Alternative Isoform Analysis of Ttc8 Expression in the Rat Pineal Gland Using a Multi-Platform Sequencing Approach Reveals Neural Regulation

Genomics and transcriptomics of the Chinese mitten crabs (Eriocheir sinensis)

To gain a deeper understanding of the genetic factors influencing the growth and development of Eriocheir sinensis, a well-known species of hairy crab found in Yangcheng Lake, this study focused on the de novo genome and full-length transcriptome information of the selected subjects. Specifically, Yangcheng Lake hairy crabs were chosen as the experimental samples. Initially, a genome analysis was performed, resulting in the identification of gene fragments with a combined length of 1266,092,319 bp. Subsequently, a transcriptome analysis was conducted on a mixture of tissues from four different sites, namely muscle, brain, eye, and heart, to further investigate the genetic characteristics at the transcriptome level. The Pacific Biosciences (Pacio) single-molecule real-time sequencing system generated a total of 36.93 G sub-fragments and 175,90041 effective inserts. This research contributes to the indirect comprehension of genetic variations underlying individual traits. Furthermore, a comparison of the obtained data with relevant literature emphasizes the advantages of this study and establishes a basis for further investigations on the Chinese mitten crab.

A novel full-length transcriptome resource from multiple immune-related tissues in turbot (Scophthalmus maximus) using Pacbio SMART sequencing

Turbot (Scophthalmus maximus) is an important cold-water economic fish. However, the production and development of turbot industry has been constantly hindered by the frequent occurrence of some diseases. Lacking full-length transcriptome for turbot limits immune gene discoveries and gene structures analysis. Therefore, we generated a full-length transcriptome using mixed immune-related tissues of turbot with PacBio Sequel platform. In this study, a total of 31.7 Gb high quality data were generated with the average subreads length of 2618 bp. According to the presence of 5' and 3' primers as well as poly (A) tails, FL (Full-length) and NFL (Non-full-length) isoforms were obtained. Meanwhile, we identified 32,003 non-redundant transcripts, 76.02% of which was novel isoforms of known genes. In addition, 12,176 alternative splicing (AS) events, 6614 polyadenylation (APA) events, 1905 transcription factors, and 2703 lncRNAs were identified. This work is a comprehensive report on the full-length transcriptome of immune-related tissues of turbot, and it also provides valuable molecular resources for future research on the adaptation mechanisms and functional genomics of turbot.

Chemical characterization of pineal neurons in perinatal rats

Ample evidence indicates that in several mammalian species the pineal body contains neurons. In adult white albino rats neurons are not present in the pineal body; however, in perinatal rats many neurons were described. It was demonstrated that in adult mammalian species the pineal neurons contained some neuropeptides and neurotransmitters such as leu-enkephalin, met-enkephalin, substance-P, somatostatin and γ-aminobutiric acid. Oxytocin, vasopressin mRNAs and peptides were also demonstrated. No data are available on the chemical nature of the neurons in perinatal rats. In the present experiment we used immunohistochemistry to clarify this issue. After paraformaldehyde fixation frozen sections were prepared and stained for immunoreactivities of several neuropeptides and neurotransmitters. Dopamine β-hydroxylase, neuropeptide-Y, vesicular acetylcholine transporter, vesicular glutamate transporter and calcitonin gene-related peptide antibodies were able to stain fibers. According to previous data these fibers may be sympathetic, parasympathetic or sensory. Vesicular glutamate transporter antibody may stain pinealocytes as well. Some cells were immunoreactive for substance-P, oxytocin, vasopressin, leu-enkefalin and glutamic acid decarboxylase. These immnoreactivities showed colocalization with neuron-specific nuclear protein immunoreactivity indicating that these cells were neurons. Calbindin was observed in oval and elongated cells resembling pinealocytes. Based on the results obtained in adult mammals, the pineal neurons may be analogue to retinal ganglion cells, or they may function as interneurons in the retino-pinealo-retinal neuronal circuit or peptidergic neurons may influence pinealocytes in a paracrine manner.

Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages

Background

Red palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control.

Methods

In this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest.

Results

Sequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus.

SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

Background

Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis.

Methods

In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus.

Results

A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.

SMRT sequencing of the full-length transcriptome of the Sunda pangolin (Manis javanica)

It is widely known that transcriptional diversity contributes greatly to biological regulation in eukaryotes. With the development of next-generation sequencing (NGS) technologies, several studies on RNA sequencing have considerably improved our understanding of transcriptome complexity. However, obtaining full-length (FL) transcripts remains a considerable challenge because of difficulties in short read-based assembly. In the present study, single-molecule real-time (SMRT) sequencing and NGS were combined to generate the complete and FL transcriptome of Manis javanica. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of the M. javanica genome. We obtained 45,530 high-confidence transcripts from 19,109 genic loci, of which 8014 genes have not yet been annotated within the M. javanica genome. Furthermore, we revealed 8824 long-chain noncoding RNAs (lncRNAs). A total of 30,199 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events were identified in the sequencing data. The structure and expression level of 59 digestive enzyme genes, including 13 carbohydrase genes, 28 lipase genes and 18 protease genes, were analyzed, which might provide original data for further research on M. javanica.

Single Cell Sequencing of the Pineal Gland: The Next Chapter

The analysis of pineal cell biology has undergone remarkable development as techniques have become available which allow for sequencing of entire transcriptomes and, most recently, the sequencing of the transcriptome of individual cells. Identification of at least nine distinct cell types in the rat pineal gland has been made possible, allowing identification of the precise cells of origin and expression of transcripts for the first time. Here the history and current state of knowledge generated by these transcriptomic efforts is reviewed, with emphasis on the insights suggested by the findings.