Long non-coding RNAs (lncRNAs) regulate various biological processes ranging from gene expression to animal behavior . Although protein-coding genes, microRNAs, and neuropeptides play important roles in the regulation of phenotypic plasticity in migratory locust, empirical studies on the function of lncRNAs in this process remain limited. Here, we applied high-throughput RNA-seq to compare the expression patterns of lncRNAs and mRNAs in the time course of locust phase change. We found that lncRNAs responded more rapidly at the early stages of phase transition. Functional annotations demonstrated that early changed lncRNAs employed different pathways in isolation and crowding phases to cope with changes in the population density. Two overlapping hub lncRNA loci in the crowding and isolation networks were screened for functional verification. One of them, LNC1010057, was validated as a potential regulator of locust phase change. This work offers insights into the molecular mechanism underlying locust phase change and expands the scope of lncRNA functions in animal behavior.

Fall armyworm (Spodoptera frugiperda), a native insect species in the Americas, is rapidly becoming a major agricultural pest worldwide and is causing great damage to corn, rice, soybeans, and other crops. To control this pest, scientists have accumulated a great deal of high-throughput data of fall armyworm, and nine versions of its genomes and transcriptomes have been published. However, easily accessing and performing integrated analysis of these omics data sets is challenging. Here, we developed the Fall Armyworm Genome Database (FAWMine, http://159.226.67.243:8080/fawmine/) to maintain genome sequences, structural and functional annotations, transcriptomes, co-expression, protein interactions, homologs, pathways, and single-nucleotide variations. FAWMine provides a powerful framework that helps users to perform flexible and customized searching, present integrated data sets using diverse visualization methods, output results tables in a range of file formats, analyze candidate gene lists using multiple widgets, and query data available in other InterMine systems. Additionally, stand-alone JBrowse and BLAST services are also established, allowing the users to visualize RNA-Seq data and search genome and annotated gene sequences. Altogether, FAWMine is a useful tool for querying, visualizing, and analyzing compiled data sets rapidly and efficiently. FAWMine will be continually updated to function as a community resource for fall armyworm genomics and pest control research.

Background Alternative splicing is the process of selecting different combinations of splice sites to produce variably spliced mRNAs. However, the relationships between alternative splicing prevalence and level (ASP/L) and variations of intron size and organism complexity (OC) remain vague. Here, we developed a robust protocol to analyze the relationships between ASP/L and variations of intron size and OC. Approximately 8 Tb raw RNA-Seq data from 37 eumetazoan species were divided into three sets of species based on variations in intron size and OC. Results We found a strong positive correlation between ASP/L and OC, but no correlation between ASP/L and intron size across species. Surprisingly, ASP/L displayed a positive correlation with mean intron size of genes within individual genomes. Moreover, our results revealed that four ASP/L-related pathways contributed to the differences in ASP/L that were associated with OC. In particular, the spliceosome pathway displayed distinct genomic features, such as the highest gene expression level, conservation level, and fraction of disordered regions. Interestingly, lower or no obvious correlations were observed among these genomic features. Conclusions The positive correlation between ASP/L and OC ubiquitously exists in eukaryotes, and this correlation is not affected by the mean intron size of these species. ASP/L-related splicing factors may play an important role in the evolution of OC.

Hepatocellular carcinoma (HCC) is a prevalent malignancy cancer worldwide with a poor prognosis. Hepatic resection is indicated as a potentially curative option for HCC patients in the early stage. However, due to multiple nodules, it leads to clinical challenges for surgical management. Approximately 41%–75% of HCC cases are multifocal at initial diagnosis, which may arise from multicentric occurrence (MO-HCC) or intrahepatic metastasis (IM-HCC) pattern with significantly different clinical outcomes. Effectively differentiating the two mechanisms is crucial to prioritize the allocation of surgery for multifocal HCC. In this study, we collected a multifocal hepatocellular carcinoma cohort of 17 patients with a total of 34 samples. We performed whole-exome sequencing and staining of pathological HE sections for each lesion. Reconstruction of the clonal evolutionary pattern using genome mutations showed that the intrahepatic metastogenesis pattern had a poorer survival performance than independent origins, with variants in the TP53, ARID1A, and higher CNV variants occurring more significantly in the metastatic pattern. Cross-modality analysis with pathology showed that molecular classification results were consistent with pathology results in 70.6% of patients, and we found that pathology results could further complement the classification for undefined patterns of occurrence. Based on these results, we propose a model to differentiate the pattern of multifocal hepatocellular carcinoma based on the pathological results and genome mutations information, which can provide guidelines for diagnosing and treating multifocal hepatocellular carcinoma.