Background: The pathogen of angiostrongyliasis is the parasite Angiostrongylus cantonensis, and the Transcriptome profiling of the male adult was unclear. We aimed to understand how the male adults adapt, so the expression profile of A. cantonensis adult males was analyzed. Methods: In order to improve the understanding of the Transcriptome of adult males, RNA from three groups of male adult A. cantonensis was extracted and reverse transcribed to construct cDNA libraries. After sequencing, annotation of unigenes and transcripts was performed by querying the NR (Non-Redundant Protein Sequence Database), GO (Gene Ontology) and COG/ KOG (Clusters of Orthologous Groups of proteins/euKaryotic Ortholog Groups) databases. Results: For each group of adults, 43, 260, 894 raw reads and 43, 200, 341 clean reads were obtained. After successful assembly, 87, 649 unigenes and 146, 895 transcripts were obtained. Annotation of the unigenes and transcripts was identical and male adults expressed a series of genes encoding proteins specific to the male gender at the adult stage, such as proteins involved in energy metabolism, energy synthesis and transport. Expression of the ribosome pathway suggests a relationship with the physical activities during the adult male stage. Conclusion: The Transcriptome analysis is a good reference to understand further the expression profile of male adult A. cantonensis.

Shoot apical meristem (SAM) and root apical meristem (RAM) are regions in the plant which contain stem cells. SAM provides cells for development of all above-ground structures such as leaves, flowers, branches and inter nodes and RAM is responsible for formation of plant underground organs. Furthermore, root is major component of plant nutrient and use of water in the plant. Therefore, the growth and development of the plant depends on the function of meristematic regions in shoot and root apex. In this study, the Transcriptome of the shoot and root tip of soybean were investigated to identify genes that are highly expressed in this regions and likely to have major role in these areas. Hence, RNA-seq data were analyzed using the CLC Genomics workbench.Results revealed 1956 and 1725 genes were specifically expressed in the shoot and root tip, respectively. Moreover in the shoot tip in comparison with the root tip, 3750 genes of differentially expressed genes had a fold change of two or greater and 3710 of down regulated genes in the shoot tip had a fold change of two or greater. Functional analysis of differentially expressed genes revealed that these genes are involved in catalytic, transcription, signaling and enzyme regulator activities.

Given the importance of Transcriptome analysis in various biological studies and considering the vast amount of whole Transcriptome sequencing data, it seems necessary to develop an algorithm to assemble Transcriptome data. In this study we propose an algorithm for Transcriptome assembly in the absence of a reference genome. First, the contiguous sequences are generated using de Bruijn graph with different k-mer lengths. Then, the eclectic mixtures of sequences are gathered in order to form the final sequences. Lastly, the contiguous sequences are clustered and the isoform groups are provided. This proposed algorithm is capable of generating long contiguous sequences and accurately clustering them into isoform groups.To evaluate our algorithm, we applied it to a simulated RNA-seq dataset of rat Transcriptome and a real RNA-seq experiment of the loricaria gr. cataphracta Transcriptome. The correctness of the assembled contigs was more than 95%, and our algorithm was able to reconstruct over 70% of the transcripts at more than 80% of the transcripts’ lengths. This study demonstrates that applying a sophisticated merging method improves Transcriptome assembly. The source code is available upon request by contacting the corresponding author by email.

Cumin (Cuminum cyminum L. ) is a flowering plant from Apiaceae family and native to the East Mediterranean to India. The main component of essential oil in cumin seeds is cumin aldehyde (63% of total oil). Despite the importance of the cumin derivative drugs little information is available on the genome and the molecular mechanisms involved in metabolic pathway of this plant. Transcriptomic studies have greatly contributed to better understand in metabolic pathways of medicinal plants. At the moment, the use of next-generation sequencing techniques, especially RNA-seq technique were considered as the suitable promising and most accurate methods of transcriptomic evaluation. In the present study, we report cumin Transcriptome for the first time. Flower tissue was used to extract RNA from four samples for RNA-seq analysis. According to the results, more than 153000000 reads with length of 50 NT were achieved. Trinity software, using 25 and 32 K-mers, was used to assemble the reads. Selection of the best assembly was followed using BUSCO software based on the integer transcript sequences. After assembly of reads, 50973 genes with an average length of 725 NT and N50 value of 1136 NT were obtained. Moreover, 53103 transcripts were identified from all genes. From this number, 35860 transcripts had at least one homologous in Nr database. More than 66. 7% of all transcripts had at least one homologous in GO database (biological process, molecular function, cellular compound). Most of the genes were related to transcriptional regulation and membrane activities. In the present study, the first Transcriptome profile is reported in cumin which data can be used in subsequent studies to assess expression of genes and other genetic studies in this plant.

Scorpions are generally an important source of bioactive components, including toxins and other small peptides as attractive molecules for new drug development. Mesobuthus eupeus, from medically important and widely distributed Buthidae family, is the most abundant species in Iran. Researchers are interesting on the gland of this scorpion due to the complexity of its venom. Here, we have analyzed the Transcriptome based on expressed sequence tag (EST) database from the venom tissue of Iranian M. eupeus by constructing a cDNA library and subsequent Sanger sequencing of obtained inserts. Sixty-three unique transcripts were identified, which were grouped in different categories, including Toxins (44 transcripts), Cell Proteins (9 transcripts), Antimicrobial Peptides (4 transcripts) and Unknown Peptides (3 transcripts). The analysis of the ESTs revealed several new components categorized among various toxin families with effect on ion channels. Sequence analysis of a new precursor provides evidence to validate the first CaTxs from M. eupeus. The results are exploration of the diversity of precursors expressed of Iranian M. eupeus venom gland. We further described comparative analysis of venom components of Iranian M. eupeus with other sibling species.