scholarly journals Transcriptomic Analysis of Seasonal Gene Expression and Regulation during Xylem Development in “Shanxin” Hybrid Poplar (Populus davidiana × Populus bolleana)

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 451
Author(s):  
Chao Zhao ◽  
Youchao He ◽  
Ying Yu ◽  
Meiqi Zhou ◽  
Leifei Zhao ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cell Expansion ◽  
Hybrid Poplar ◽  
Wood Formation ◽  
Differentially Expressed ◽  
Cell Wall Biosynthesis ◽  
Growth Stages ◽  
Xylem Development ◽  
Go Terms ◽  
Different Growth Stages

Xylem development is a key process for wood formation in woody plants. To study the molecular regulatory mechanisms related to xylem development in hybrid poplar P. davidiana × P. bolleana, transcriptome analyses were conducted on developing xylem at six different growth stages within a single growing season. Xylem development and differentially expressed genes in the six time points were selected for a regulatory analysis. Xylem development was observed in stem sections at different growth stages, which showed that xylem development extended from the middle of April to early August and included cell expansion and secondary cell wall biosynthesis. An RNA-seq analysis of six samples with three replicates was performed. After transcriptome assembly and annotation, the differentially expressed genes (DEGs) were identified, and a Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and expression analysis of the DEGs were performed on each sample. On average, we obtained >20 million clean reads per sample, which were assembled into 84,733 nonredundant transcripts, of which there were 17,603 unigenes with lengths >1 kb. There were 14,890 genes that were differentially expressed among the six stages. The upregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S1 vs. S2 or S3 vs. S4 and, in GO terms, related to phytohormones in the S1 vs. S2 or S4 vs. S5 comparisons. The downregulated DEGs were enriched in GO terms related to cell wall biosynthesis between S4 vs. S5 or S5 vs. S6 and, in GO terms, related to hormones between S1 vs. S2 or S2 vs. S3. The KEGG pathways in the DEGs related to “phenylpropanoid biosynthesis”, “plant hormone signal transduction” and “starch and sucrose metabolism” were significantly enriched among the different stages. The DEGs related to cell expansion, polysaccharide metabolism and synthesis, lignin synthesis, transcription factors and hormones were identified. The identification of genes involved in the regulation of xylem development will increase our understanding of the molecular regulation of wood formation in trees and, also, offers potential targets for genetic manipulation to improve the properties of wood.

scholarly journals Identification of Differentially Expressed Genes Associated With Precocious Puberty by Suppression Subtractive Hybridization in Goat Pituitary Tissues

2020 ◽  
Author(s):  
Yufang Liu ◽  
Guiling Cao ◽  
Yujing Xie ◽  
Mingxing Chu
Keyword(s):  
Differentially Expressed Genes ◽  
Suppression Subtractive Hybridization ◽  
Precocious Puberty ◽  
Subtractive Hybridization ◽  
Differentially Expressed ◽  
Growth Stages ◽  
Kegg Pathways ◽  
Oocyte Meiosis ◽  
Go Terms ◽  
Different Growth Stages

Abstract Background Our study aimed to identify genes related to precocious puberty expressed in the pituitary of different growth stages goats using suppression subtractive hybridization (SSH) screening. Pituitary tissues at 30 day and 90 day and 180 day growth stages of Jining gray goats and Liaoning cashmere goats were used in this study. To identify differentially expressed genes in the pituitary tissues, mRNA from these tissues was extracted and SSH libraries were constructed for screening (API, EPI and BPI groups). ResultsA total of 60, 49 and 58 differently expression genes were annotation in the database. 222 Gene Ontology (GO) terms and 75 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were matched to those genes. Most differentially expressed genes (DEGs) related to the GO terms “structural constituent of ribosome”, “translation” and “GTP binding” were significantly enriched while numerous DEGs related to the Jak-STAT signaling and oocyte meiosis pathways were also significantly enriched. Candidate genes to be involved in precocious puberty and sexual development were retrieved from the SSH libraries. These related genes were discussed taking into account whether they were expressed in different growth stages of pituitary tissues, and of which them influenced the hypothalamic-pituitary-gonadal (HPG) axis. ConclusionsInteresting findings about precocious puberty related genes from an evolutionary perspective (such as PRLP0, EIF5A and YWHAH) and for putative future goats breeding applications are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of goats.

scholarly journals Differences in xylem development between Dutch and Japanese tomato (Solanum lycopersicum) correlate with cytokinin levels in hypocotyls

2020 ◽  
Vol 126 (2) ◽  
pp. 315-322 ◽  
Author(s):  
Xiaohua Qi ◽  
Hirokazu Takahashi ◽  
Yasushi Kawasaki ◽  
Yuya Ohta ◽  
Masahide Isozaki ◽  
...  
Keyword(s):  
High Yield ◽  
Growth Stages ◽  
Cytokinin Biosynthesis ◽  
Xylem Development ◽  
Isopentenyl Adenine ◽  
Use Efficiency ◽  
The Difference ◽  
Leaf Photosynthetic Rate ◽  
The Relationship ◽  
Different Growth Stages

Abstract Background and Aims Dutch tomato cultivars tend to have a greater yield than Japanese cultivars even if they are grown under the same conditions. Factors contributing to the increased yield of the Dutch cultivars were a greater light use efficiency and greater leaf photosynthetic rate. On the other hand, the relationship between tomato yields and anatomical traits is still unclear. The aim of this study is to identify the anatomical traits related to the difference in yield between Dutch and Japanese cultivars. Methods Anatomical properties were compared during different growth stages of Dutch and Japanese tomatoes. Hormone profiles and related gene expression in hypocotyls of Dutch and Japanese cultivars were compared in the hypocotyls of 3- and 4-week-old plants. Key results Dutch cultivars have a more developed secondary xylem than Japanese cultivars, which would allow for greater transport of water, mineral nutrients and phytohormones to the shoots. The areas and ratios of the xylem in the hypocotyls of 3- to 6-week-old plants were larger in the Dutch cultivars. In reciprocal grafts of the Japanese and Dutch cultivars, xylem development at the scion and rootstock depended on the scion cultivar, suggesting that some factors in the scion are responsible for the difference in xylem development. The cytokinin content, especially the level of N6-(Δ 2-isopentenyl) adenine (iP)-type cytokinin, was higher in the Dutch cultivars. This result was supported by the greater expression of Sl-IPT3 (a cytokinin biosynthesis gene) and Sl-RR16/17 (a cytokinin-responsive gene) in the Dutch cultivars. Conclusions These results suggest that iP-type cytokinins, which are locally synthesized in the hypocotyl, contribute to xylem development. The greater xylem development in Dutch cultivars might contribute to the high yield of the tomato.

Analysis of the Crushing Effect about Ultrasound on E. coli and B. subtilis

2012 ◽  
Vol 260-261 ◽  
pp. 1017-1021
Author(s):  
Xin Ying Wang ◽  
Yong Tao Liu ◽  
Min Hui ◽  
Ji Fei Xu
Keyword(s):  
Escherichia Coli ◽  
Cell Wall ◽  
Bacillus Subtilis ◽  
Bacterial Cell ◽  
Logarithmic Phase ◽  
Growth Stages ◽  
Bacterial Cells ◽  
E Coli ◽  
Different Growth Stages ◽  
Main Factor

Escherichia coli and Bacillus subtilis as objects of the study, ultrasonic fragmentation acted on the bacterial cells in different growth stages, results showed that, it’s similar to the crushing effect of ultrasound on E. coli and B. subtilis cells of different growth stages, the highest crushing rate in the logarithmic phase, reached to 95.8% and 94.3% respectively, the crushing rate of adjustment phase is lowest, maintained at around 60%, the crushing rate stability cell was centered, which can be achieved 90%. The structure of the bacterial cell wall didn’t the main factor to decide the ultrasonic fragmentation effect, but different growth periods of bacterial cells did the determinant.

scholarly journals Transcriptomic Profiling of Cryptomeria fortunei Hooibrenk Vascular Cambium Identifies Candidate Genes Involved in Phenylpropanoid Metabolism

Forests ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 766
Author(s):  
Junjie Yang ◽  
Zhenhao Guo ◽  
Yingting Zhang ◽  
Jiaxing Mo ◽  
Jiebing Cui ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Southern China ◽  
Expression Profiles ◽  
Wood Formation ◽  
Differentially Expressed ◽  
Myb Transcription Factor ◽  
Growth Stages ◽  
Phenylpropanoid Metabolism ◽  
Protein Database ◽  
Cambial Zone

Cryptomeria fortunei Hooibrenk (Chinese cedar) is a coniferous tree from southern China that has an important function in landscaping and timber production. Lignin is one of the key components of secondary cell walls, which have a crucial role in conducting water and providing mechanical support for the upward growth of plants. It is mainly biosynthesized via the phenylpropanoid metabolic pathway, of which the molecular mechanism remains so far unresolved in C. fortunei. In order to obtain further insight into this pathway, we performed transcriptome sequencing of the C. fortunei cambial zone at 5 successive growth stages. We generated 78,673 unigenes from transcriptome data, of which 45,214 (57.47%) were successfully annotated in the non-redundant protein database (NR). A total of 8975 unigenes were identified to be significantly differentially expressed between Sample_B and Sample_A after analyzing their expression profiles. Of the differentially expressed genes (DEGs), 6817 (75.96%) and 2158 (24.04%) were up- and down-regulated, respectively. 83 DEGs were involved in phenylpropanoid metabolism, 37 DEGs that encoded v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factor (TF), and many candidates that encoded lignin synthesizing enzymes. These findings contribute to understanding the expression pattern of C. fortunei cambial zone transcriptome. Furthermore, our results provide additional insight towards understanding the molecular mechanisms of wood formation in C. fortunei.

scholarly journals Free and Cell Wall-Bound Polyamines under Long-Term Water Stress Applied at Different Growth Stages of ×Triticosecale Wittm

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0135002 ◽  
Author(s):  
Tomasz Hura ◽  
Michał Dziurka ◽  
Katarzyna Hura ◽  
Agnieszka Ostrowska ◽  
Kinga Dziurka
Keyword(s):  
Cell Wall ◽  
Water Stress ◽  
Growth Stages ◽  
Different Growth Stages

scholarly journals Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane

2021 ◽  
Vol 12 ◽  
Author(s):  
Guilherme Kenichi Hosaka ◽  
Fernando Henrique Correr ◽  
Carla Cristina da Silva ◽  
Danilo Augusto Sforça ◽  
Fernanda Zatti Barreto ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cellulose Synthase ◽  
Carbon Partitioning ◽  
Differentially Expressed ◽  
Soluble Solids ◽  
Time Shift ◽  
Cell Wall Biosynthesis ◽  
Sucrose Accumulation ◽  
Time Points ◽  
Genes Encoding

Multiple genes in sugarcane control sucrose accumulation and the biosynthesis of cell wall components; however, it is unclear how these genes are expressed in its apical culms. To better understand this process, we sequenced mRNA from +1 stem internodes collected from four genotypes with different concentrations of soluble solids. Culms were collected at four different time points, ranging from six to 12-month-old plants. Here we show differentially expressed genes related to sucrose metabolism and cell wall biosynthesis, including genes encoding invertases, sucrose synthase and cellulose synthase. Our results showed increased expression of invertases in IN84-58, the genotype with lower sugar and higher fiber content, as well as delayed expression of secondary cell wall-related cellulose synthase for the other genotypes. Interestingly, genes involved with hormone metabolism were differentially expressed across time points in the three genotypes with higher soluble solids content. A similar result was observed for genes controlling maturation and transition to reproductive stages, possibly a result of selection against flowering in sugarcane breeding programs. These results indicate that carbon partitioning in apical culms of contrasting genotypes is mainly associated with differential cell wall biosynthesis, and may include early modifications for subsequent sucrose accumulation. Co-expression network analysis identified transcription factors related to growth and development, showing a probable time shift for carbon partitioning occurred in 10-month-old plants.

Effects of Molybdenum on Cell Wall Component of Wheat Leaf Under Different Growth Stages

2021 ◽  
Author(s):  
Xiaozhen Yang ◽  
Qiaoqiao Gan ◽  
Xuecheng Sun ◽  
Songwei Wu ◽  
Qiling Tan ◽  
...  
Keyword(s):  
Cell Wall ◽  
Growth Stages ◽  
Cell Wall Component ◽  
Wheat Leaf ◽  
Different Growth Stages
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