Recent studies have suggested that long non-coding RNAs (lncRNAs) can interact with microRNAs (miRNAs) and indirectly regulate miRNA targets though competing interactions. However, the molecular mechanisms underlying these interactions are still largely unknown. In this study, these lncRNA–miRNA–gene interactions were defined as lncRNA-associated competing triplets (LncACTs), and an integrated pipeline was developed to identify lncACTs that are active in cancer. Competing lncRNAs had sponge features distinct from non-competing lncRNAs. In the lncACT cross-talk network, disease-associated lncRNAs, miRNAs and coding-genes showed specific topological patterns indicative of their competence and control of communication within the network. The construction of global competing activity profiles revealed that lncACTs had high activity specific to cancers. Analyses of clustered lncACTs revealed that they were enriched in various cancer-related biological processes. Based on the global cross-talk network and cluster analyses, nine cancer-specific sub-networks were constructed. H19- and BRCA1/2-associated lncACTs were able to discriminate between two groups of patients with different clinical outcomes. Disease-associated lncACTs also showed variable competing patterns across normal and cancer patient samples. In summary, this study uncovered and systematically characterized global properties of human lncACTs that may have prognostic value for predicting clinical outcome in cancer patients.

Background: Acyl-CoA:lysophosphatidylcholine acyltransferase (LPCAT) enzymes have central roles in acyl editing of phosphatidylcholine.Results: Plant LPCATs were expressed in yeast and biochemically characterized.Conclusion: LPCATs can edit acyl composition of phosphatidylcholine through their combined forward and reverse reactions.Significance: Plant LPCATs play a role in editing both sn-positions of PC and remove ricinoleic acid with high selectivity from this lipid.

Recent phylogenetic analysis using mitochondrial cytochrome oxidase I (mtCOI) sequences of Bemisia tabaci worldwide indicates that the whitefly comprises at least 24 morphologically indistinguishable but genetically distinct cryptic species. While evidence of reproductive isolation has been reported for some of the putative species, more extensive crossing experiments are required to clarify the systematics of this species complex. In this study, we established laboratory cultures for six putative species of B. tabaci collected in China. We conducted 22 inter‐species crosses among the six putative species. The data and those reported previously were collated, and the combined dataset covered all the 30 possible inter‐species crosses among the six putative species. Intra‐species controls always produced female and male progeny and the proportions of females in the first generation (F1) ranged from 56% to 70%. However, in inter‐species crosses female progeny were rarely produced, and the few F1 females produced in four of the 30 inter‐species crosses were either sterile or significantly weaker in viability. These results demonstrate a pattern of complete reproductive isolation among the six putative species and show that they are six cryptic species in the B. tabaci complex.

Polyacetylenic lipids accumulate in various Apiaceae species after pathogen attack, suggesting that these compounds are naturally occurring pesticides and potentially valuable resources for crop improvement. These compounds also promote human health and slow tumor growth. Even though polyacetylenic lipids were discovered decades ago, the biosynthetic pathway underlying their production is largely unknown. To begin filling this gap and ultimately enable polyacetylene engineering, we studied polyacetylenes and their biosynthesis in the major Apiaceae crop carrot (Daucus carota subsp. sativus). Using gas chromatography and mass spectrometry, we identified three known polyacetylenes and assigned provisional structures to two novel polyacetylenes. We also quantified these compounds in carrot leaf, petiole, root xylem, root phloem, and root periderm extracts. Falcarindiol and falcarinol predominated and accumulated primarily in the root periderm. Since the multiple double and triple carbon-carbon bonds that distinguish polyacetylenes from ubiquitous fatty acids are often introduced by Δ12 oleic acid desaturase (FAD2)-type enzymes, we mined the carrot genome for FAD2 genes. We identified a FAD2 family with an unprecedented 24 members and analyzed public, tissue-specific carrot RNA-Seq data to identify coexpressed members with root periderm-enhanced expression. Six candidate genes were heterologously expressed individually and in combination in yeast and Arabidopsis (Arabidopsis thaliana), resulting in the identification of one canonical FAD2 that converts oleic to linoleic acid, three divergent FAD2-like acetylenases that convert linoleic into crepenynic acid, and two bifunctional FAD2s with Δ12 and Δ14 desaturase activity that convert crepenynic into the further desaturated dehydrocrepenynic acid, a polyacetylene pathway intermediate. These genes can now be used as a basis for discovering other steps of falcarin-type polyacetylene biosynthesis, to modulate polyacetylene levels in plants, and to test the in planta function of these molecules.

The whitefly Bemisia tabaci has a global distribution and extensive genetic diversity. Recent phylogenetic analyses as well as crossing experiments suggest that B. tabaci is a complex composed of > 20 cryptic species, but more crossing studies are required to examine the reproductive compatibility among the putative species and thus further clarify the systematics of this species complex. We conducted crossing experiments and behavioral observations to investigate the reproductive compatibility between the Mediterranean, Asia II 3, and Asia II 1 putative species of B. tabaci collected from Zhejiang, China. Female progeny were never produced in inter‐species crosses, demonstrating a lack of egg fertilization; while 55%–75% females were produced in all the intra‐species treatments. Continuous behavioral observations showed that frequent courtship events occurred in both intra‐species treatments and inter‐putative species crosses. However, copulation events occurred only in the three intra‐species treatments with one exception: that one copulation event occurred between Asia II 3 and Mediterranean in the crosses where two cohorts of females and males of different putative species were enclosed together in a small arena but were not allowed access to their intra‐specific mates for a long period of time. These data demonstrated complete reproductive isolation between the Mediterranean, Asia II 3, and Asia II 1 putative species, and further showed that the isolation is due to lack of copulation. Demonstration of reproductive isolation between the Mediterranean and two indigenous putative species from China provides further evidence for the existence of cryptic species within the B. tabaci complex.

BackgroundCOI (CORONATINE INSENSITIVE), an F-box component of the Skp1-Cullin-F-box protein (SCFCOI1) ubiquitin E3 ligase, plays important roles in the regulation of plant growth and development. Recent studies have shown that COIs are involved in pollen fertility. In this study, we identified and characterized COI genes in the wheat genome and analyzed expression patterns under abiotic stress.ResultsA total of 18 COI candidate sequences for 8 members of COI gene family were isolated in wheat (Triticum aestivum L.). Phylogenetic and structural analyses showed that these COI genes could be divided into seven distinct subfamilies. The COI genes showed high expression in stamens and glumes. The qRT-PCR results revealed that wheat COIs were involved in several abiotic stress responses and anther/glume dehiscence in the photoperiod-temperature sensitive genic male sterile (PTGMS) wheat line BS366.ConclusionsThe structural characteristics and expression patterns of the COI gene family in wheat as well as the stress-responsive and differential tissue-specific expression profiles of each TaCOI gene were examined in PTGMS wheat line BS366. In addition, we examined SA- and MeJA-induced gene expression in the wheat anther and glume to investigate the role of COI in the JA signaling pathway, involved in the regulation of abnormal anther dehiscence in the PTGMS wheat line. The results of this study contribute novel and detailed information about the TaCOI gene family in wheat and could be used as a benchmark for future studies of the molecular mechanisms of PTGMS in other crops.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5116-9) contains supplementary material, which is available to authorized users.

Within the tumour microenvironment, cells exhibit different behaviours driven by fine-tuning of gene regulation. Identification of cellular-specific gene regulatory networks will deepen the understanding of disease pathology at single-cell resolution and contribute to the development of precision medicine. Here, we describe a database, LnCeCell (http://www.bio-bigdata.net/LnCeCell/ or http://bio-bigdata.hrbmu.edu.cn/LnCeCell/), which aims to document cellular-specific long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) networks for personalised characterisation of diseases based on the ‘One Cell, One World’ theory. LnCeCell is curated with cellular-specific ceRNA regulations from >94 000 cells across 25 types of cancers and provides >9000 experimentally supported lncRNA biomarkers, associated with tumour metastasis, recurrence, prognosis, circulation, drug resistance, etc. For each cell, LnCeCell illustrates a global map of ceRNA sub-cellular locations, which have been manually curated from the literature and related data sources, and portrays a functional state atlas for a single cancer cell. LnCeCell also provides several flexible tools to infer ceRNA functions based on a specific cellular background. LnCeCell serves as an important resource for investigating the gene regulatory networks within a single cell and can help researchers understand the regulatory mechanisms underlying complex microbial ecosystems and individual phenotypes.

This study demonstrates the first practical use of CSILs for the transfer of fiber quality QTLs into Upland cotton cultivars using SSR markers without detrimentally affecting desirable agronomic characteristics. Gossypium hirsutum is characterized by its high lint production and medium fiber quality compared to extra-long staple cotton G. barbadense. Transferring valuable traits or genes from G. barbadense into G. hirsutum is a promising but challenging approach through a traditional interspecific introgression strategy. We developed one set of chromosome segment introgression lines (CSILs), where TM-1, the genetic standard in G. hirsutum, was used as the recipient parent and the long staple cotton G. barbadense cv. Hai7124 was used as the donor parent by molecular marker-assisted selection (MAS). Among them, four CSILs, IL040-A4-1, IL080-D6-1, IL088-A7-3 and IL019-A2-6, found to be associated with superior fiber qualities including fiber length, strength and fineness QTL in Xinjiang were selected and backcrossed, and transferred these QTLs into three commercial Upland cotton cultivars such as Xinluzao (XLZ) 26, 41 and 42 grown in Xinjiang. By backcrossing and self-pollinating twice, five improved lines (3262-4, 3389-2, 3326-3, 3380-4 and 3426-5) were developed by MAS of background and introgressed segments. In diverse field trials, these QTLs consistently and significantly offered additive effects on the target phenotype. Furthermore, we also pyramided two segments from different CSILs (IL080-D6-1 and IL019-A2-6) into cultivar 0768 to accelerate breeding process purposefully with MAS. The improved lines pyramided by these two introgressed segments showed significant additive epistatic effects in four separate field trials. No significant alteration in yield components was observed in these modified lines. In summary, we first report that these CSILs have great potential to improve fiber qualities in Upland cotton MAS breeding programs.