Comparative transcriptome analysis of the cold resistance of the sterile rice line 33S

Rice (Oryza sativa L.) is one of the most important species for food production worldwide. Low temperature is a major abiotic factor that affects rice germination and reproduction. Here, the underlying regulatory mechanism in seedlings of a TGMS variety (33S) and a cold-sensitive variety (Nipponbare) was investigated by comparative transcriptome. There were 795 differentially expressed genes (DEGs) identified only in cold-treated 33S, suggesting that 33S had a unique cold-resistance system. Functional and enrichment analysis of these DEGs revealed that, in 33S, several metabolic pathways, such as photosynthesis, amino acid metabolism, secondary metabolite biosynthesis, were significantly repressed. Moreover, pathways related to growth and development, including starch and sucrose metabolism, and DNA biosynthesis and damage response/repair, were significantly enhanced. The expression of genes related to nutrient reserve activity were significantly up-regulated in 33S. Finally, three NAC and several ERF transcription factors were predicted to be important in this transcriptional reprogramming. This present work provides valuable information for future investigations of low-temperature response mechanisms and genetic improvement of cold-tolerant rice seedlings.

Comparative Transcriptome and WGCNA RevealKey Genes Involved in Lignocellulose Degradation in Sarcomyxa Edulis

In order to explore the molecular mechanism of Sarcomyxa edulis response to lignocelluloses degradation, the developmental transcriptomes was analyzed for six stages covering the whole developmental process, including mycelium growing to half bag (B1), mycelium in cold stimulation after full bag (B2), mycelium in primordia appearing (B3), primordia (B4), mycelium at the harvest stage (B5) and mature fruiting body (B6). A total of 6 samples were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, we constructed a co-expression network of weighted genes associated with extracellular enzyme physiological traits by WGCNA, and obtained 19 gene co-expression modules closely related to lignocelluloses degradation. In addition, a number of key genes involved in lignocelluloses degradation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of Sarcomyxa edulis lignocelluloses degradation.

Comparative Transcriptome Analysis of Gayal (Bos frontalis), Yak (Bos grunniens), and Cattle (Bos taurus) Reveal the High-Altitude Adaptation

Gayal and yak are well adapted to the local high-altitude environments, yet the transcriptional regulation difference of the plateau environment among them remains obscure. Herein, cross-tissue and cross-species comparative transcriptome analysis were performed for the six hypoxia-sensitive tissues from gayal, yak, and cattle. Gene expression profiles for all single-copy orthologous genes showed tissue-specific expression patterns. By differential expression analysis, we identified 3020 and 1995 differentially expressed genes (DEGs) in at least one tissue of gayal vs. cattle and yak vs. cattle, respectively. Notably, we found that the adaptability of the gayal to the alpine canyon environment is highly similar to the yak living in the Qinghai-Tibet Plateau, such as promoting red blood cell development, angiogenesis, reducing blood coagulation, immune system activation, and energy metabolism shifts from fatty acid β-oxidation to glycolysis. By further analyzing the common and unique DEGs in the six tissues, we also found that numerous expression regulatory genes related to these functions are unique in the gayal and yak, which may play important roles in adapting to the corresponding high-altitude environment. Combined with WGCNA analysis, we found UQCRC1, COX5A are the shared differentially expression hub genes related to the energy supply of myocardial contraction in the heart-related modules of gayal and yak, and CAPS is a shared differentially hub gene among the hub genes of the lung-related module, which is related to pulmonary artery smooth muscle contraction. Additionally, EDN3 is the unique differentially expression hub gene related to the tracheal epithelium and pulmonary vasoconstriction in the lung of gayal. CHRM2 is a unique differentially expression hub gene that was identified in the heart of yak, which has an important role in the autonomous regulation of the heart. These results provide a basis for further understanding the complex transcriptome expression pattern and the regulatory mechanism of high-altitude domestication of gayal and yak.

Transcriptome Analysis Reveals the Inducing Effect of Bacillus siamensis on Disease Resistance in Postharvest Mango Fruit

Postharvest anthracnose, caused by the fungus Colletotrichum gloeosporioides, is one of the most important postharvest diseases of mangoes worldwide. Bacillus siamensis (B. siamensis), as a biocontrol bacteria, has significant effects on inhibiting disease and improving the quality of fruits and vegetables. In this study, pre-storage application of B. siamensis significantly induced disease resistance and decreased disease index (DI) of stored mango fruit. To investigate the induction mechanisms of B. siamensis, comparative transcriptome analysis of mango fruit samples during the storage were established. In total, 234,808 unique transcripts were assembled and 56,704 differentially expressed genes (DEGs) were identified by comparative transcriptome analysis. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs showed that most of the DEGs involved in plant-pathogen interaction, plant hormone signal transduction, and biosynthesis of resistant substances were enriched. Fourteen DEGs related to disease-resistance were validated by qRT-PCR, which well corresponded to the FPKM value obtained from the transcriptome data. These results indicate that B. siamensis treatment may act to induce disease resistance of mango fruit by affecting multiple pathways. These findings not only reveal the transcriptional regulatory mechanisms that govern postharvest disease, but also develop a biological strategy to maintain quality of post-harvest mango fruit.