scholarly journals Comparing Time Series Transcriptome Data Between Plants Using A Network Module Finding Algorithm

2019 ◽  
Author(s):  
Jiyoung Lee ◽  
Lenwood S. Heath ◽  
Ruth Grene ◽  
Song Li
Keyword(s):  
Plant Species ◽  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Network Module ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
R Programming Language ◽  
Homologous Genes ◽  
R Programming

ABSTRACTComparative transcriptome analysis is the comparison of expression patterns between homologous genes in different species. Since most molecular mechanistic studies in plants have been performed in model species including Arabidopsis and rice, comparative transcriptome analysis is particularly important for functional annotation of genes in other plant species. Many biological processes, such as embryo development, are highly conserved between different plant species. The challenge is to establish one-to-one mapping of the developmental stages between two species. In this protocol, we solve this problem by converting the gene expression patterns into a co-expression network and then apply network module-finding algorithms to the cross-species co-expression network. We describe how to perform such analysis using bash scripts for preliminary data processing and R programming language, which implemented simulated annealing method for module finding. We also provide instructions on how to visualize the resulting co-expression networks across species.

scholarly journals Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Huini Tang ◽  
...  
Keyword(s):  
Circadian Rhythm ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Genetic Constitution ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Extracellular Region

Abstract Background: Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in cotton is poorly understood. Results: Three stable performing F1 hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation, and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results. Conclusions: Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic process may control vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.

scholarly journals Comparative Transcriptome Analysis of Two Races of Heterodera glycines at Different Developmental Stages

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e91634 ◽  
Author(s):  
Gaofeng Wang ◽  
Deliang Peng ◽  
Bingli Gao ◽  
Wenkun Huang ◽  
Lingan Kong ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Heterodera Glycines ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis

A Comprehensive Ultrastructure and Transcriptome Analyses of Early Regeneration in Ophryotrocha Xiamen Sp. Nov. (Annelida: Dorvilleidae)

2020 ◽  
Author(s):  
Ruanni Chen ◽  
Irum Mukhtar ◽  
Shurong Wei ◽  
Siyi Wu ◽  
Jianming Chen
Keyword(s):  
Transcriptome Analysis ◽  
Expression Patterns ◽  
Model Organisms ◽  
Suitable Model ◽  
Potential Candidate ◽  
Comparative Transcriptome ◽  
Coastal Zones ◽  
Model Species ◽  
Comparative Transcriptome Analysis ◽  
Early Regeneration

Abstract BackgroundIn recent years, significant progress has been made using powerful genetic approaches with newly developed models for understanding on regeneration, however, the molecular and cellular basis of early regeneration remains unclear. Annelids of the genus Ophryotrocha have long been subjects of research use as model species in ecological, toxicological, reproductive, and regenerative investigations. Although, Ophryotrocha spp., are amenable to molecular, cellular, and functional analyses, still in need to explore new model organisms in this genus to understand regeneration mechanisms. Here, we focus on a newly identified Ophryotrocha species for its early regeneration developmental mode.ResultsBased on detailed morphological (K-maxillae, rosette gland, and chromosome number) and molecular analyses, we present, O. xiamen as a new suitable model species to investigate the early regeneration mechanism. The comparative transcriptome analysis showed the gene expression patterns were related to transcriptional regulation, energy metabolism profiles and structure and signal transduction during early stages of regeneration. Data also exhibited that genes such as neurotrypsin, Nos2, DMBT1, SCO spondin, and endotubin associated to regulate inflammation, enterocyte differentiation, apoptosis, and neuroepithelial, were up-regulated during early regeneration stages (wound healing and blastema formation). Additionally, most of the known regeneration-related genes of annelids were also identified in O. xiamen which enabled to explore the precise functions of genes involved in regeneration process.ConclusionsThis study enriches the identification of genus Ophryotrocha in Chinese coastal zones, an area with high abundances of annelids. The comparative transcriptome analysis provided the whole expression changes during early regeneration process. Morphology and molecular shred of evidences in O. xiamen revealed similar features of early regeneration with other invertebrates. Information on potential candidate genes associated with early regeneration in O. xiamen, will be useful for further studies.

scholarly journals Comparative transcriptome analysis reveals ectopic delta-5 and delta-6 desaturases enhance protective gene expression upon Vibrio vulnificus challenge in Tilapia (Oreochromis niloticus)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pin-Yang Tu ◽  
Shin-Jie Huang ◽  
Venugopal Rajanbabu ◽  
Jen-Leih Wu ◽  
Jyh-Yih Chen
Keyword(s):  
Transcriptome Analysis ◽  
Post Infection ◽  
Vibrio Vulnificus ◽  
Expression Patterns ◽  
Comparative Transcriptome ◽  
Wild Type ◽  
Comparative Transcriptome Analysis ◽  
Enhanced Resistance ◽  
Gene Enrichment ◽  
Transgenic Tilapia

Abstract Background Tilapia (Oreochromis niloticus) cultures are frequently infected by Vibrio vulnificus, causing major economic losses to production units. Previously, tilapia expressing recombinant delta-5 desaturase and delta-6 desaturase (D56) were found to be resistant to V. vulnificus infection. In this report, we profile the D56-mediated molecular changes underlying this resistance in tilapia. A comparative transcriptome analysis was performed on V. vulnificus-infected wild-type and D56-transgenic tilapia using Illumina’s sequencing-by-synthesis approach. Gene enrichment analysis on differentially expressed unigenes was performed, and the expression patterns were validated by real-time PCR. Results Comparative transcriptome analysis was performed on RNA-sequence profiles obtained from wild-type and D56-transgenic tilapia at 0, 6 and 24 h post-infection with V. vulnificaus. GO and KEGG gene enrichment analyses showed that D56 regulates several pathways and genes, including fatty acid (FA) metabolism associated, and inflammatory and immune response. Expression of selected FA metabolism-associated, inflammatory and immune responsive genes was validated by qPCR. The inflammatory and immune responsive genes that are modulated by FA-associated D56 likely contribute to the enhanced resistance against V. vulnificus infection in Tilapia. Conclusions Transcriptome profiling and filtering for two-fold change variation showed that 3795 genes were upregulated and 1839 genes were downregulated in D56-transgenic tilapia. These genes were grouped into pathways, such as FA metabolism, FA elongation, FA biosynthesis, biosynthesis of unsaturated FA, FA degradation, inflammation, immune response, and chemokines. FA-associated genes and immune-related genes were modulated by D56 at 6 h and 24 h post infection with V. vulnificus. The expression patterns of FA-related genes, inflammatory genes, antimicrobial peptide genes and immune responsive genes at 0, 3, 6, 12, 24 and 48 h post-infection suggests these genes are involved in the enhanced resistance of D56 transgenic tilapia to V. vulnificus.

Comparative transcriptome analysis of developmental stages of theLimonium bicolorleaf generates insights into salt gland differentiation

2015 ◽  
Vol 38 (8) ◽  
pp. 1637-1657 ◽  
Author(s):  
FANG YUAN ◽  
MING-JU AMY LYU ◽  
BING-YING LENG ◽  
GUANG-YONG ZHENG ◽  
ZHONG-TAO FENG ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Salt Gland ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis

scholarly journals Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton

2019 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Huini Tang ◽  
...  
Keyword(s):  
Circadian Rhythm ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
F1 Hybrids ◽  
Pcr Analysis ◽  
Genetic Constitution ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Extracellular Region

Abstract Background: Heterosis breeding is the most useful method for yield increment around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in hybrid cotton is poorly understood. Results: Three stable performing F1 hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated that expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found that several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results. Conclusions: Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic processes may be controlled vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.

scholarly journals Comparative transcriptome analysis reveals sesquiterpenoid biosynthesis among 1-, 2- and 3-year old Atractylodes chinensis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jianhua Zhao ◽  
Chengzhen Sun ◽  
Fengyu Shi ◽  
Shanshan Ma ◽  
Jinshuang Zheng ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Squalene Epoxidase ◽  
Sequencing Analysis ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Qrt Pcr

Abstract Background Atractylodes chinensis (DC.) Koidz is a well-known medicinal plant containing the major bioactive compound, atractylodin, a sesquiterpenoid. High-performance liquid chromatography (HPLC) analysis demonstrated that atractylodin was most abundant in 3-year old A. chinensis rhizome, compared with those from 1- and 2-year old rhizomes, however, the molecular mechanisms underlying accumulation of atractylodin in rhizomes are poorly understood. Results In this study, we characterized the transcriptomes from rhizomes of 1-, 2- and 3-year old (Y1, Y2 and Y3, respectively) A. chinensis, to identify differentially expressed genes (DEGs). We identified 240, 169 and 131 unigenes encoding the enzyme genes in the mevalonate (MVA), methylerythritol phosphate (MEP), sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. To confirm the reliability of the RNA sequencing analysis, eleven key gene encoding factors involved in the sesquiterpenoid and triterpenoid biosynthetic pathway, as well as in pigment, amino acid, hormone and transcription factor functions, were selected for quantitative real time PCR (qRT-PCR) analysis. The results demonstrated similar expression patterns to those determined by RNA sequencing, with a Pearson’s correlation coefficient of 0.9 between qRT-PCR and RNA-seq data. Differential gene expression analysis of rhizomes from different ages revealed 52 genes related to sesquiterpenoid and triterpenoid biosynthesis. Among these, seven DEGs were identified in Y1 vs Y2, Y1 vs Y3 and Y2 vs Y3, of which five encoded four key enzymes, squalene/phytoene synthase (SS), squalene-hopene cyclase (SHC), squalene epoxidase (SE) and dammarenediol II synthase (DS). These four enzymes directly related to squalene biosynthesis and subsequent catalytic action. To validate the result of these seven DEGs, qRT-PCR was performed and indicated most of them displayed lower relative expression in 3-year old rhizome, similar to transcriptomic analysis. Conclusion The enzymes SS, SHC, SE and DS down-regulated expression in 3-year old rhizome. This data corresponded to the higher content of sesquiterpenoid in 3-year old rhizome, and confirmed by qRT-PCR. The results of comparative transcriptome analysis and identified key enzyme genes laid a solid foundation for investigation of production sesquiterpenoid in A. chinensis.

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