Genome-Wide Functional Analysis of Cotton (Gossypium hirsutum) in Response to Drought

Cotton is one of the most important crops for its natural textile fibers in the world. However, it often suffered from drought stress during its growth and development, resulting in a drastic reduction in cotton productivity. Therefore, study on molecular mechanism of cotton drought-tolerance is very important for increasing cotton production. To investigate molecular mechanism of cotton drought-resistance, we employed RNA-Seq technology to identify differentially expressed genes in the leaves of two different cultivars (drought-resistant cultivar J-13 and drought-sensitive cultivar Lu-6) of cotton. The results indicated that there are about 13.38% to 18.75% of all the unigenes differentially expressed in drought-resistant sample and drought-sensitive control, and the number of differentially expressed genes was increased along with prolonged drought treatment. DEG (differentially expression gene) analysis showed that the normal biophysical profiles of cotton (cultivar J-13) were affected by drought stress, and some cellular metabolic processes (including photosynthesis) were inhibited in cotton under drought conditions. Furthermore, the experimental data revealed that there were significant differences in expression levels of the genes related to abscisic acid signaling, ethylene signaling and jasmonic acid signaling pathways between drought-resistant cultivar J-13 and drought-sensitive cultivar Lu-6, implying that these signaling pathways may participate in cotton response and tolerance to drought stress.     

Transcriptome analysis of Arabidopsis clubroots indicate a key role for cytokinins in disease development

The clubroot disease of the family Brassicaceae is caused by the obligate biotrophic protist Plasmodiophora brassicae. Infected roots undergo a developmental switch that results in the formation of aberrant roots (clubs). To investigate host gene expression during the development of the disease, we have used the Arabidopsis ATH1 genome array. Two timepoints were chosen, an early timepoint at which the pathogen has colonized the root but has induced only very limited change of host cell and root morphology and a later timepoint at which more than 60% of the host root cells were colonized and root morphology was drastically altered. At both timepoints, more than 1,000 genes were differentially expressed in infected versus control roots. These included genes associated with growth and cell cycle, sugar phosphate metabolism, and defense. The involvement of plant hormones in club development was further supported; genes involved in auxin homeostasis, such as nitrilases and members of the GH3 family, were upregulated, whereas genes involved in cytokinin homeostasis (cytokinin synthases and cytokinin oxidases/dehydrogenases) were already strongly downregulated at the early timepoint. Cytokinin oxidase/dehydrogenase overexpressing lines were disease resistant, clearly indicating the importance of cytokinin as a key factor in clubroot disease development.     

利用RNA-seq数据分析肝细胞癌差异表达基因及蛋白相互作用

RNA-Seq已成为当前转录组学研究的强有力工具,尤其在肿瘤差异表达基因的筛选方面有重要的应用价值。为进一步阐明肝细胞癌(HCC)的分子机制,本研究对GEO中1个包括12对HCC组织标本的RNA-Seq数据集(GSE63863)进行了生物信息学分析。采用edgeR、DESeq2、voom等3种不同算法的软件进行统计分析,共获得976个差异表达基因(adj. p-value<0.01或FDR<0.01,|logFC|≥2),其中上调表达422个(43.2%),下调554个(56.8%)。GO富集分析显示这些差异表达基因主要涉及离子结合、氧化还原酶活性等分子功能以及氧化还原、细胞分裂等生物学过程;KEGG通路分析显示,这些差异表达基因主要涉及细胞周期、视黄醇等代谢通路。STRING分析显示,共有654个基因编码的蛋白质存在相互作用,进一步利用MCODE分析显示,169个基因编码蛋白构成4个子网络,相应的中心节点基因分别为UBE2C、GNG4、TTR、FOS,这些基因的异常表达可能在HCC的发生发展过程中具有重要作用。上述研究结果将为进一步阐明HCC分子发病机制、寻找新型生物标志物提供初步的依据。     

Gene expression profiling during gland morphogenesis of a mutant and a glandless upland cotton

To identify genes involved in pigment gland morphogenesis in cotton, gene expression was profiled using genechip (Affymetrix) during pigment gland morphogenesis in cotton variety Xiangmian-18, which has glandless seeds but glanded plants, and a glandless line, N5. The results showed that 303 genes were differentially expressed by a factor greater than two during gland morphogenesis; 59% (180) of these genes shared similarity with known genes in GenBank. These genes play roles in defense response, response to oxidative stress, peroxidase activity, and other metabolic pathways. KOBAS (KEGG Orthology-Based Annotation System) indicate that these genes are involved in 68 biochemical pathways. These findings suggest that the related defense response, gossypol biosynthesis pathway and other complex regulation may be associated with pigment gland morphogenesis in cotton. The results may provide a basis for further study and serve as a guide for related research.     

Chromatin reorganization and endogenous auxin/cytokinin dynamic activity during somatic embryogenesis of cultured cotton cell

We conducted a systematic assessment and comparative study on the biochemical and cellular characteristics of cultured cotton cells during the entire process of somatic embryogenesis (SE). All staged cultures were widely investigated in this assay. Cell and tissue ectogenesis manipulation combined with flow cytometry (FCM) was employed to cellular study during the whole totipotency process of dedifferentiation and redifferentiation. We identified two phases of chromatin decondensation during the dedifferentiation and redifferentiation. At the same time, sharp increase in the ratio of indoleacetic acid (IAA), isopentenyladenosine group (iPAs) at the same stage of cell dedifferentiation and redifferentiation process serve as distinct biochemical maker of dedifferentiation and SE initiation with the unique feature. Our results suggest the two phases of chromatin reorganization associated with endogenous auxin/cytokinin dynamic activity may underlie dedifferentiation and redifferentiation during the entire SE process in cotton.