Characterization and analysis of the transcriptome response to drought in Larix kaempferi using PacBio full-length cDNA sequencing integrated with de novo RNA-seq reads

Li, Wenlong; Lee, Joobin; Yu, Sen; Wang, Fude; Lv, Wanqiu; Zhang, Xin; Li, Chenghao; Yang, Jingli

doi:10.1007/s00425-020-03555-3

Cited by 17 publications

(24 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, in this study, we identified some AP2/ERF and NAC TF family members whose expression levels were significantly altered by PEG-induced drought stress. Similar results were obtained with other plants, such as V. riparia , P. davidiana and L. kaempferi [ 8 , 27 , 38 ]. Furthermore, the genes encoding DRE1D , ERF5 , NAC2 , and NAC72 / RD26 were up-regulated under PEG-induced drought stress in this study.…”

Section: Discussionsupporting

confidence: 88%

“…Increased expression of genes involved in lignin biosynthesis, such as PAL , 4CL , CAD , CCR , C4H , and COMT homologous genes, was observed in the roots of P. ussuriensis under PEG-induced drought stress ( Table S11 ). Similar results were obtained in Paeonia ostii [ 68 ] and L. kaempferi [ 38 ], which suggested that plants might promote lignin biosynthesis resulting in enhanced tolerance to drought stress.…”

Section: Discussionsupporting

confidence: 78%

“…In this study, most of the differentially expressed TFs were members of the AP2/ERF, C2H2, MYB, NAC, C2C2, and WRKY TF families ( Figure 5 A). A substantial amount of evidence has shown that these TF subfamilies were involved in plant drought resistance [ 12 , 38 , 39 , 40 ].…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing

Liu

et al. 2022

IJMS

Self Cite

View full text Add to dashboard Cite

In this study, we characterized the gene expression profile in the roots of Populus ussuriensis at 0, 6, 12, 24, 48 and 120 h after the start of polyethylene glycol (PEG)-induced drought stress using PacBio single-molecule real-time sequencing (SMRT-seq) and Illumina RNA sequencing. Compared to the control, 2244 differentially expressed genes (DEGs) were identified, and many of these DEGs were associated with the signal transduction, antioxidant system, ion accumulation and drought-inducing proteins. Changes in certain physiological and biochemical indexes, such as antioxidant activity and the contents of Ca2+, proline, and total soluble sugars, were further confirmed in P. ussuriensis roots. Furthermore, most of the differentially expressed transcription factors were members of the AP2/ERF, C2H2, MYB, NAC, C2C2 and WRKY families. Additionally, based on PacBio SMRT-seq results, 5955 long non-coding RNAs and 700 alternative splicing events were identified. Our results provide a global view of the gene expression profile that contributes to drought resistance in P. ussuriensis and meaningful information for genetic engineering research in the future.

show abstract

Section: Discussionsupporting

confidence: 88%

Section: Discussionsupporting

confidence: 78%

See 1 more Smart Citation

Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing

Liu

et al. 2022

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…It is a closed loop with no 5' and 3' ends, and its structure makes it more stable in cells. CircRNA has developmental stage specificity and tissue specificity, rich in content, and conserved among species [ 9 ]. Increasing evidence shows that circRNA plays an indispensable role in various tumors, such as circFBLIM1, circABCB, and circHIPK3.…”

Section: Introductionmentioning

confidence: 99%

CircINTS4 Facilitates Chemoresistance of TNBC by Competitively Binding miR-129-5p/POM121 Axis

Tang

Zhou

Yang

et al. 2022

Journal of Oncology

View full text Add to dashboard Cite

Objectives. To detect the expression of circular RNA (circRNA) circINTS4 in triple-negative breast cancer (TNBC) and to analyze the relationship between the expression of circRNA circINTS4 and the clinicopathological characteristics and chemotherapy resistance of patients with TNBC. Methods. Bioinformatics was used to predict that circINTS4 and POM121 could bind to miR-129-5p, and dual luciferase reporter genes proved that circINTS4 could bind to miR-129-5p and miR-129-5p could bind to POM121. RNA immunoprecipitation (RIP) and RNA pull-down experiments confirmed that circINTS4 binds to miR-129-5p. The correlation among circINTS4, miR-129-5p, and POM121 was detected by qRT-PCR. Results. In ADR-resistant TNB cells, circINTS4 was significantly up-regulated, miR-129-5p was down-regulated, and POM121 protein expression was significantly up-regulated. Experimental results showed that circINTS4 knockdown inhibited proliferation, migration, invasion, and autophagy. Knocking down miR-129-5p or overexpression of POM121 reversed the inhibitory effect of sh-circints4 on the development of ADR-resistant TNBC cells. In addition, CIRCINTS4 regulates POM121 expression by sponge-adsorbed miR-129-5p. CIRCINTS4 knockdown prevents ADR-resistant tumor growth by regulating the miR-129-5p/POM121 axis in vivo. Conclusions. CircRNA circINTS4 may act as the ceRNA of miR-129-5p to regulate the expression of target gene POM121, thereby promoting the progress of TNBC molecular mechanism and providing scientific basis for circINTS4 as a new molecular target for clinical diagnosis and drug resistance therapy of TNBC.

show abstract

“…However, according to current research, SMRT-seq often provides inaccurate gene information, and low gene coverage leads to a high error rate (Li et al, 2021). The incompleteness of Illumina HiSeq can be supplemented by more complete reading of SMRT-seq, while the inaccurate reading of SMRT-seq can be corrected by more accurate data of Illumina Hiseq (Li et al, 2021). Full-length transcripts that do not require assembly can be used to detect alternative splicing (AS) events, APA events, long noncoding RNAs (LncRNAs), and fusion transcripts.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the gene expression profile response to drought stress in Haloxylon Bunge using PacBio SMRT and Illumina sequencing

Yang

2022

Preprint

View full text Add to dashboard Cite

Haloxylon ammodendron and Haloxylon persicum are important drought-tolerant plants in northwest China. The whole-genome sequencing of H. ammodendron and H. persicum grown in their natural environment is incomplete, and their transcriptional regulatory network in response to drought environment remains unclear. To reveal the transcriptional responses of H. ammodendron and H. persicum to an arid environment, we performed single-molecule real-time (SMRT) and Illumina RNA sequencing. In total, 20,246,576 and 908,053 subreads and 435,938 and 210,334 circular consensus sequencing reads were identified by SMRT sequencing of H. ammodendron and H. persicum, and 15238 and 10135 unigenes, respectively, were successfully collected. In addition, 9794 and 7330 simple sequence repeats (SSRs) and 838 and 71 long noncoding RNAs were identified. In an arid environment, the growth of H. ammodendron was restricted; plant height decreased significantly; and the base and branch diameters became thinner. Hydrogen peroxide (H O ) content and peroxidase activity were increased. Under dry and wet conditions, 11,803 and 15,217 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum, respectively. There were 319 and 415 DEGs in the signal transduction pathways related to drought stress signal perception and transmission, including the Ca signal pathway, the ABA signal pathway, and the MAPK signal cascade. In addition, 217 transcription factors (TFs) and 398 TFs of H. ammodendron and H. persicum were differentially expressed, including FAR1, MYB, and AP2/ERF. Bioinformatic analysis showed that under drought stress, the expression patterns of genes related to active oxygen (reactive oxygen species) scavenging, functional proteins, lignin biosynthesis, and glucose metabolism pathways were altered. This is the first full-length transcriptome report concerning the responses of H. ammodendron and H. persicum to drought stress. The results provide a foundation for further study of the adaptation to drought stress. The full-length transcriptome can be used in genetic engineering research.

show abstract

Characterization and analysis of the transcriptome response to drought in Larix kaempferi using PacBio full-length cDNA sequencing integrated with de novo RNA-seq reads

Cited by 17 publications

References 50 publications

Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing

Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing

CircINTS4 Facilitates Chemoresistance of TNBC by Competitively Binding miR-129-5p/POM121 Axis

Characterization of the gene expression profile response to drought stress in Haloxylon Bunge using PacBio SMRT and Illumina sequencing

Contact Info

Product

Resources

About