Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa.

BACKGROUND: The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, relative fewer phasiRNA biogenesis pathways have been discovered in rice compared to other plant species, which limits the comprehensive understanding of phasiRNA biogenesis and the miRNA-derived regulatory network. RESULTS: In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further investigation of their regulatory function revealed that eleven novel phasiRNAs in 21-nt length recognized forty-one target genes. Most of these genes were involved in the growth and development of rice. In addition, five novel 24-nt phasiRNAs targeted to the promoter of an OsCKI1 gene and thereafter resulted in higher level of methylation in panicle, which implied their regulatory function in transcription of OsCKI1,which acted as a regulator of rice development. CONCLUSIONS: These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.

sRNATargetDigger: A bioinformatics software for bidirectional identification of sRNA-target pairs with co-regulatory sRNAs information.

Identification of the target genes of microRNAs (miRNAs), trans-acting small interfering RNAs (ta-siRNAs), and small interfering RNAs (siRNAs) is an important step for understanding their regulatory roles in plants. In recent years, many bioinformatics software packages based on small RNA (sRNA) high-throughput sequencing (HTS) and degradome sequencing data analysis have provided strong technical support for large-scale mining of sRNA-target pairs. However, sRNA-target regulation is achieved using a complex network of interactions since one transcript might be co-regulated by multiple sRNAs and one sRNA may also affect multiple targets. Currently used mining software can realize the mining of multiple unknown targets using known sRNA, but it cannot rule out the possibility of co-regulation of the same target by other unknown sRNAs. Hence, the obtained regulatory network may be incomplete. We have developed a new mining software, sRNATargetDigger, that includes two function modules, "Forward Digger" and "Reverse Digger", which can identify regulatory sRNA-target pairs bidirectionally. Moreover, it has the ability to identify unknown sRNAs co-regulating the same target, in order to obtain a more authentic and reliable sRNA-target regulatory network. Upon re-examination of the published sRNA-target pairs in Arabidopsis thaliana, sRNATargetDigger found 170 novel co-regulatory sRNA-target pairs. This software can be downloaded from http://www.bioinfolab.cn/sRNATD.html.

Identification of novel phasiRNAs loci on long non-coding RNAs in Arabidopsis thaliana.

Long non-coding RNAs (lncRNAs) are the "dark matters"involved in gene regulation with complex mechanisms. However, the functions of most lncRNAs remain to be determined. Our previous work revealed a massive number of degradome-supported cleavage signatures on Arabidopsis lncRNAs. Some of them have been confirmed associated with miRNAs-like sRNAs production, while others without long stem structure remain unexplored. A systematical search for phasiRNAs generating ability of these lncRNAs was conducted. Eight novel small RNA triggered lncRNA-phasiRNA pathways were discovered and three of them were found to be conserved in Arabidopsis, Oryza sativa, Glycine max and Gossypium hirsutum. Besides, Five novel ta-siRNAs derived from these lncRNAs were further identified to be involved in the regulation of plant development, stress responses and aromatic amino acids synthesis. These results substantially expanded the gene regulation mechanisms of lncRNAs.

Genome-wide identification and characterization of novel microRNAs in seed development of soybean.

MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA-target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.

Formation of zona radiata and ultrastructural analysis of egg envelope during oogenesis of Chinese perch Siniperca chuatsi.

During oocyte maturation, egg envelope undergoes a series of changes in structure and function. We investigated the follicular envelope, zona radiata and plasmalemma of Chinese perch, Siniperca chuatsi at five different developmental stages by light, scanning and transmission electron microscopy. An octopus-like structure in the zona radiata was observed for the first time. The increasing thickness of zona radiata during these stages suggests the microvilli's functional transition from transferring vital materials for the protection of the oocyte. That the egg envelope fully matures later than the oocyte is well supported by the disappearance of the follicular envelope. We have discovered several characteristic structures in the semi-floating egg and propose that the octopus-like structure is essential for oocyte migration and fertilization.

Ultrastructural observation on genesis and morphology of cortical granules in Macrobrachium nipponense (Crustacea, Caridea).

Cortical granules are secretory vesicles in oocytes that develop from the Golgi complex. In the freshwater shrimp, Macrobrachium nipponense, mitochondria participates in the formation of cortical granules. We investigated the structural changes of mitochondria and the distribution cortical granules in different stages of oocyte development. Transmission electron microscopy provided evidence for the involvement of mitochondria and a particular spiral lamellar organization and an electron-lucent area in internal cortical granules. The ooplasm provided material for the cortical granules in early oocyte development. We demonstrated that mitochondria play a role in coalescence and maturation of cortical granules in this species. Additionally, a concept of cortical granules regarded as a functional integration is put forward. The genesis of shrimp cortical granules exhibited a particular pathway of maturation. The outer shape and inner organization considering different taxa suggested general as well as specific features of the development of cortical granules.