#Gene construction kit torrent software
#Gene construction kit torrent torrent

The MIRA-Illumina and TRINITY-Ion Torrent assemblies annotated the highest number of total transcripts (62,628 and 74,058 respectively). MIRA-Ion Torrent showed the highest number of shared sequences (84.8%) with the oak transcriptome. All the assembled transcripts from the hybrid transcriptome were annotated with gene ontology grouping them in terms of biological processes, molecular functions and cellular components. In addition, an in silico proteomic analysis was carried out using the translated assemblies as databases. Those from Ion Torrent showed more proteins compared to the Illumina and hybrid assemblies.

This new generated transcriptome represents a valuable tool to conduct differential gene expression studies in response to biotic and abiotic stresses and to assist and validate the ongoing Q. Holm oak ( Quercus ilex L.) forms natural forests or “dehesa” ecosystems, playing an important role from an environmental and socio-economic point of view. Holm oak, as with other forest tree species, can be defined as an orphan and recalcitrant experimental system, whose study at the molecular and genomic level represents a challenge. To date, partial studies using classical biochemical and proteomics approaches have shed some light on different aspects of Q. Ilex biology such as natural variation, seed germination, seedling growth, physiology and, biotic and abiotic stress-responses. The holm oak genome has not yet been sequenced, however, transcriptome analysis, using RNA-sequencing (RNA-Seq), offers an alternative technology now widely used to identify and characterize gene sequences. In order to generate transcriptomes, a set of read sequences are obtained first by next generation sequencing (NGS) technologies. Of these, Illumina is the most commonly used. However, an alternative technology is provided by Ion Torrent instruments. The raw read data obtained using both platforms differ in some parameters such as fragment length, probability of base substitutions or insertion/deletion alterations in homopolymeric regions. Once generated, these reads must be de novo assembled to produce a transcriptome. Several de novo transcriptome assemblers are currently available that, combined with user-tunable parameters, enable the generation of a large figure of candidate assemblies for a single data set. Recent studies have shown that the evaluation of de novo transcriptome assemblies remains a challenge,, and there is not a universal accepted optimal assembler identified for de novo generation. Recently, a de novo transcriptome assembly of Q. ilex was published using an Illumina Hiseq 2500 platform.

#Gene construction kit torrent software

Initially, 31,973 total sequences were annotated using the Blast2Go software and later, the total number of transcripts was increased to 62,628 total sequences using the Sma3s v2 software. #Where can i torrent gene construction kit software #Where can i torrent gene construction kit software.