Differences in hepatic gene expression as a major distinguishing factor between Korean native pig and Yorkshire

There are phenotypic differences between Korean native pig (KNP) and Yorkshire (YS) breeds due to different interests in selection. YS has been selected for industrial interests such as a growth rate and lean meat production, while KNP has been maintained as a regional breed with local interests such as disease resistance and fat content in and between muscle. A comparison of gene expression profiles from liver tissue reflected overall long-term effects of artificial selection for these two pig breeds. Based on minimum positive false discovery rate (less than 10%) and fold change (|FC|>1.5), 73 differentially expressed genes (DEGs) were identified. Functional analysis of these DEGs indicated clear distinctions in signaling capacity related to epidermal growth factor (EGF), extracellular structure, protein metabolism, and detoxification. Hepatic DEGs demonstrated the importance of hormonal and metabolic capabilities to differences between these two pig breeds.     

Transcriptional alteration of p53 related processes as a key factor for skeletal muscle characteristics in <Emphasis Type="Italic">Sus scrofa</Emphasis>

The pig could be a useful model to characterize molecular aspects determining several delicate phenotypes because they have been bred for those characteristics. The Korean native pig (KNP) is a regional breed in Korea that was characterized by relatively high intramuscular fat content and reddish meat color compared to other western breeds such as Yorkshire (YS). YS grew faster and contained more lean muscle than KNP. We compared the KNP to Yorksire to find molecular clues determining muscle characteristics. The comparison of skeletal gene expression profiles between these two breeds showed molecular differences in muscle. We found 82 differentially expressed genes (DEGs) defined by fold change (more than 1.5 fold difference) and statistical significance (within 5% of false discovery rate). Functional analyses of these DEGs indicated up-regulation of most genes involved in cell cycle arrest, down-regulation of most genes involved in cellular differentiation and its inhibition, down-regulation of most genes encoding component of muscular-structural system, and up-regulation of most genes involved in diverse metabolism in KNP. Especially, DEGs in above-mentioned categories included a large number of genes encoding proteins directly or indirectly involved in p53 pathway. Our results indicated a possible role of p53 to determine muscle characteristics between these two breeds.     

西方蜜蜂工蜂蛹响应低温胁迫的差异表达基因分析

【目的】本研究旨在从转录组水平筛选和分析西方蜜蜂Apis mellifera工蜂不同时期蛹对低温胁迫反应的差异表达基因(DEGs)。【方法】将西方蜜蜂工蜂封盖后3 d预蛹以及封盖后6和9 d蛹分别置于低温环境(20℃)和最适发育温度(35℃)中4 h,分别作为处理组和对照组,通过转录组学技术筛选低温处理组与对应的对照组之间的DEGs,并进行GO功能分类和KEGG通路分析。利用RT qPCR分别对封盖后3 d预蛹以及封盖后6和9 d蛹的8, 6和5个DEGs的表达谱进行验证。【结果】与对照组相比,封盖后3 d预蛹以及封盖后6和9 d蛹受低温胁迫后的DEGs分别有220, 50和26个;GO功能分类发现,DEGs富集数最多的条目为代谢进程、细胞进程、催化活性和结合,封盖后3 d预蛹的DEGs在生物学进程调控、细胞部分和细胞器等有较多富集。KEGG通路分析显示,处理组和对照组间西方蜜蜂各日龄DEGs在整体概述图、氨基酸代谢、信号转导、运输和分解代谢有富集。封盖后3 d预蛹以及封盖后6和9 d蛹受低温胁迫后共有的DEG 3-磷酸肌醇依赖性蛋白激酶1基因PDK1上调表达,同时富集在自噬-动物、mTOR和FoxO信号通路。低温胁迫后,封盖后3 d预蛹的胰岛素受体底物1-B基因IRS1-B和Kruppel同源物1基因Kr-h1上调表达,而核激素受体FTZ-F1基因Ftz-F1与蜕皮启动激素基因Eth显著下调表达,说明封盖后3 d预蛹响应低温细胞自噬和蜕皮受到抑制程度更大。在低温胁迫后封盖后6 d蛹中与昆虫角质层着色与免疫相关的酪氨酸羟化酶基因TyHyd下调表达;与对照组相比,在低温胁迫后封盖后9 d蛹中DEGs最少,说明在3个蛹期中,其受低温的影响较小。【结论】本研究测定了西方蜜蜂3个不同发育阶段蛹响应低温的DEGs,结果显示大部分DEGs为阶段特有,说明西方蜜蜂不同发育阶段响应低温的机制不同。一些共有DEGs以及阶段特有DEGs的功能研究和其作用机制是进一步研究蜜蜂对低温响应机制的重点内容,为探究蜜蜂蛹期响应低温胁迫的分子机制提供了基础数据。     

金针菇成熟期和伸长期菌盖的转录组与蛋白组比较分析

菌盖是大型真菌的重要组成部分,也是其产生有性孢子的部位,但是其发育机制仍不明确。本研究以金针菇Flammulina filiformis为材料,采用转录组和蛋白组联合分析的方法,比较分析了金针菇成熟期和伸长期菌盖的差异基因与蛋白,并对其进行GO (gene ontology)功能聚类分析、KEGG (Kyoto encyclopedia of genes and genomes)富集分析和蛋白互作网络分析。本研究筛选到差异表达基因有1 391个,差异表达蛋白147个,均以上调表达为主。GO功能聚类分析结果表明,催化活性(catalytic activity)条目富集基因最多,其次是细胞组分(cell part)、细胞过程(cellular process)和细胞器(organelle)。KEGG富集分析结果表明,差异表达基因和蛋白主要富集在碳水化合物代谢通路(carbohydrate metabolism)和氨基酸代谢通路(amino acid metabolism)等。本研究选取了9个关键的差异表达基因,使用实时荧光定量PCR (real-time quantitative PCR,RT-qPCR)对其表达量进行了验证。RT-qPCR验证结果与转录组测序结果相一致。蛋白互作网络分析表明,水解酶类、结构域类和转录调节类蛋白为互作网络的主要结点。本研究联合转录组、蛋白组测序数据,通过分析差异基因与蛋白,为深入了解金针菇菌盖发育机制提供数据参考。     

低温胁迫下意大利蜜蜂预蛹的差异表达基因趋势分析

【目的】蜜蜂是典型的具有发育狭温性的全变态昆虫。本研究以对低温最敏感的意大利蜜蜂Apis mellifera ligustica预蛹为研究对象,通过低温胁迫不同时间的差异表达基因(differentially expressed genes, DEGs)趋势分析,探讨低温胁迫对蜜蜂发育影响的关键基因。【方法】对3日龄意大利蜜蜂封盖子预蛹进行20℃低温胁迫18 h(T18)和36 h(T36),以未经低温胁迫的预蛹为对照(CK),通过Illumina HiSeq~(TM)平台进行转录组学测定。利用Short Time-series Expression Miner(STEM)软件对2个处理组与对照组比较共有的差异表达基因进行趋势分析,再进一步对显著富集趋势模式中富集的差异表达基因进行GO分类和KEGG pathway分析。利用RT-qPCR对随机挑选的5个DEGs的表达模式进行验证。【结果】对检测到1 062个T18 vs CK和T36 vs CK共有的DEGs进行趋势分析,发现3个显著的基因表达模式,包括2个上调表达模式(Profile 6,有539个基因;Profile 7,有271个基因),1个下调表达模式(Profile 1,有183个基因)。对3个显著富集趋势模式DEGs分别进行GO富集分析和KEGG pathway分析,在Profile 6中找到同时富集在FoxO信号通路和寿命调节信号通路上的胰岛素样肽基因ILP和叉头蛋白O基因FoxO持续上调,说明低温胁迫会影响蜜蜂预蛹蜕皮激素信号传递;在Profile 7中CREB结合蛋白基因CBP持续上调,蜜蜂预蛹受到低温胁迫会影响细胞发育;在Profile 1中细胞色素P450基因CYP450 306a1 (phm)和WNT1显著下调,说明化蛹时受到低温胁迫会影响蜕皮激素的合成。通过RT-qPCR分析挑选的5个基因的表达结果和高通量测序结果一致。【结论】通过对蜜蜂响应低温胁迫的差异表达基因趋势分析发现,蜜蜂胰岛素和蜕皮激素共同调控的FoxO可能是低温胁迫抑制蜜蜂化蛹的一个关键基因。本研究为探索低温胁迫影响蜜蜂发育变态的分子调控机制奠定了基础。