Identification and characterization of the Remorin gene family in Saccharum and the involvement of ScREM1.5e-1/-2 in SCMV infection on sugarcane

IntroductionRemorins (REMs) are plant-specific membrane-associated proteins that play important roles in plant–pathogen interactions and environmental adaptations. Group I REMs are extensively involved in virus infection. However, little is known about the REM gene family in sugarcane (Saccharum spp. hyrid), the most important sugar and energy crop around world.MethodsComparative genomics were employed to analyze the REM gene family in Saccharum spontaneum. Transcriptomics or RT-qPCR were used to analyze their expression files in different development stages or tissues under different treatments. Yeast two hybrid, bimolecular fluorescence complementation and co-immunoprecipitation assays were applied to investigate the protein interaction.ResultsIn this study, 65 REMs were identified from Saccharum spontaneum genome and classified into six groups based on phylogenetic tree analysis. These REMs contain multiple cis-elements associated with growth, development, hormone and stress response. Expression profiling revealed that among different SsREMs with variable expression levels in different developmental stages or different tissues. A pair of alleles, ScREM1.5e-1/-2, were isolated from the sugarcane cultivar ROC22. ScREM1.5e-1/-2 were highly expressed in leaves, with the former expressed at significantly higher levels than the latter. Their expression was induced by treatment with H2O2, ABA, ethylene, brassinosteroid, SA or MeJA, and varied upon Sugarcane mosaic virus (SCMV) infection. ScREM1.5e-1 was localized to the plasma membrane (PM), while ScREM1.5e-2 was localized to the cytoplasm or nucleus. ScREM1.5e-1/-2 can self-interact and interact with each other, and interact with VPgs from SCMV, Sorghum mosaic virus, or Sugarcane streak mosaic virus. The interactions with VPgs relocated ScREM1.5e-1 from the PM to the cytoplasm.DiscussionThese results reveal the origin, distribution and evolution of the REM gene family in sugarcane and may shed light on engineering sugarcane resistance against sugarcane mosaic pathogens

An Extractive-and-Abstractive Framework for Source Code Summarization

(Source) Code summarization aims to automatically generate summaries/comments for a given code snippet in the form of natural language. Such summaries play a key role in helping developers understand and maintain source code. Existing code summarization techniques can be categorized into extractive methods and abstractive methods. The extractive methods extract a subset of important statements and keywords from the code snippet using retrieval techniques, and generate a summary that preserves factual details in important statements and keywords. However, such a subset may miss identifier or entity naming, and consequently, the naturalness of generated summary is usually poor. The abstractive methods can generate human-written-like summaries leveraging encoder-decoder models from the neural machine translation domain. The generated summaries however often miss important factual details. To generate human-written-like summaries with preserved factual details, we propose a novel extractive-and-abstractive framework. The extractive module in the framework performs a task of extractive code summarization, which takes in the code snippet and predicts important statements containing key factual details. The abstractive module in the framework performs a task of abstractive code summarization, which takes in the entire code snippet and important statements in parallel and generates a succinct and human-written-like natural language summary. We evaluate the effectiveness of our technique, called EACS, by conducting extensive experiments on three datasets involving six programming languages. Experimental results show that EACS significantly outperforms state-of-the-art techniques in terms of all three widely used metrics, including BLEU, METEOR, and ROUGH-L