scholarly journals Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Kathleen Greenham ◽  
Ryan C Sartor ◽  
Stevan Zorich ◽  
Ping Lou ◽  
Todd C Mockler ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Network Models ◽  
Transcript Level ◽  
Rapid Expansion ◽  
Genetic Redundancy ◽  
Circadian Expression ◽  
Genome Wide ◽  
Important Challenge

An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Here we describe the circadian transcriptome in the polyploid crop Brassica rapa. Strikingly, almost three-quarters of the expressed genes exhibited circadian rhythmicity. Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. We observed genome-wide expansion of the circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal evidence for divergence between B. rapa paralogs that may be driven in part by variation in conserved non-coding sequences (CNS). Additionally, differential drought response among retained paralogous pairs suggests further functional diversification. These findings support the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new approach for assessing paralog activity at the transcript level.

Expression characterisation of cyclophilin BrROC1 during light treatment and abiotic stresses response in Brassica rapa subsp. rapa ‘Tsuda’

2018 ◽  
Vol 45 (12) ◽  
pp. 1223 ◽  
Author(s):  
Haifang Yan ◽  
Bo Zhou ◽  
Wei He ◽  
Yuzhe Nie ◽  
Yuhua Li
Keyword(s):  
Blue Light ◽  
Brassica Rapa ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Transcript Level ◽  
Light Treatment ◽  
Anthocyanin Synthesis ◽  
Root Epidermis ◽  
High Or Low Temperature ◽  
Level Analysis

ROC1 is a prototypic peptidyl prolyl cis/trans isomerase (PPIase) of the plant cytosol belonging to the large subfamily of cyclophilins that are associated with diverse functions through foldase, scaffolding, chaperoning or other unknown activities. Although many functions of plant cyclophilins have been reported, the molecular basis of stress-responsive expression of plant cyclophilins is still largely unknown. To characterise the roles of BrROC1 during light treatment and their responses in various abiotic stresses, we identified BrROC1 genes and characterised their expression patterns in Brassica rapa subsp. rapa ‘Tsuda’. Our results showed that BrROC1 genes are multi-family genes. Transcript level analysis showed BrROC1-2 expressed higher than BrROC1-1 in 0 to 6-day-old seedlings under natural light. Moreover, BrROC1-2 genes were also induced to highly express in the cotyledon, upper hypocotyls and lower hypocotyls of seedlings under UV-A and blue-light treatment. In addition, the transcript level of BrROC1-1 was higher in pigment tissues than that in unpigment tissues (cotyledon and lower hypocotyl) under UV-A and blue-light treatment. Furthermore, when the unpigment epidermis (shaded light) of 2-month-old ‘Tsuda’ turnip roots was exposed to UV-A light, transcript levels of the BrROC1-1 and BrROC1-2 were significantly increased with time prolongation. These two BrROC1 genes might be involved in UV-A-induced anthocyanin synthesis in the root epidermis of ‘Tsuda’ turnip, which accumulates high levels of anthocyanin. These two BrROC1 genes were also induced to be regulated by abiotic stresses such as high or low temperature, dehydration, osmotic and salt stresses. Then, the results indicate that BrROC1 genes are involved in light induction response and may play important roles in adaptation of plants to various environmental stresses.

scholarly journals Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

2020 ◽  
Author(s):  
Kathleen Greenham ◽  
Ryan C. Sartor ◽  
Stevan Zorich ◽  
Ping Lou ◽  
Todd C. Mockler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Regulatory Network ◽  
Time Course ◽  
Expression Patterns ◽  
Time Of Day ◽  
Circadian Regulation ◽  
Genome Wide ◽  
Circadian Control ◽  
Gene Regulatory

AbstractAn important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Gene expression is one method for determining the activity of paralogs; however, the majority of transcript abundance data represents a static point that does not consider the spatial and temporal dynamics of the transcriptome. Studies in Arabidopsis have estimated up to 90% of the transcriptome to be under diel or circadian control depending on the condition. As a result, time of day effects on the transcriptome have major implications on how we characterize gene activity. In this study, we aimed to resolve the circadian transcriptome in the polyploid crop Brassica rapa and explore the fate of multicopy orthologs of Arabidopsis circadian regulated genes. We performed a high-resolution time course study with 2 h sampling density to capture the genes under circadian control. Strikingly, more than two-thirds of expressed genes exhibited rhythmicity indicative of circadian regulation. To compare the expression patterns of paralogous genes, we developed a program in R called DiPALM (Differential Pattern Analysis by Linear Models) that analyzes time course data to identify transcripts with significant pattern differences. Using DiPALM, we identified genome-wide divergence of expression patterns among retained paralogs. Cross-comparison with a previously generated diel drought experiment in B. rapa revealed evidence for differential drought response for these diverging paralog pairs. Using gene regulatory network models we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal additional evidence for divergence in expression between B. rapa paralogs that may be driven in part by variation in conserved non coding sequences. These findings provide new insight into the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new method for assessing paralog activity at the transcript level.SignificanceThe circadian regulation of the transcriptome leads to time of day changes in gene expression that coordinates environmental conditions with physiological responses. Brassica rapa, a morphologically diverse crop species, has undergone whole genome triplication since diverging from Arabidopsis resulting in an expansion of gene copy number. To examine how this expansion has influenced the circadian transcriptome we developed a new method for comparing gene expression patterns. This method facilitated the discovery of genome-wide expansion of expression patterns for genes present in multiple copies and divergence in temporal abiotic stress response. We find support for conserved sequences outside the gene body contributing to these expression pattern differences and ultimately generating new connections in the gene regulatory network.

scholarly journals Genome-wide identification of expansin gene family reveals expansin genes are involved in fibre cells growth in cotton

2019 ◽  
Author(s):  
Limin Lv ◽  
Dongyun Zuo ◽  
Xingfen Wang ◽  
Hailiang Cheng ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Cotton Fibre ◽  
Plant Cell Walls ◽  
Biological Functions ◽  
Qpcr Analysis ◽  
Genome Wide ◽  
Fibre Development ◽  
Initiation Stage

Abstract Background : Expansins ( EXPs ), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family are still unknown in cotton. Results: In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum . These genes were classified into four subfamilies, including 67 GhEXPAs , eight GhEXPBs , six GhEXLAs , and 12 GhEXLBs , and divided into 15 subgroups. All 93 expansin genes are distributed over 24 chromosomes excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns in different stages of cotton fibre development. Among them, three genes ( GhEXPA4o , GhEXPA1A , and GhEXPA8h ) were highly expressed in the initiation stage, nine genes ( GhEXPA4a , GhEXPA13a , GhEXPA4f , GhEXPA4q , GhEXPA8f , GhEXPA2 , GhEXPA8g , GhEXPA8a , and GhEXPA4n ) had high expression during the fast elongation stage, while GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. Conclusions: Our results provide a solid basis for further elucidation of biological functions of expansin genes in cotton fibre development and valuable genetic resources used for crop improvement in the future.

scholarly journals Genome-Wide Identification, Phylogeny, Evolution and Expression Patterns of AP2/ERF Genes and Cytokinin Response Factors in Brassica rapa ssp. pekinensis

PLoS ONE ◽  
2013 ◽  
Vol 8 (12) ◽  
pp. e83444 ◽  
Author(s):  
Zhenning Liu ◽  
Lijun Kong ◽  
Mei Zhang ◽  
Yanxia Lv ◽  
Yapei Liu ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Expression Patterns ◽  
Response Factors ◽  
Genome Wide ◽  
Cytokinin Response

scholarly journals Genome-wide identification of the expansin gene family reveals that expansin genes are involved in fibre cell growth in cotton

2020 ◽  
Author(s):  
Limin Lv ◽  
Dongyun Zuo ◽  
Xingfen Wang ◽  
Hailiang Cheng ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Cell Growth ◽  
Gene Family ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Cotton Fibre ◽  
Plant Cell Walls ◽  
Biological Functions ◽  
Genome Wide ◽  
Fibre Development ◽  
Initiation Stage

Abstract Background : Expansins ( EXPs ), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family in cotton are still unknown. Results: In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum . These genes were classified into four subfamilies, including 67 GhEXPAs , 8 GhEXPBs , 6 GhEXLAs , and 12 GhEXLBs , and divided into 15 subgroups. The 93 expansin genes are distributed over 24 chromosomes, excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons, and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns among different stages of cotton fibre development. Among them, 3 genes ( GhEXPA4o , GhEXPA1A , and GhEXPA8h ) were highly expressed in the initiation stage, 9 genes ( GhEXPA4a , GhEXPA13a , GhEXPA4f , GhEXPA4q , GhEXPA8f , GhEXPA2 , GhEXPA8g , GhEXPA8a , and GhEXPA4n ) had high expression during the fast elongation stage, and GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. Conclusions: Our results provide a solid basis for further elucidation of the biological functions of expansin genes in relation to cotton fibre development and valuable genetic resources for future crop improvement.

scholarly journals Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10934
Author(s):  
Ruihua Wang ◽  
Taili Han ◽  
Jifeng Sun ◽  
Ligong Xu ◽  
Jingjing Fan ◽  
...  
Keyword(s):  
Gene Family ◽  
Brassica Rapa ◽  
Expression Patterns ◽  
Structural Evolution ◽  
Amino Acid Residues ◽  
Rna Seq ◽  
Cis Acting ◽  
Genome Wide ◽  
Genome Triplication

Ovate family proteins (OFPs) are a class of proteins with a conserved OVATE domain that contains approximately 70 amino acid residues. OFP proteins are plant-specific transcription factors that participate in regulating plant growth and development and are widely distributed in many plants. Little is known about OFPs in Brassica rapa to date. We identified 29 OFP genes in Brassica rapa and found that they were unevenly distributed on 10 chromosomes. Intron gain events may have occurred during the structural evolution of BraOFP paralogues. Syntenic analysis verified Brassica genome triplication, and whole genome duplication likely contributed to the expansion of the OFP gene family. All BraOFP genes had light responsive- and phytohormone-related cis-acting elements. Expression analysis from RNA-Seq data indicated that there were obvious changes in the expression levels of six OFP genes in the Brassica rapa hybrid, which may contribute to the formation of heterosis. Finally, we found that the paralogous genes had different expression patterns among the hybrid and its parents. These results provide the theoretical basis for the further analysis of the biological functions of OFP genes across the Brassica species.

scholarly journals Genome-wide identification of expansin gene family reveals expansin genes are involved in fibre cells growth in cotton

2019 ◽  
Author(s):  
Limin Lv ◽  
Dongyun Zuo ◽  
Xingfen Wang ◽  
Hailiang Cheng ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Cotton Fibre ◽  
Plant Cell Walls ◽  
Biological Functions ◽  
Qpcr Analysis ◽  
Genome Wide ◽  
Fibre Development ◽  
Initiation Stage

Abstract Background : Expansins ( EXPs ), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family are still unknown in cotton. Results: In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum . These genes were classified into four subfamilies, including 67 GhEXPAs , 8 GhEXPBs , 6 GhEXLAs , and 12 GhEXLBs , and divided into 15 subgroups. All 93 expansin genes are distributed over 24 chromosomes excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns in different stages of cotton fibre development. Among them, 3 genes ( GhEXPA4o , GhEXPA1A , and GhEXPA8h ) were highly expressed in the initiation stage, 9 genes ( GhEXPA4a , GhEXPA13a , GhEXPA4f , GhEXPA4q , GhEXPA8f , GhEXPA2 , GhEXPA8g , GhEXPA8a , and GhEXPA4n ) had high expression during the fast elongation stage, while GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. Conclusions: Our results provide a solid basis for further elucidation of biological functions of expansin genes in cotton fibre development and valuable genetic resources used for crop improvement in the future.

scholarly journals Genome-wide identification of expansin gene family reveals expansin genes are involved in fibre cells growth in cotton

2020 ◽  
Author(s):  
Limin Lv ◽  
Dongyun Zuo ◽  
Xingfen Wang ◽  
Hailiang Cheng ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Cotton Fibre ◽  
Plant Cell Walls ◽  
Biological Functions ◽  
Qpcr Analysis ◽  
Genome Wide ◽  
Fibre Development ◽  
Initiation Stage

Abstract Background : Expansins ( EXPs ), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family are still unknown in cotton. Results: In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum . These genes were classified into four subfamilies, including 67 GhEXPAs , 8 GhEXPBs , 6 GhEXLAs , and 12 GhEXLBs , and divided into 15 subgroups. All 93 expansin genes are distributed over 24 chromosomes excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns in different stages of cotton fibre development. Among them, 3 genes ( GhEXPA4o , GhEXPA1A , and GhEXPA8h ) were highly expressed in the initiation stage, 9 genes ( GhEXPA4a , GhEXPA13a , GhEXPA4f , GhEXPA4q , GhEXPA8f , GhEXPA2 , GhEXPA8g , GhEXPA8a , and GhEXPA4n ) had high expression during the fast elongation stage, while GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. Conclusions: Our results provide a solid basis for further elucidation of biological functions of expansin genes in cotton fibre development and valuable genetic resources used for crop improvement in the future.

scholarly journals Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types

2021 ◽  
Vol 12 ◽  
Author(s):  
Natalia Petrova ◽  
Alsu Nazipova ◽  
Oleg Gorshkov ◽  
Natalia Mokshina ◽  
Olga Patova ◽  
...  
Keyword(s):  
Cell Wall ◽  
Higher Plants ◽  
Expression Patterns ◽  
Transcript Level ◽  
Genome Wide ◽  
Distinct Cell ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Search ◽  
Encoding Genes

The genomes of higher plants encode a variety of proteins with lectin domains that are able to specifically recognize certain carbohydrates. Plants are enriched in a variety of potentially complementary glycans, many of which are located in the cell wall. We performed a genome-wide search for flax proteins with lectin domains and compared the expression of the encoding genes in different stem tissues that have distinct cell wall types with different sets of major polysaccharides. Over 400 genes encoding proteins with lectin domains that belong to different families were revealed in the flax genome; three quarters of these genes were expressed in stem tissues. Hierarchical clustering of the data for all expressed lectins grouped the analyzed samples according to their characteristic cell wall type. Most lectins differentially expressed in tissues with primary, secondary, and tertiary cell walls were predicted to localize at the plasma membrane or cell wall. These lectins were from different families and had various architectural types. Three out of four flax genes for proteins with jacalin-like domains were highly upregulated in bast fibers at the stage of tertiary cell wall deposition. The dynamic changes in transcript level of many genes for lectins from various families were detected in stem tissue over the course of gravitropic response induced by plant gravistimulation. The data obtained in this study indicate a large number of lectin-mediated events in plants and provide insight into the proteins that take part in tissue specialization and reaction to abiotic stress.

scholarly journals Author response: Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

2020 ◽  
Author(s):  
Kathleen Greenham ◽  
Ryan C Sartor ◽  
Stevan Zorich ◽  
Ping Lou ◽  
Todd C Mockler ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Expression Patterns ◽  
Author Response ◽  
Genome Wide
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