两种家猪心脏组织基因表达谱的分析

选取丹麦成年长白母猪的心脏、肌肉、主动脉、左心室和中国成年二花脸母猪心脏共5种组织,建立相应的cDNA文库,在此基础上测定了35180条表达序列标签。通过比较分析长白猪4种组织的基因表达,找出了长白猪心脏组织中3个显著高表达的功能群和47个显著高表达的基因。长白猪心脏组织在分子伴侣活动、马达活动和生理过程中表达的基因较多,47个显著高表达的基因都是和运动、运动调节、能量及保护有关的基因。两种家猪心脏组织表达差异显著的基因有74个,并且绝大部分是在长白猪心脏中表达更高,显示出长白猪心脏组织生理活动的高效与旺盛。     

南蛇藤假种皮形成过程中萜类合成基因的表达分析

为探究南蛇藤（Celastrus orbiculatus Thunb.）假种皮发育过程中萜类物质合成相关基因的表达差异,本文选取3个不同发育时期（盛花期、落花期和幼果期）的南蛇藤雌花为实验材料,构建3个cDNA文库,通过Illumina HiSeq^TM 2000平台进行转录组测序,共获得87600个unigene序列,平均长度为453bp,N50/N90比值为4.64。通过3个不同发育阶段基因差异表达的比较及功能富集分析,鉴定出16个萜类合成相关基因,其中8个基因的编码蛋白参与调控7个萜类合成代谢位点。还确定了与萜类合成相关的7个转录因子家族的成员数量以及相对表达量最高的基因。     

Systematic isolation of genes expressed at low levels in inflorescence apices of Arabidopsis thaliana.

We constructed an equalized cDNA library from Arabidopsis inflorescence shoot apices including inflorescence meristem, floral meristem and flower tissue collected before stage 5 of flower development. The cDNA clones were arrayed on membranes and were differentially screened using cDNA pools from vegetative and inflorescence tissues as probes. Each clone was classified by expression specificity and expression level. By removing the clones that displayed hybridization signals, 384 out of 3264 clones in this library remained as candidates for inflorescence-specific mRNAs expressed at low levels. Sequence analysis of all selected clones indicated that 53 were identical and 120 were homologous to genes in public protein databases. The remaining 211 selected clones had no significant amino acid sequence similarities with those deduced from any reported genes, though 62 of them appeared in Arabidopsis expressed sequenced tags (ESTs). About 40% of the selected clones were novel, validating the present approach for gene discovery. Northern blot analysis of 22 randomly selected clones confirmed that most were expressed preferentially in inflorescence tissues. In addition, many clones were transcribed at relatively low levels. We demonstrate that the screening method of the present study is useful for systematic classification of cDNA species based on expression specificity.     

光诱导香菇菌丝转色阶段的转录因子表达分析

转录因子在真菌环境响应及生理过程中发挥重要的调节作用。本文利用转录组测序（RNA-Seq）技术研究光诱导香菇菌丝转色过程中的转录因子表达变化。转录组测序结果表明,在光照条件下转色的菌丝（313C）与黑暗条件下未转色的菌丝（313W）相比,香菇菌丝中共有68个转录因子基因表达发生变化（48个转录因子上调表达,20个转录因子下调表达）;转色的菌丝（313C）与初始未转色的菌丝（118）相比,香菇菌丝中有80个转录因子基因表达发生变化（49个转录因子上调表达,31个转录因子下调表达）。这些差异表达的转录因子包括WD40、MADS-box、MYB和GATA等家族。另外,样品的两两比较中差异表达的转录因子既存在部分重叠,也表现特异性。其中,313C/313W中有14个特异性差异表达转录因子,313C/118中有26个特异差异表达的转录因子。重叠的转录因子有64个,其中有39个表达水平上调,15个表达水平下调。采用实时荧光定量PCR对几个转录因子进行了表达检测,其中部分转录因子的表达趋势与转录组分析基本相同。这些数据为进一步研究香菇转色的转录调控奠定了一定的基础。     

Genome-Wide Identification and Analysis of Genes Encoding Proteolytic Enzymes in Pineapple

Pineapple, Ananas comosus, is an economically important fruit crop. Recently its genome was completely sequenced and a total of 27,024 protein coding genes were predicted. Using a set of well evaluated bioinformatics tools we have predicted the protein subcellular locations and comparatively analyzed the protein conserved domains of the predicted proteomes in pineapple, Oryza sativa (rice), Sorghum bicolor (sorghum), and Brachypodium distachyson. Our analysis revealed that ~24–26 % of proteins were located in nucleus, 17–21 % in cytosol, 9–11 % in chloroplast, and 8–11 % proteins were secreted in these monocot plants. The secretomes in the four species were analyzed comparatively and a large number of secreted glycosyl hydrolases were identified. As pineapple proteolytic enzymes, knowns as bromelains, have been used for medical treatments, we focused on genome-wide identification and analysis of pineapple genes encoding proteases. A total of 512 pineapple genes encoding putative proteolytic enzymes were identified, with 152 secreted, 74 localized in cytosol, 67 in nucleus, 60 in chloroplast, 18 in mitochondria, and the remaining in other subcellular locations. The top large protease families in pineapple were papain family cysteine protease (62 genes), peptidase S8 family (56 genes), aspartyl protease family (38 genes), and serine carboxypeptidase (33 genes). Gene expression analysis revealed that among 512 protease genes 432 were expressed in various tissues and 72 genes were differentially expressed. The highly expressed protease genes were identified including 7 papain family cysteine proteases. The protease genes with the predicted protein subcellular locations will facilitate the efforts for examining their biological roles in pineapple growth and development and for expressing the recombinant proteases for medical use. The information of protein subcellular location of all plant species can be accessed at the PlantSecKB website (http://proteomics.ysu.edu/secretomes/plant.php).