Characterization by Suppression Subtractive Hybridization of Transcripts That Are Differentially Expressed in Leaves of Anthracnose-Resistant Ramie Cultivar

For the purpose of screening putative anthracnose resistance-related genes of ramie (Boehmeria nivea L. Gaud), a cDNA library was constructed by suppression subtractive hybridization using anthracnose-resistant cultivar Huazhu no. 4. The cDNAs from Huazhu no. 4, which were infected with Colletotrichum gloeosporioides, were used as the tester and cDNAs from uninfected Huazhu no. 4 as the driver. Sequencing analysis and homology searching showed that these clones represented 132 single genes, which were assigned to functional categories, including 14 putative cellular functions, according to categories established for Arabidopsis. These 132 genes included 35 disease resistance and stress tolerance-related genes including putative heat-shock protein 90, metallothionein, PR-1.2 protein, catalase gene, WRKY family genes, and proteinase inhibitor-like protein. Partial disease-related genes were further analyzed by reverse transcription PCR and RNA gel blot. These expressed sequence tags are the first anthracnose resistance-related expressed sequence tags reported in ramie

Survival and Genome Diversity of <i>Vibrio parahaemolyticus</i> Isolated from Edible Aquatic Animals

Vibrio parahaemolyticus can cause acute gastroenteritis, wound infection, and septicemia in humans. The waterborne bacterium is frequently isolated from aquatic products worldwide. Nevertheless, little information in genome evolution of V. parahaemolyticus isolated from aquatic animals is yet available. Here we overcome this limitation by specifying six V. parahaemolyticus isolates recovered from edible shellfish, fish, and crustacean. Most isolates with multiple resistance phenotypes grew optimally at 3% NaCl and pH 8.5. Draft genome sequences of the six V. parahaemolyticus isolates (4,937,042 bp to 5,067,778 bp) were determined using the Illumina Hiseq × 10 sequencing platform. Comparative genomic analyses revealed 4622 to 4791 predicted protein-encoding genes, of which 1064 to 1107 were of unknown function. Various mobile genetic elements (MGEs) were identified in the V. parahaemolyticus genomes, including genome islands (n = 5 to 9), prophage gene clusters (n = 0 to 2), integrons (n = 1 to 11), and insertion sequences (n = 0 to 3). A number of antibiotic-resistant (n = 17 to 20), virulence-associated (n = 77 to 79), and strain-specific (n = 131 to 287) genes were also identified, indicating possible horizontal gene transfer via the MGEs and considerable genome variation in the V. parahaemolyticus isolates. Altogether, the results of this study fill prior gaps in our knowledge of the genome evolution of V. parahaemolyticus, as isolated from edible aquatic animals

Identification and Expression Analysis of the PIN and AUX/LAX Gene Families in Ramie (Boehmeria nivea L. Gaud)

Auxin regulates diverse aspects of growth and development. Furthermore, polar auxin transport, which is mediated by the PIN-FORMED (PIN) and AUXIN1/LIKE-AUX (AUX/LAX) proteins, plays a crucial role in auxin distribution. In this study, six PIN and four AUX/LAX genes were identified in ramie (Boehmeria nivea L.). We used qRT-PCR to characterize and analyze the two gene families, including phylogenetic relationships, intron/exon structures, cis-elements, subcellular localization, and the expression patterns in different tissues. The expression of these genes in response to indole-3-acetic acid (IAA) treatment and drought stress was also assessed; the results indicate that most of the BnAUX/LAX and BnPIN genes were regulated as a result of IAA treatment and drought stress. Our study provides insights into ramie auxin transporters and lays the foundation for further analysis of their biological functions in ramie fiber development and adaptation to environmental stresses

Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)-Based Comparative Proteome Analysis of the Response of Ramie under Drought Stress

In this study, we conducted the first isobaric tags for relative and absolute quantitation (isobaric tags for relative and absolute quantitation (iTRAQ))-based comparative proteomic analysis of ramie plantlets after 0 (minor drought stress), 24 (moderate drought stress), and 72 h (severe drought stress) of treatment with 15% (w/v) poly (ethylene glycol)6000 (PEG6000) to simulate drought stress. In our study, the association analysis of proteins and transcript expression revealed 1244 and 968 associated proteins identified in leaves and roots, respectively. L1, L2, and L3 are leaf samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups, a total of 118, 216, and 433 unique proteins were identified as differentially expressed during L1 vs. L2, L2 vs. L3, and L1 vs. L3, respectively. R1, R2, and R3 are root samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups，a total of 124, 27, and 240 unique proteins were identified as differentially expressed during R1 vs. R2, R2 vs. R3, and R1 vs. R3, respectively. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was significantly upregulated in roots in response to drought stress. This enhancement may result in more glycolytically generated adenosine triphosphate (ATP) in roots to adapt to adverse environmental conditions. To obtain complementary information related to iTRAQ data, the mRNA levels of 12 proteins related to glycolysis/gluconeogenesis in leaves and 7 in roots were further analyzed by qPCR. Most of their expression levels were higher in R3 than R1 and R2, suggesting that these compounds may promote drought tolerance by modulating the production of available energy

Transcriptome Profiling and Identification of Transcription Factors in Ramie (Boehmeria nivea L. Gaud) in Response to PEG Treatment, Using Illumina Paired-End Sequencing Technology

Ramie (Boehmeria nivea L. Gaud), commonly known as China grass, is a perennial bast fiber plant of the Urticaceae. In China, ramie farming, industry, and trade provide income for about five million people. Drought stress severely affects ramie stem growth and causes a dramatic decrease in ramie fiber production. There is a need to enhance ramie’s tolerance to drought stress. However, the drought stress regulatory mechanism in ramie remains unknown. Water stress imposed by polyethylene glycol (PEG) is a common and convenient method to evaluate plant drought tolerance. In this study, transcriptome analysis of cDNA collections from ramie subjected to PEG treatment was conducted using Illumina paired-end sequencing, which generated 170 million raw sequence reads. Between leaves and roots subjected to 24 (L2 and R2) and 72 (L3 and R3) h of PEG treatment, 16,798 genes were differentially expressed (9281 in leaves and 8627 in roots). Among these, 25 transcription factors (TFs) from the AP2 (3), MYB (6), NAC (9), zinc finger (5), and bZIP (2) families were considered to be associated with drought stress. The identified TFs could be used to further investigate drought adaptation in ramie

Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of Ramie (Boehmeria nivea L. Gaud).

In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system

Comparation Test on High-Quality Flax Resources for Oil and Fiber Production in Kazakhstan

Oil flax stems are often burnt because of the low fiber content; this issue is especially serious in Kazakhstan. To solve this problem, this study aimed to determine which flax resources could exhibit a significant increase in stem yield without a decrease in seed yield. In a previous study in 2019, we tested seven types of flax stems at the research site of the S. Seifullin KATU campus. Here, a further investigation of the same resources, which was conducted in 2020, is described. According to the results, the UF03, UF05, and UF06 showed higher dynamics of plant height in the budding and blooming stages compared to a local Kazakhstani variety; this result greatly differed compared with the data from 2019. UF03 yielded the best oil quality, especially in terms of the linolenic acid and linoleic acid contents. UF02 had good performance in terms of yield and the largest fat content of all resources. More foreign flax resources should be introduced to improve the development of the flax industry in Kazakhstan

The Mechanisms Underlying Physiological and Molecular Responses to Waterlogging in Flax

Waterlogging due to excessive rainfall has become a factor limiting flax production in southern China. This has led to morphology alteration, and biomass and yield reduction in field crop production. Flax variety Zhongyama 1 was planted in sand culture, and the adaptive mechanisms of the responses to waterlogging in the fast growth and harvest stage were determined. According to the results, height and total biomass decreased significantly under waterlogged conditions during the fast growth period; furthermore, in the harvest stage, flax height increased significantly, whereas the technical length, fork diameter, and weight decreased significantly. For gene expression, the gene of glucose, glutathione metabolism, was up-regulated in shoot, and the gene of phenylpropanoid metabolic, lignin, was up-regulated in root. The results suggested that the synthesis and degradation of lignin is involved in flax resistance to waterlogging, especially in terms of phenylpropanoid biosynthesis, glycolysis, and metabolism of plant hormone signal transduction. Furthermore, unpaired electrons flowing through the electron transport chain may react with oxygen to produce ROS and hamper plant growth, development, and survival