De Novo Assembly and Transcriptome Profiling of Ethiopian Lowland Bamboo Oxytenanthera Abyssinica (A. rich) Munro Under Drought and Salt Stresses

Background: Bamboos are perennial grasses classified under family Poaceae and subfamily Bambusoideae and are among the fastest growing plants on earth. Despite ecological and economic significances, Ethiopian lowland bamboo (O. abyssinica) lacks global gene expression under abiotic stress. Methods: Plastic pot germinated seedlings of O. abyssinica were subjected to 200 µm NaCl and 25% PEG-6000 (Poly Ethylene glycol) to induce salt and drought stress, respectively. Using the Illumina sequencing platform, fifteen cDNA libraries were constructed and sequenced to generate the first drought and salt stress transcriptome profiling of the species so as to elucidate genome-wide transcriptome changes in response to such stresses. Results: Following quality control, 754,444,646 clean paired-ends reads were generated, and then de novo assembled into 406,181 unigenes. Functional annotation against the public databases presented annotation of 217,067 (53.4%) unigenes, where NCBI-Nr 203,777, Swissport 115,741, COG 81,632 and KEGG 80,587. Prediction of Transcripts Factors (TFs) have generated 4,332 TFs organized into 64 TF families. Analysis of Differentially Expressed Genes (DEGs) provided 65,471 genes where 569 genes belong to all stresses. Protein families with a higher number of differentially expressed genes include bZIP (49), WRKY (43), MYB (38), AP2/ERF (30), HD-ZIP (25) and MYB related (21). Conclusion: In addition to revealing the genome-wide level appraisal of transcriptome resources of the species, this study also uncovered the comprehensive understanding of key stress responsive protein-coding genes, protein families and pathways which could be used as the basis for further studies.

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De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

BMC Genomics ◽

10.1186/s12864-021-07715-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yu-Fu Gao ◽

Dong-Hui Zhao ◽

Jia-Qi Zhang ◽

Jia-Shuo Chen ◽

Jia-Lin Li ◽

...

Keyword(s):

Differentially Expressed Genes ◽

De Novo ◽

Regulatory Genes ◽

Differentially Expressed ◽

Anthocyanin Synthesis ◽

Leaf Color ◽

Metabolite Analysis ◽

Color Formation ◽

Content Change ◽

Final Color

Abstract Background Leaf color is an important ornamental trait of colored-leaf plants. The change of leaf color is closely related to the synthesis and accumulation of anthocyanins in leaves. Acer pseudosieboldianum is a colored-leaf tree native to Northeastern China, however, there was less knowledge in Acer about anthocyanins biosynthesis and many steps of the pathway remain unknown to date. Results Anthocyanins metabolite and transcript profiling were conducted using HPLC and ESI-MS/MS system and high-throughput RNA sequencing respectively. The results demonstrated that five anthocyanins were detected in this experiment. It is worth mentioning that Peonidin O-hexoside and Cyanidin 3, 5-O-diglucoside were abundant, especially Cyanidin 3, 5-O-diglucoside displayed significant differences in content change at two periods, meaning it may be play an important role for the final color. Transcriptome identification showed that a total of 67.47 Gb of clean data were obtained from our sequencing results. Functional annotation of unigenes, including comparison with COG and GO databases, yielded 35,316 unigene annotations. 16,521 differentially expressed genes were identified from a statistical analysis of differentially gene expression. The genes related to leaf color formation including PAL, ANS, DFR, F3H were selected. Also, we screened out the regulatory genes such as MYB, bHLH and WD40. Combined with the detection of metabolites, the gene pathways related to anthocyanin synthesis were analyzed. Conclusions Cyanidin 3, 5-O-diglucoside played an important role for the final color. The genes related to leaf color formation including PAL, ANS, DFR, F3H and regulatory genes such as MYB, bHLH and WD40 were selected. This study enriched the available transcriptome information for A. pseudosieboldianum and identified a series of differentially expressed genes related to leaf color, which provides valuable information for further study on the genetic mechanism of leaf color expression in A. pseudosieboldianum.

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Corrigendum to “Transcriptome de novo assembly and analysis of differentially expressed genes related to cytoplasmic male sterility in onion” [Plant Physiol. Biochem. 125 (2018) 35–44]

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2018.06.038 ◽

2018 ◽

Vol 129 ◽

pp. 437

Author(s):

Qiaoling Yuan ◽

Ce Song ◽

Luyao Gao ◽

Huihui Zhang ◽

Cuicui Yang ◽

...

Keyword(s):

Cytoplasmic Male Sterility ◽

Male Sterility ◽

Differentially Expressed Genes ◽

De Novo Assembly ◽

De Novo ◽

Differentially Expressed ◽

Onion Plant

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Suppression Subtractive Hybridization cDNA Libraries to Identify Differentially Expressed Genes from Contrasting Fish Habitats

Marine Biotechnology ◽

10.1007/s10126-004-3146-6 ◽

2004 ◽

Vol 6 (4) ◽

pp. 386-399 ◽

Cited By ~ 22

Author(s):

Peter F. Straub ◽

Mary L. Higham ◽

Arnaud Tanguy ◽

Brenda J. Landau ◽

William C. Phoel ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Suppression Subtractive Hybridization ◽

Subtractive Hybridization ◽

Differentially Expressed ◽

Cdna Libraries ◽

Fish Habitats

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Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

BioMed Research International ◽

10.1155/2016/3702789 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Liangbin Zeng ◽

Airong Shen ◽

Jia Chen ◽

Zhun Yan ◽

Touming Liu ◽

...

Keyword(s):

Protein Function ◽

Molecular Mechanisms ◽

Defense Mechanism ◽

Natural Fiber ◽

De Novo ◽

Average Length ◽

Expression Patterns ◽

Transcriptome Profiling ◽

Cdna Libraries ◽

Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

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Transcriptome analysis ofSchistosoma mansonilarval development using serial analysis of gene expression (SAGE)

Parasitology ◽

10.1017/s0031182009005733 ◽

2009 ◽

Vol 136 (5) ◽

pp. 469-485 ◽

Cited By ~ 22

Author(s):

A. S. TAFT ◽

J. J. VERMEIRE ◽

J. BERNIER ◽

S. R. BIRKELAND ◽

M. J. CIPRIANO ◽

...

Keyword(s):

Gene Expression ◽

Sequence Data ◽

Subsequent Development ◽

Differentially Expressed ◽

Cdna Libraries ◽

Genome Wide ◽

A Genome ◽

Genome Wide Expression ◽

Cell Conditioned Medium

SUMMARYInfection of the snail,Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke,Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of theS. mansonimiracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia andin vitrocultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of theB. glabrataembryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to theS. mansonigene predictions (v4.0e) either by estimating theoretical 3′ UTR lengths or using existing 3′ EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

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RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.662002 ◽

2021 ◽

Vol 8 ◽

Author(s):

Kirsten E. McLoughlin ◽

Carolina N. Correia ◽

John A. Browne ◽

David A. Magee ◽

Nicolas C. Nalpas ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Mycobacterium Bovis ◽

Peripheral Blood ◽

Post Infection ◽

Time Course ◽

De Novo ◽

Differentially Expressed Gene ◽

Differentially Expressed ◽

Infection Time ◽

Time Point

Bovine tuberculosis, caused by infection with members of the Mycobacterium tuberculosis complex, particularly Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including RNA sequencing, has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analysed the transcriptome of bovine whole peripheral blood samples collected at −1 week pre-infection and +1, +2, +6, +10, and +12 weeks post-infection time points. Differentially expressed genes were catalogued and evaluated at each post-infection time point relative to the −1 week pre-infection time point and used for the identification of putative candidate host transcriptional biomarkers for M. bovis infection. Differentially expressed gene sets were also used for examination of cellular pathways associated with the host response to M. bovis infection, construction of de novo gene interaction networks enriched for host differentially expressed genes, and time-series analyses to identify functionally important groups of genes displaying similar patterns of expression across the infection time course. A notable outcome of these analyses was identification of a 19-gene transcriptional biosignature of infection consisting of genes increased in expression across the time course from +1 week to +12 weeks post-infection.

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Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries (Fragaria×ananassa)

PeerJ ◽

10.7717/peerj.4976 ◽

2018 ◽

Vol 6 ◽

pp. e4976 ◽

Cited By ~ 10

Author(s):

Panpan Hu ◽

Gang Li ◽

Xia Zhao ◽

Fengli Zhao ◽

Liangjie Li ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Fruit Ripening ◽

Fruit Development ◽

Transcriptome Profiling ◽

Differentially Expressed ◽

Fragaria Ananassa ◽

Mads Box ◽

Cell Wall Modification ◽

Ripening Process ◽

Fruit Development And Ripening

Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste, and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. A total of fiveubiquitin-conjugating enzymesand 10MADS-box transcription factorswere differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics inFragaria × ananassa.

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