Transcriptional identification and characterization of differentially expressed genes associated with embryogenesis in radish (Raphanus sativus L.)

Zhai, Limin; Xu, Liang; Wang, Yan; Zhu, Xiaoming; Feng, Haiyang; Li, Chao; Luo, Xiaobo; Everlyne, Muleke M.; Liu, Liwang

doi:10.1038/srep21652

Cited by 41 publications

(26 citation statements)

References 68 publications

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“…The similar result was reported about enrichment of the phenylpropanoid pathway in strawberry embryogenic callus [19]. In addition, external stimuli and plant hormones related genes played a key role in the SE process [47,48]. Sucrose were added to culture medium as exogenous carbon sources in conifers SE [49,50].…”

Section: Discussionsupporting

confidence: 77%

Transcriptomes Analysis Reveals Novel Insight Into the Molecular Mechanisms of Somatic Embryogenesis in Hevea Brasiliensis

Wang

Zhou

et al. 2020

Preprint

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Background Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes had been identified and the molecular regulation mechanisms of late SE still not well understood. Results In this study, the transcriptomes of embryogenic calluses (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, more than 85.92% of the clean reads were mapped to the rubber tree genome. The de novo assembly generated 36937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs mainly involved in phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcript factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. Conclusions This study provides important information to elucidate the molecular regulation during rubber tree late SE.

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Section: Discussionsupporting

confidence: 77%

Transcriptomes Analysis Reveals Novel Insight Into the Molecular Mechanisms of Somatic Embryogenesis in Hevea Brasiliensis

Wang

Zhou

et al. 2020

Preprint

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“…The results indicated a strong correlation (R2 = 0.908) between the expression fold changes detected by DGE and qRT-PCR (Figure 6). This finding is comparable with other studies analyzing correlations between RNA-seq and qRT-PCR results (Camarena et al, 2010;Zhang et al, 2013;Zhai et al, 2016). The qRT-PCR validation results confirmed the accuracy and reliability of the expression changes detected by DGE analysis.…”

Section: Validation Of Degs By Qrt-pcrsupporting

confidence: 81%

Characterization and Identification of Differentially Expressed Genes Involved in Thermal Adaptation of the Hong Kong Oyster Crassostrea hongkongensis by Digital Gene Expression Profiling

Zhang

Mao

et al. 2017

Front. Mar. Sci.

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Thermal exposure of sessile marine animals inhabiting estuarine intertidal regions is a serious concern with respect to their physiological processes. Organisms living in this region can be exposed to high temperature (>40 • C) during the low tide, which may affect the survival of these organisms. The Hong Kong oyster, Crassostrea hongkongensis, distributed along the coast waters of the South China Sea, is one of the dominant sessile inhabitants of marine intertidal region which undergoes large seasonal temperature fluctuations (up to 10-20 • C during diurnal cycles) every year. To cope with acute thermal stress, it has developed several adaptation mechanisms, e.g., the firmly shut of the shells. However, the genetic basis of these mechanisms remain largely unclear. To better understand how acute thermal exposure affects the biology of the oyster, two cDNA libraries obtained from the gill of oysters exposed to 37 • C thermal stress and ambient temperature were sequenced using the Digital Gene Expression (DGE) tag profiling strategy. In total, 5.9 and 6.2 million reads were obtained from thermal stress and control libraries, respectively, with approximately 74.25 and 75.02% of the reads mapping to the Crassostrea hongkongensis reference sequence. A total of 605 differentially expressed transcripts could be detected in the thermal stress group as compared to the control group, of which 378 are up-regulated and 227 are down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these Differentially Expressed Genes (DEGs) were enriched with a broad spectrum of biological processes and pathways, including those associated with chaperones, antioxidants, immunity, apoptosis and cytoskeletal reorganization. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum was the most affected metabolic pathway, which plays an important role in the unfolded protein response (UPR) and ER-associated degradation (ERAD) processes. Our results demonstrate the complex multi-modal cellular response to thermal stress in C. hongkongensis.

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“…ARF4 and AUX22B genes were selected from the plant hormone signal transduction pathway, which are the two key transcription factors involved in regulating the expression of auxin-responsive genes. Auxin response factor (ARFs) is considered as essential SE genes that are specifically activated during embryogenic differentiation [31][32][33][34]. ARFs bind auxin response promoter elements, mediate transcriptional responses to auxin and regulate auxin-mediated transcriptional activation/repression, together with Aux/IAA [35,36].…”

Section: Candidate Gene Expression Pattern Validationmentioning

confidence: 99%

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton

Fan

Guo

et al. 2020

IJMS

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The somatic embryogenesis (SE) process of plants is regulated by exogenous hormones. During the SE, different genes sensitively respond to hormone signals through complex regulatory networks to exhibit plant totipotency. When cultured in indole-3-butyric acid (IBA) concentration gradient medium supplemented with 0 mg dm −3 , 0.025 mg dm −3 , and 0.05 mg dm −3 IBA, the callus differentiation rate first increased then decreased in cotton. To characterize the molecular basis of IBA-induced regulating SE, transcriptome analysis was conducted on embryogenic redifferentiation. Upon the examination of the IBA's embryogenic inductive effect, it was revealed that pathways related to plant hormone signal transduction and alcohol degradation were significantly enriched in the embryogenic responsive stage (5 days). The photosynthesis, alcohol metabolism and cell cycle pathways were specifically regulated in the pre-embryonic initial period (20 days). Upon the effect of the IBA dose, in the embryogenic responsive stage (5 days), the metabolism of xenobiotics by the cytochrome P450 pathway and secondary metabolism pathways of steroid, flavonoid, and anthocyanin biosynthesis were significantly enriched. The phenylpropanoid, brassinosteroid, and anthocyanin biosynthesis pathways were specifically associated in the pre-embryonic initial period (20 days). At different developmental stages of embryogenic induction, photosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling, xenobiotics metabolism by cytochrome P450, and brassinosteroid biosynthesis pathways were enriched at low a IBA concentration. Meanwhile, at high IBA concentration, the carbon metabolism, alcohol degradation, circadian rhythm and biosynthesis of amino acids pathways were significantly enriched. The results reveal that complex regulating pathways participate in the process of IBA-induced redifferentiation in cotton somatic embryogenesis. In addition, collections of potential essential signaling and regulatory genes responsible for dose IBA-induced efficient embryogenic redifferentiation were identified. Quantitative real-time PCR (qRT-PCR) was performed on the candidate genes with different expression patterns, and the results are basically consistent with the RNA-seq data. The results suggest that the complicated and concerted IBA-induced mechanisms involving multiple cellular pathways are responsible for dose-dependent plant growth regulator-induced SE. This report represents a systematic study and provides new insight into molecular signaling and regulatory basis underlying the process of dose IBA-induced embryogenic redifferentiation during SE.

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Transcriptional identification and characterization of differentially expressed genes associated with embryogenesis in radish (Raphanus sativus L.)

Cited by 41 publications

References 68 publications

Transcriptomes Analysis Reveals Novel Insight Into the Molecular Mechanisms of Somatic Embryogenesis in Hevea Brasiliensis

Transcriptomes Analysis Reveals Novel Insight Into the Molecular Mechanisms of Somatic Embryogenesis in Hevea Brasiliensis

Characterization and Identification of Differentially Expressed Genes Involved in Thermal Adaptation of the Hong Kong Oyster Crassostrea hongkongensis by Digital Gene Expression Profiling

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton

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