Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of the key genes and pathways that involved in CIMS were important to understand the underlying molecular mechanism. In the present report, a multi-omics integrative analysis, including of the proteomic, transcriptomic and miRNAs, combined with morphological and physiological analysis were conducted. Earlier degeneration of the tapetosomes and elaioplasts, aberrantly stacking in tapetal cells and incompletely deposition in tryphine of pollen wall were observed in chemical hybridization agent (CHA) of SX-1 treated B. napus through SEM and TEM analysis. It was revealed that the deficiencies in protein processing in endoplasmic reticulum (ER) and flavonoids biosynthesis were occurred at early stage in the SX-1 treated materials. Subsequently, plant hormone signal transduction, biosynthesis of amino acids, fatty acids and steroid in anther at later stages were identified down-regulated after SX-1 treatment. 144 transcript factors (TFs) were also indentified to down-regulated at early stage, which suggested the early regulation in anther and pollen wall development were disordered in CHA treated B. napus. In addition, 7 important miRNAs were identified and 2 of the predicted target genes of miRNAs were Rf-like genes. Taken together, an interaction network of candidate genes and the putative metabolism pathways were constructed based on the multi-omics integrative analysis, it provided a new insight into the male sterility induced by CHA of SX-1 in B. napus.

Background: Osmanthus fragrans is an important economical plant containing multiple secondary metabolites including flavonoids and anthocyanins. During the past years, the roles of miRNAs in regulating the biosynthesis of secondary metabolites in plants have been widely investigated. However, few studies on miRNA expression profiles and the potential roles in regulating flavonoid biosynthesis have been reported in O. fragrans. Results: In this study, we used high-throughput sequencing technology to analyze the expression profiles of miRNAs in leaf and flower tissues of O. fragrans. As a result, 106 conserved miRNAs distributed in 47 families and 88 novel miRNAs were identified. Further analysis showed there were 133 miRNAs differentially expressed in leaves and flowers. Additionally, the potential target genes of miRNAs as well as the related metabolic pathways were predicted. In the end, flavonoid content was measured in flower and leaf tissues and potential role of miR858 in regulating flavonoid synthesis was illustrated in O. fragrans. Conclusions: This study not only provided the genome-wide miRNA profiles in the flower and leaf tissue of O. fragrans, but also investigated the potential regulatory role of miR858a in flavonoid synthesis in O. fragrans. The results specifically indicated the connection of miRNAs to the regulation of secondary metabolite biosynthesis in non-model economical plant.

As a medicinal plant widely planted in southwest karst of China, the study of adaptation mechanisms ofLonicera confusa, especially to karst calcium-rich environment, can provide important theoretical basis for repairing desertification by genetic engineering. In this study, the Ca²⁺imaging in the leaves ofL. confusawas explored by LSCM (Laser Scanning Confocal Microscopy) and TEM (Transmission Electron Microscopy), which revealed that the calcium could be transported to gland, epidermal hair and stoma in the leaves ofL. confusain high-Ca²⁺environment. In addition, we simulated the growth environment ofL. confusaand identified DEGs (Differentially Expressed Genes) under different Ca²⁺concentrations by RNA sequencing. Further analysis showed that these DEGs were assigned with some important biological processes. Furthermore, a complex protein-protein interaction network among DEGs inL. Confusawas constructed and some important regulatory genes and transcription factors were identified. Taken together, this study displayed the Ca²⁺transport and the accumulation of Ca²⁺channels and pools inL. Confusawith high-Ca²⁺treatment. Moreover, RNA sequencing provided a global picture of differential gene expression patterns inL. Confusawith high-Ca²⁺treatment, which will help to reveal the molecular mechanism of the adaptation ofL. confusato high-Ca²⁺environment in the future.

Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported. Here, we apply small RNA sequencing to explore miRNA expression patterns between B. napus, B. rapa and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel miRNAs in B. napus, B. rapa and the F1 hybrid, respectively. Moreover, 213 miRNAs were found to be differentially expressed between B. napus, B. rapa and the F1 hybrid. The present study also shows 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, to be nonadditively expressed in the F1 hybrid. Furthermore, miRNA synteny analysis revealed high genomic conservation between the genomes of B. napus, B. rapa and their F1 hybrid, with some miRNA loss and gain events in the F1 hybrid. This study not only provides useful resources for exploring global miRNA expression patterns and genome structure but also facilitates genetic research on the roles of miRNAs in genomic interactions of Brassica allopolyploids.

Chinese sturgeon (Acipenser sinensis) is a critically endangered fish inhabiting the Yangtze River and Chinese coastal waters. Numerous research projects and conservation efforts have focused on artificial propagation and release to restore this endangered species. However, genomic and full-length transcriptomic sequencing of Chinese sturgeon has rarely been reported. In this study, a total of 10 Chinese sturgeon tissues were used for PacBio Iso-seq and RNA-seq analyses. A total of 19,538 full-length transcripts were obtained with sizes from 51 bp to 7,033 bp. Moreover, cluster analysis of gene families and phylogenetic analysis of 14 species were performed. Furthermore, lncRNAs and coding sequence (CDS) were identified in all Chinese sturgeon tissues. Finally, gene expression profiles and differentially expressed genes (DEGs) were analyzed among 10 tissues in Chinese sturgeon. Taken together, full-length transcripts and the gene expression profile from Chinese sturgeon tissues will provide gene sequences and expression information for future functional genomic study and be very helpful for comprehensive understanding of the genetic mechanism of endangerment in Chinese sturgeon.