Department of Biotechnology and Systems Biology, Ljubljana, SloveniaĢEcole Nationale Supérieure Agronomique de Toulouse, Toulouse, France Reference leaftTranscriptomes for potato cultivars: Desiree and PW363
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