#Where can i torrent gene construction kit 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. ilex was published using an Illumina Hiseq 2500 platform. Recently, a de novo transcriptome assembly of Q. 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. 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. Once generated, these reads must be de novo assembled to produce a transcriptome. 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. However, an alternative technology is provided by Ion Torrent instruments. Of these, Illumina is the most commonly used. In order to generate transcriptomes, a set of read sequences are obtained first by next generation sequencing (NGS) technologies. 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.
ilex biology such as natural variation, seed germination, seedling growth, physiology and, biotic and abiotic stress-responses. To date, partial studies using classical biochemical and proteomics approaches have shed some light on different aspects of Q.
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. Holm oak ( Quercus ilex L.) forms natural forests or “dehesa” ecosystems, playing an important role from an environmental and socio-economic point of view. 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. Those from Ion Torrent showed more proteins compared to the Illumina and hybrid assemblies. In addition, an in silico proteomic analysis was carried out using the translated assemblies as databases. 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. MIRA-Ion Torrent showed the highest number of shared sequences (84.8%) with the oak transcriptome. The MIRA-Illumina and TRINITY-Ion Torrent assemblies annotated the highest number of total transcripts (62,628 and 74,058 respectively). The RAY-hybrid assembly generated the most complete transcriptome (1,116 complete sequences of which 1,085 were single copy) with a E90N50 of 1,122 bp.
A hybrid transcriptome combining both sequencing technologies was also obtained in this study. In this study, Quercus ilex raw sequencing reads were obtained from Illumina and Ion Torrent and assembled by three different algorithms, MIRA, RAY and TRINITY. Genomic analysis of this forest tree species is a major challenge considering its recalcitrant character and the absence of previous molecular studies. Here, we compare Illumina and Ion Torrent sequencing platforms for the construction and analysis of the holm oak ( Quercus ilex) transcriptome. Currently, next generation sequencing platforms are used to obtain a high amount of raw data to build the transcriptome of any plant. Transcriptome analysis is widely used in plant biology research to explore gene expression across a large variety of biological contexts such as those related to environmental stress and plant-pathogen interaction.