The transcriptome of a “sleeping” invader: de novo assembly and annotation of the transcriptome of aestivating Cornu aspersum

Abstract

Background Cornu aspersum is a quite intriguing species from the point of view of ecology and evolution and its potential use in medical and environmental applications. It is a species of economic importance since it is farmed and used for culinary purposes. However, the genomic tools that would allow a thorough insight into the ecology, evolution, nutritional and medical properties of this highly adaptable organism, are missing. In this work, using next-generation sequencing (NGS) techniques we assessed a significant portion of the transcriptome of this non-model organism.ResultsOut of the 9445 de novo assembled contigs, 2886 (30.6%) returned significant hits and for 2261 (24%) of them Gene Ontology (GO) terms associated to the hits were retrieved. A high percentage of the contigs (69.4%) produced no BLASTx hits. The GO terms were grouped to reflect biological processes, molecular functions and cellular components. Certain GO terms were dominant in all groups. After scanning the assembled transcriptome for microsatellites (simple sequence repeats, SSRs), a total of 563 SSRs were recovered. Among the identified SSRs, trinucleotide repeats were the predominant followed by tetranucleotide and dinucleotide repeats.ConclusionThe annotation success of the transcriptome of C. aspersum was relatively low. This is probably due to the very limited number of annotated reference genomes existing for mollusc species, especially terrestrial ones. Several biological processes being active in the aestivating species were revealed through the association of the transcripts to enzymes relating to the pathways. The genomic tools provided herein will eventually aid in the study of the global genomic diversity of the species and the investigation of aspects of the ecology, evolution, behavior, nutritional and medical properties of this highly adaptable organism.

Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop

“…Our transcriptome assembly had the vast majority of all reads mapping back to the assembly, and 100% of the mapped fragments were found mapped as proper pairs (yielding concordant alignments 1 or more times to the reconstructed transcriptome). Furthermore, our findings are superior to Parmakelis et al [57], Diray-Arce et al [58], and Khudyakov et al [59] who found that 65.58%, 72.91%, and 86.60% of the total raw reads could be mapped back to the assembly. This high concordance in our transcriptome might be due to the K-mer which was set at the maximal value of 32-mer [60].…”

Alternative Splicing Detection Tool—a novel PERL algorithm for sensitive detection of splicing events, based on next-generation sequencing data analysis

“…As it can be easily assumed, given the vast amount of data produced by NGS, developing a massive data storage and management solution and creating bioinformatic tools to effectively analyze it will be the most crucial step for the successful application of NGS methodology (72). The full benefit of NGS will not be achieved until bioinformatics are able to maximally utilize and interpret these enormous short-read sequences into molecular and genetic useful information (73).…”

Non-coding RNAs: the riddle of the transcriptome and their perspectives in cancer

“…Simultaneously, the databases including annotated ncRNA transcripts [e.g., miRBase (5), lncRNAdb (6), NONCODE (7) etc.] are expanding constantly with novel sequences, mainly due to the technological advancement through the establishment of high-throughput next-generation (NGS) technologies (8,9). In particular, NGS has revealed many ncRNAs originating from protein-coding genes (10)(11)(12)(13)(14)(15)(16).…”