- 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. - Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. - grandis x urophylla (low embryogenetic potential).. - Compared to the differentiated tissues, we identified 9229 and 8989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. - embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E.. - grandis x urophylla.. - 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.. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - However, it is still unknown about the gene changes and gene regulations in the SE and dedif- ferentiation of Eucalyptus.. - In the present study, we analyzed the transcriptome profiles and gene variants in the dedifferentiation process of two Eucalyptus species – E. - It will improve our understanding about the molecular mechanisms in the SE of Eucalyptus. - grandis x urophylla). - The callus which had been cultured in the induction medium for 10 days were used for transcriptome sequencing.. - Table 1 showed an overview of the. - Then, the reads were aligned to the E. - Out of the total 36,349 E. - 1 in the differentiated and dedifferen- tiated tissues of Eucalyptus (Additional file 1). - 1 Morphological characterization of somatic callus and overview of the transcriptome sequencing. - a Morphological characterization of the dedifferentiation from stem to callus. - grandis x urophylla. - b Growth curves of the callus tissue of E.. - c Number of genes identified in the stem and callus of E. - grandis x urophylla (B1, B2). - grandis x urophylla shared 8 highly expressed genes including Eucgr.H01085 (ethyl- ene-responsive transcription factor ERF071), Eucgr.G03106 (wound-induced protein 1) and Eucgr.F00114 (zinc finger protein ZAT10). - To study the possible functional genes/pathways in the SE of Eucalyptus, we first identified DEGs in the dedifferen- tiated tissue of E. - camaldulensis compared to the differen- tiated tissue. - It showed that Eucgr.H02264 (probable indole-3-acetic acid-amido synthetase GH3.1), Eucgr.D02625 (phosphori- bulokinase, chloroplastic), Eucgr.J03055 (hypothetical pro- tein), Eucgr.H02600 (protein SRG1) and Eucgr.B03016 (LOB domain-containing protein 40) were the top 5 up- regulated genes while Eucgr.J00794 (DNA-damage-repair/. - toleration protein DRT100), Eucgr.I02271 (endochiti- nase), Eucgr.A01080 (glycine-rich RNA-binding protein), Eucgr.D00703 (beta-galactosidase 8) and Eucgr.A01881 (trans-resveratrol di-O-methyltransferase) were the top 5 down-regulated genes, according to the FDR (false discov- ery rate) values (Additional file 2). - Then, we analyzed some gene groups might be in- volved in the dedifferentiation process of E. - In addition, 41 DEGs encoding auxin related prod- ucts were found in the callus of E. - camaldulensis compared to the stem (Table 2), including 7 auxin response factors, 3 auxin-binding proteins, 2 auxin-induced in root clusters proteins and 16 auxin-responsive proteins (Additional file 2). - Furthermore, we found and 272 DEGs (Table 2) encoding RP, ZFP, HSP, histone and TF, respect- ively, might be involved in the dedifferentiation process of E. - regulated embryogenesis related genes were identified in the callus of E. - Details of these cell wall related DEGs in different categories, such as “GO:0009505~plant-type cell wall” and “GO:0009834~plant-type secondary cell wall biogenesis”, can be accessed in the additional file 3.. - We next identified 4200 up-regulated and 4708 down- regulated genes in the dedifferentiated tissue of E.. - grandis x urophylla compared to the differentiated tissue (Fig. - According to the FDR, top 5 DEGs include Eucgr.B03016 (LOB domain-containing protein 40), Eucgr.H02264 (probable indole-3-acetic acid-amido synthe- tase GH3.1), Eucgr.I02271 (endochitinase), Eucgr.L02894 and Eucgr.L02534 (Additional file 2). - 8.36E-14), which indicates that these DEGs may play key roles in the SE of E. - Table 2 showed the numbers of DEGs from the seven gene groups identified in the dedifferentiation process of E. - grandis x urophylla (Table 2). - Figure 2e showed an overview of all the DEGs identified in the dedifferentiated tissues com- pared to the differentiated tissues in both E. - grandis x urophylla, which might relate to the regenerative ability of Eucalyptus.. - We next compared the DEGs identified in the dediffer- entiation process of E. - It showed in the upper panel of Fig. - they shared 2687 up-regulated genes in the dedifferen- tiated tissue compared to differentiated tissue, including Eucgr.H01085 (ethylene-responsive transcription factor ERF071), Eucgr.A01538 (fructose-bisphosphate aldolase 6, cytosolic), Eucgr.G03106 (wound-induced protein 1), Eucgr.K02614 (NDR1/HIN1-Like protein 3), Eucgr.F00114 (zinc finger protein ZAT10) and Eucgr.H03082 (early nodulin-75) (Additional file 2). - There were 2003 and 1513 up-regulated genes specifically identified in the callus of E. - 3a), in- cluding Eucgr.J00025 (heat shock cognate 70 kDa pro- tein 2), Eucgr.B01596 (probable xyloglucan endotransglucosylase/hydrolase protein 23), Eucgr.A01080 (glycine-rich RNA-binding protein), Eucgr.F00590 (snakin-2) and Eucgr.H03983 (major al- lergen Pru ar 1) (Additional file 2). - 2 DEGs identified in the callus compared to the stem of E. - a Volcano plot showing up- and down-regulated genes in the callus of E. - camaldulensis compared to the stem. - c Volcano plot of the DEGs identified in the callus of E. - grandis x urophylla compared to the stem. - grandis x urophylla showing the genes expression patterns in the dedifferentiation process. - Interestingly, we identified and 98 DEGs related to the embryogenesis, ethylene, auxin, RP, ZFP, HSP, histone, cell wall and TF, respect- ively, only in the dedifferentiation process of E. - camaldu- lensis, Eucgr.K02992 (auxin transporter-like protein 4) and Eucgr.C02984 (auxin-responsive protein IAA26) were down-regulated and Eucgr.H03171 (auxin-induced protein 22D) was up-regulated in E. - All the DEGs related to ethylene and specifically identified in the callus of E. - 3d and e) showed that most of the E. - camaldulensis specific DEGs encoding HSP and RP were down-regulated in the dedifferentiated tissue compared to the differentiated tissue. - It is interesting that Eucgr.F01000 (formin-like. - protein 5, log2FC = 1.65, p = 5.67E-05) were the only DEG involved in the “GO:0005199 ~ structural constitu- ent of cell wall”. - In addition, some other gene families were identified to be specifically differentially expressed in the SE of E. - We used qRT-PCR to confirm the expression patterns of DEGs in the dedifferentiation process of E. - We randomly selected 9 genes (Eucgr.A00971, Eucgr.A01091, Eucgr.B03715, Eucgr.C03048, Eucgr.D01811, Eucgr.F00490, Eucgr.F01164, Eucgr.H03077 and Eucgr.K01605) for the qRT-PCR experiment and the H2B gene was used as the internal control. - The primer sequences for all these genes can be accessed in the Additional file 4. - It is notable that the increase of WRKY TF (Eucgr.D01811) and the decrease of RP gene (Eucgr.A00971) in E. - The dysregulation of Eucgr.B03715, Eucgr.C03048 and Eucgr.F00490 in E. - Initially, we obtained 97,504 and 75,582 variants in the differentiated and dedifferentiated tissues of E. - Likewise, 72,208 and 66,311 variants were found in the differentiated and dedifferentiated tissues. - Interestingly, these 13,434 variants were derived from 4723 Eucalyptus genes, such as annexin (Eucgr.F02423, Eucgr.H00564), ARF guanine-nucleotide exchange factor GNOM (Eucgr.B03196), AP2-like ER. - 3 DEGs related to the SE of Eucalyptus. - TF (Eucgr.I00278, Eucgr.J02113), auxin response factors (Eucgr.G00076, Eucgr.C02178, Eucgr.C03293, Eucgr.J00923, Eucgr.F02090, Eucgr.D00264, Eucgr.E00888) and wall- associated receptor kinas-like (Eucgr.I01022). - SERK2 is significantly increased in the embryogenic callus and the maturation stage compared to non- embryogenic callus [30]. - In the present study we identi- fied the up-regulation of some SERK genes in the dedif- ferentiated tissue compared to differentiated tissue in both E. - The functions of SERK genes in the SE of Eucalyp- tus require further experiments to be explored.. - In the present study, three genes (Eucgr.B00948, Eucgr.G02187, Eucgr.A02229) encoding auxin efflux carrier were up- regulated only in the dedifferentiation process of E.. - Among them, one ABA receptor and two ABA 8′-hydroxylase genes were specifically down-regulated in the dedifferentiated tissue of E. - Interestingly, we found seven genes encoding LEA in the callus compared to the stem (Add- itional file 3). - However, the expression level of down- regulated LEA gene (Eucgr.E00787) was much higher than the five up-regulated LEA genes. - Among them, three (Eucgr.K01312, Eucgr.I01292, Eucgr.A02687) were specifically up-regulated in the callus of E. - It is also involved in the specification of apical-basal pattern formation in the early embryo and the root formation [40, 41]. - In this study we identified some dysregulated TF genes exclusively in the callus of E. - Also, WRKY TF was up-regulated in the Eucalyptus camaldulensis seeding subjected to the water stress [46].. - Interestingly, Eucgr.A01158 (fasciclin-like arabi- nogalactan protein 11), a protein involved in the plant- type secondary cell wall biogenesis, was found with up- regulation in the SE of E. - camaldulensis but down- regulation in the SE of E. - have been reported to function in the vegetative propa- gation in plants. - While very few studies have been dem- onstrated to investigate their functions and associations in the SE of Eucalyptus, our results indicate that the dys- regulation of these genes and pathways like metabolisms involved by these genes might play important roles in the SE of Eucalyptus.. - Our results showed dysregu- lated genes from some gene families like auxin, ethylene, SERK, RP, ZFP, HSP, histone, ABA, LEA and TF might play key roles in the SE and the regenerative ability of Eucalyptus. - Our findings provide a valuable resource for future studies in the field of Euca- lyptus and, more importantly, will benefit the Eucalyptus breeding program.. - Dongyun Xiang and were maintained in the experimental fields of Guangxi Forestry Research Institute. - We used strelka (2.9.10–4-gd737744) to call the variants, including SNPs and small indels, in the stem and callus tissues of both E. - A total of nine genes (Eucgr.A00971, Eucgr.A01091, Eucgr.B03715, Eucgr.C03048, Eucgr.D01811, Eucgr.F00490, Eucgr.F01164, Eucgr.H03077 and Eucgr.K01605) were randomly selected and the H2B gene was used as the internal control. - Then, ΔΔCt was used to show the difference of a gene in the callus compared to the stem. - Differentially expressed genes in the dedifferentiated tissues compared to the differentiated tissues of E. - Cell wall related DEGs identified in the SE of E.. - The authors declare that the funding bodies have no role in the research design, the data collection and analysis, and the manuscript preparation.. - Alterations in the transcriptome of soybean in response to enhanced somatic embryogenesis promoted by orthologs of Agamous- like15 and Agamous-like18. - Dynamic changes in the transcriptome of Populus hopeiensis in response to abscisic acid. - Cell wall alterations in the arabidopsis emb30 mutant
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