Genome-wide identification of microRNAs associated with the somatic embryogenesis in Eucalyptus

Abstract Background: MicroRNAs (miRNAs) are a class of small noncoding RNAs with 18-24 nucleotides in length and function in many biological processes in plant. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis of Eucalyptus is still poor. Here we reported for the first time the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus cultivars and identified miRNAs involved in the somatic embryogenesis of Eucalyptus.Results: Stem and tissue-culture induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla, and were used as differentiated and dedifferentiated samples, respectively. We generated 346.4 million reads for 12 samples (n=3) and identified 888 miRNA precursors (197 known and 691 novel) which can produce 1,067 mature miRNAs. These miRNAs were mainly distributed in chromosomes Chr03, Chr05 and Chr08, and can produce 46 miRNA clusters. In these samples we detected 998 miRNAs with TPM (transcripts per million reads) > 5 and found that highly expressed miRNAs varied across samples. We identified 327 and 343 differentially expressed miRNAs in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. Dysregulated miRNAs shared by the two cultivars might be involved in the development of embryonic callus of Eucalyptus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399 and MIR482. We also identified 81 up-regulated (e.g., miR159c-3p, miR167a-5p, miR397a-3p, miR397c-5p, miR397d-3p, miR397d-5p, N-miR1-5p and N-miR5-5p) and 67 down-regulated (e.g., miR482b-3p, N-miR3-3p, miR156a-3p, N-miR40-3p and N-miR18-5p) miRNAs specific to E. camaldulensis. Target prediction and functional analysis showed they might be involved in longevity regulating and plant hormone signal transduction pathways. Then, the expression patterns of these miRNAs were confirmed by qRT-PCR. Conclusions: This is the first time to study the miRNAs profiles in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, our findings will improve our understanding of miRNA regulation and molecular mechanisms during the somatic embryogenesis of Eucalyptus, and the output of this study will benefit the Eucalyptus breeding program.

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Genome-wide identification of microRNAs involved in the somatic embryogenesis of Eucalyptus

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab070 ◽

2021 ◽

Author(s):

Zihai Qin ◽

Junji Li ◽

Ye Zhang ◽

Yufei Xiao ◽

Xiaoning Zhang ◽

...

Keyword(s):

Somatic Embryogenesis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Target Prediction ◽

Small Rna Sequencing ◽

Eucalyptus Species ◽

Mirna Regulation ◽

Small Noncoding Rnas ◽

First Time ◽

Dedifferentiation Process

Abstract MicroRNAs (miRNAs) are small noncoding RNAs (18∼24 nt) and function in many biological processes in plants. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis (SE) of Eucalyptus is still poor. Here we reported, for the first time, the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus species and identified miRNAs involved in SE of Eucalyptus. Stem and tissue-culture induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla, and were used as differentiated and dedifferentiated samples, respectively. Small RNA sequencing generated 304.2 million clean reads for the Eucalyptus samples (n = 3) and identified 888 miRNA precursors (197 known and 691 novel) for Eucalyptus. These miRNAs were mainly distributed in chromosomes Chr03, Chr05 and Chr08, and can produce 46 miRNA clusters. Then, we identified 327 and 343 differentially expressed miRNAs (DEmiRs) in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. DEmiRs shared by the two Eucalyptus species might be involved in the development of embryonic callus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399 and MIR482. Notably, we identified 81 up-regulated and 67 down-regulated miRNAs specific to E. camaldulensis, which might be associated with the high embryogenic potential. Target prediction and functional analysis showed they might be involved in longevity regulating and plant hormone signal transduction pathways. Further, using the gene expression profiles we observed the negative regulation of miRNA∼target pairs, such as MIR160∼ARF18, MIR396∼GRF6, MIR166∼ATHB15/HD-ZIP and MIR156/MIR157∼SPL1. Interestingly, transcription factors such as WRKY, MYB, GAMYB, TCP4 and PIL1 were found to be regulated by the DEmiRs. The genes encoding PIL1 and RPS21C, regulated by up-regulated miRNAs (e.g., egd-N-miR63-5p, egd-N-miR63-5p and MIR169,) were down-regulated exclusively in the dedifferentiation of E. camaldulensis. This is the first time to study the miRNA regulation in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, it will improve our understanding of miRNA regulation during the somatic embryogenesis of Eucalyptus and benefit the Eucalyptus breeding program.

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Chemerin-ChemR23 Signaling in Tooth Development

Journal of Dental Research ◽

10.1177/0022034512464777 ◽

2012 ◽

Vol 91 (12) ◽

pp. 1147-1153 ◽

Cited By ~ 3

Author(s):

T. Ohira ◽

D. Spear ◽

N. Azimi ◽

V. Andreeva ◽

P.C. Yelick

Keyword(s):

Progenitor Cells ◽

Molecular Mechanisms ◽

Tooth Development ◽

Expression Patterns ◽

Cell Interactions ◽

Specific Expression ◽

Ribosomal Protein S6 ◽

First Time

Our long-term goal is to identify and characterize molecular mechanisms regulating tooth development, including those mediating the critical dental epithelial-dental mesenchymal (DE-DM) cell interactions required for normal tooth development. The goal of this study was to investigate Chemerin (Rarres2)/ChemR23(Cmklr1) signaling in DE-DM cell interactions in normal tooth development. Here we present, for the first time, tissue-specific expression patterns of Chemerin and ChemR23 in mouse tooth development. We show that Chemerin is expressed in cultured DE progenitor cells, while ChemR23 is expressed in cultured DM cells. Moreover, we demonstrate that ribosomal protein S6 (rS6) and Akt, downstream targets of Chemerin/ChemR23 signaling, are phosphorylated in response to Chemerin/ChemR23 signaling in vitro and are expressed in mouse tooth development. Together, these results suggest roles for Chemerin/ChemR23-mediated DE-DM cell signaling during tooth morphogenesis.

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Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

10.21203/rs.3.rs-47390/v3 ◽

2020 ◽

Author(s):

Yufei Xiao ◽

Junji Li ◽

Ye Zhang ◽

Xiaoning Zhang ◽

Hailong Liu ◽

...

Keyword(s):

Transcription Factor ◽

Somatic Embryogenesis ◽

Large Scale ◽

Molecular Mechanisms ◽

Zinc Finger Protein ◽

Expression Patterns ◽

Late Embryogenesis Abundant ◽

Arabinogalactan Protein ◽

Late Embryogenesis Abundant Protein ◽

Eucalyptus Species

Abstract Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2,687 up-regulated and 2,581 down-regulated genes shared. Next, we identified 2,003 up-regulated and 1,958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

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Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

BMC Genomics ◽

10.1186/s12864-020-07214-5 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Yufei Xiao ◽

Junji Li ◽

Ye Zhang ◽

Xiaoning Zhang ◽

Hailong Liu ◽

...

Keyword(s):

Transcription Factor ◽

Somatic Embryogenesis ◽

Large Scale ◽

Molecular Mechanisms ◽

Zinc Finger Protein ◽

Expression Patterns ◽

Late Embryogenesis Abundant ◽

Arabinogalactan Protein ◽

Late Embryogenesis Abundant Protein ◽

Eucalyptus Species

Abstract Background Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE. Results We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9229 and 8989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2687 up-regulated and 2581 down-regulated genes shared. Next, we identified 2003 up-regulated and 1958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

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Plant miRNA regulation is environmentally and developmentally-sensitive

10.1101/136762 ◽

2017 ◽

Author(s):

Patrick von Born ◽

Ignacio Rubio-Somoza

Keyword(s):

Developmental Stage ◽

Target Genes ◽

Expression Patterns ◽

Mature Mirnas ◽

Dependent Manner ◽

Mirna Regulation ◽

Vegetative Development ◽

Plant Mirna ◽

Translational Inhibition ◽

Temperature And Growth

AbstractDevelopment and fitness of any organism rely on properly controlled gene expression. This is especially true for plants, as their development is determined by both internal and external cues. MicroRNAs (miRNAs) are embedded in the genetic cascades that integrate and translate those cues into developmental programs. miRNAs negatively regulate their target genes mainly post-transcriptionally through two co-existing mechanisms; mRNA cleavage and translational inhibition. It is unclear whether the efficiency of miRNA-guided regulation is generally influenced by factors like ambient temperature or developmental stage. Here we show that plant miRNA accumulation, as well as miRNAs’ mode of action can be temperature- and development-sensitive. Higher temperatures tend to induce a more pronounced accumulation of mature miRNAs. Both parameters have also an impact on the expression patterns of the core players involved in miRNA performance. We show that efficiency of miRNA-mediated gene silencing declines with age during vegetative development in a temperature-dependent manner. Co-existence of cleavage and translational inhibition was also found to be dependent on temperature and developmental stage. Therefore, each miRNA family specifically regulates their respective targets, while temperature and growth influence the performance of miRNA-dependent regulation in a more general way.

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Transcriptome Analysis Identifies Genes Involved in the Somatic Embryogenesis of Eucalyptus

10.21203/rs.3.rs-47390/v1 ◽

2020 ◽

Author(s):

Yufei Xiao ◽

Junji Li ◽

Ye Zhang ◽

Xiaoning Zhang ◽

Hailong Liu ◽

...

Keyword(s):

Transcription Factor ◽

Somatic Embryogenesis ◽

Large Scale ◽

Molecular Mechanisms ◽

Zinc Finger Protein ◽

Expression Patterns ◽

Late Embryogenesis Abundant ◽

Arabinogalactan Protein ◽

Late Embryogenesis Abundant Protein ◽

Transcriptional Level

Abstract Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood due to its increasing importance for fiber and energy in the word. Somatic embryogenesis is one method to provide large-scale commercial use for the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the SE of Eucalyptus on transcriptional level.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus cultivars – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). In total, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively. Comparison of DEGs showed that they shared 2,687 up-regulated and 2,581 down-regulated genes. Next, we found 2,003 up-regulated and 1,958 down-regulated genes specifically identified in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. Our results will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

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MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish

Molecular Biology and Evolution ◽

10.1093/molbev/msz168 ◽

2019 ◽

Vol 36 (11) ◽

pp. 2498-2511 ◽

Cited By ~ 7

Author(s):

Paolo Franchini ◽

Peiwen Xiong ◽

Carmelo Fruciano ◽

Ralf F Schneider ◽

Joost M Woltering ◽

...

Keyword(s):

Gene Regulation ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Mirna Gene ◽

Evolutionary Divergence ◽

Mirna Regulation ◽

Gene Target ◽

Gene Pairs ◽

Phenotypic Diversification

AbstractCichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.

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Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

10.21203/rs.3.rs-47390/v2 ◽

2020 ◽

Author(s):

Yufei Xiao ◽

Junji Li ◽

Ye Zhang ◽

Xiaoning Zhang ◽

Hailong Liu ◽

...

Keyword(s):

Transcription Factor ◽

Somatic Embryogenesis ◽

Large Scale ◽

Molecular Mechanisms ◽

Zinc Finger Protein ◽

Expression Patterns ◽

Late Embryogenesis Abundant ◽

Arabinogalactan Protein ◽

Late Embryogenesis Abundant Protein ◽

Eucalyptus Species

Abstract Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2,687 up-regulated and 2,581 down-regulated genes shared. Next, we identified 2,003 up-regulated and 1,958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

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Somatic Embryogenesis and In vitro Plant Regeneration in Vigna trilobata (L.) Verd. - A Potential Pasture Legume

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v19i1.4990 ◽

1970 ◽

Vol 19 (1) ◽

pp. 89-99

Author(s):

K. Choudhary ◽

M. Singh ◽

M. S. Rathore ◽

N. S. Shekhawat

Keyword(s):

Somatic Embryogenesis ◽

Growth Regulators ◽

Somatic Embryos ◽

Basal Medium ◽

Long Term Study ◽

Continuous Application ◽

First Time ◽

Pasture Legume

This long term study demonstrates for the first time that it is possible to propagate embryogenic Vigna trilobata and to subsequently initiate the differentiation of embryos into complete plantlets. Initiation of callus was possible on 2,4-D. Somatic embryos differentiated on modified MS basal nutrient medium with 1.0 mg/l of 2,4-D and 0.5 mg/l of Kn. Sustained cell division resulted in globular and heart shape stages of somatic embryos. Transfer of embryos on to a fresh modified MS basal medium with 0.5 mg/l of Kn and 0.5 mg/l of GA3 helped them to attain maturation and germination. However, the propagation of cells, as well as the differentiation of embryos, were inhibited by a continuous application of these growth regulators. For this reason, a long period on medium lacking these growth regulators was necessary before the differentiation of embryos occurred again. The consequences for improving the propagation of embryogenic cultures in Vigna species are discussed. Key words: Pasture legume, Vigna trilobata, Globular, Heart shape, somatic embryogenesis D.O.I. 10.3329/ptcb.v19i1.4990 Plant Tissue Cult. & Biotech. 19(1): 89-99, 2009 (June)

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