Expression and localization of the Spodoptera frugiperda allatotropin (Spofr-AT) and allatostatin (Spofr-AS) genes

Manduca sexta allatotropin and allatostatin were the first corpora allata (CA) regulating neuropeptides identified from Lepidoptera. Recently, we cloned the allatotropin (Spofr-AT) and the allatostatin (Spofr-AS) genes from the fall armyworm Spodoptera frugiperda. Using one-step RT-PCR for semi-quantification of the gene expression, we now demonstrate that three mRNA isoforms of the Spofr-AT gene and the Spofr-AS gene are expressed in brain, digestive tract, and reproductive organs of larvae, pupae, and adults in a time- and tissue-specific manner. Expression rates in the brain and in various parts of the digestive tract prove the dual role of the peptides as brain/gut (neuro)peptides. The functional meaning of ovarian and testes expression of the genes is not yet clear, although myoregulatory properties of the peptides are probable. The tissue-specific localization of the prohormone expression, as demonstrated by whole mount in situ hybridization, confirms the overall distribution of the prohormones as shown by RT-PCR and supports the pleiotropic functions of the peptides.     

Rice Expression Database(RED):An integrated RNA-Seq-derived gene expression database for rice

Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED(Rice Expression Database;http://expression.ic4r.org),an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.     

ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq

Experimental variance is a major challenge when dealing with high-throughput sequencing data. This variance has several sources: sampling replication, technical replication, variability within biological conditions, and variability between biological conditions. The high per-sample cost of RNA-Seq often precludes the large number of experiments needed to partition observed variance into these categories as per standard ANOVA models. We show that the partitioning of within-condition to between-condition variation cannot reasonably be ignored, whether in single-organism RNA-Seq or in Meta-RNA-Seq experiments, and further find that commonly-used RNA-Seq analysis tools, as described in the literature, do not enforce the constraint that the sum of relative expression levels must be one, and thus report expression levels that are systematically distorted. These two factors lead to misleading inferences if not properly accommodated. As it is usually only the biological between-condition and within-condition differences that are of interest, we developed ALDEx, an ANOVA-like differential expression procedure, to identify genes with greater between- to within-condition differences. We show that the presence of differential expression and the magnitude of these comparative differences can be reasonably estimated with even very small sample sizes.     

盐胁迫下两个甜瓜品种转录因子的转录组分析

利用新一代高通量测序手段——转录组测序（RNA-Seq）技术研究在300 mmol.L-1NaCl胁迫下两个甜瓜（Cucumis melo L.）品种‘玉露’和‘冰雪脆’的转录因子基因表达变化。这两个甜瓜品种在叶绿素荧光参数上的差异表明其在盐胁迫下有不同的生理反应。转录组测序结果表明,盐胁迫与对照相比,‘玉露’共有属于19个转录因子家族的56个转录因子基因表达发生变化（在转录水平,属于7个转录因子家族的22个转录因子上调表达,属于14个转录因子家族的34个转录因子下调表达）。‘冰雪脆’有属于20个转录因子家族的47个转录因子基因表达发生变化（在转录水平上,属于5个转录因子家族的17个转录因子上调表达,属于17个转录因子家族的30个转录因子下调表达）。盐胁迫下,两个甜瓜品种差异表达的转录因子既表现特异性,也存在部分重叠。‘玉露’有29个转录因子特异响应,‘冰雪脆’有20个特异响应。盐胁迫响应重叠的转录因子有27个,其中9个上调表达,18个下调表达。采用实时荧光定量PCR对几个转录因子进行了盐胁迫下的表达检测,其趋势与转录组分析结果基本一致。