Integrated analysis of small RNA, transcriptome and degradome sequencing reveals that micro-RNAs regulate anther development in CMS cotton

2022 ◽  
Vol 176 ◽  
pp. 114422
Author(s):  
Yongqi Li ◽  
Taili Nie ◽  
Meng Zhang ◽  
Xuexian Zhang ◽  
Kashif Shahzad ◽  
...  
Keyword(s):  
Small Rna ◽  
Anther Development ◽  
Integrated Analysis ◽  
Degradome Sequencing ◽  
Micro Rnas

scholarly journals Integrated Analysis of MicroRNA and Target Genes in Brachypodium distachyon Infected by Magnaporthe oryzae by Small RNA and Degradome Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Weiye Peng ◽  
Na Song ◽  
Wei Li ◽  
Mingxiong Yan ◽  
Chenting Huang ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Small Rna ◽  
Target Genes ◽  
Brachypodium Distachyon ◽  
Grass Species ◽  
Integrated Analysis ◽  
Post Inoculation ◽  
New Approach ◽  
Degradome Sequencing ◽  
Differentially Expressed Mirnas

Rice blast caused by Magnaporthe oryzae is one of the most important diseases that seriously threaten rice production. Brachypodium distachyon is a grass species closely related to grain crops, such as rice, barley, and wheat, and has become a new model plant of Gramineae. In this study, 15 small RNA samples were sequenced to examine the dynamic changes in microRNA (miRNA) expression in B. distachyon infected by M. oryzae at 0, 24, and 48 h after inoculation. We identified 432 conserved miRNAs and 288 predicted candidate miRNAs in B. distachyon. Additionally, there were 7 and 19 differentially expressed miRNAs at 24 and 48 h post-inoculation, respectively. Furthermore, using degradome sequencing, we identified 2,126 genes as targets for 308 miRNAs; using quantitative real-time PCR (qRT-PCR), we validated five miRNA/target regulatory units involved in B. distachyon–M. oryzae interactions. Moreover, using co-transformation technology, we demonstrated that BdNAC21 was negatively regulated by miR164c. This study provides a new approach for identifying resistance genes in B. distachyon by mining the miRNA regulatory network of host–pathogen interactions.

scholarly journals Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

2019 ◽  
Author(s):  
Paulina Glazinska ◽  
Milena Kulasek ◽  
Wojciech Glinkowski ◽  
Waldemar Wojciechowski ◽  
Jan Kosiński
Keyword(s):  
Information Processing ◽  
Small Rna ◽  
Target Genes ◽  
Signal Transduction Pathway ◽  
Lupinus Luteus ◽  
Integrated Analysis ◽  
Degradome Sequencing ◽  
Kegg Pathways ◽  
Legume Crop ◽  
Yellow Lupine

Abstract Background Yellow lupine (Lupinus luteus L., Taper c.) is an important legume crop. However, its flower development and pod formation are often affected by excessive abscission. Organ detachment occurs within the abscission zone (AZ) and in L. luteus primarily affects flowers formed at the top of the inflorescence. The top flowers’ fate appears determined before anthesis. The organ development and abscission mechanisms utilize a complex molecular network, not yet not fully understood, especially as to the role of miRNAs and siRNAs. We aimed at identifying differentially expressed (DE) small ncRNAs in lupine by comparing small RNA-seq libraries generated from developing upper and lower raceme flowers, and flower pedicels with active and inactive AZs. Their target genes were also identified using transcriptome and degradome sequencing. Results Within all the libraries, 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development, 30 miRNAs displayed DE in the upper and 29 in the lower parts of the raceme. In comparisons between upper and lower raceme flowers, a total of 46 DE miRNAs were identified. miR393 and miR160 were related to the upper and miR396 to the lower flowers and pedicels of non-abscising flowers. In flower pedicels we identified 34 DE miRNAs, with miR167 being the most abundant of all. Most siRNAs seem to play a marginal role in the processes studied herein, with the exception of tasiR-ARFs, which were DE in the developing flowers. The target genes of these miRNAs were predominantly categorized into the following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: ‘Metabolism’ (15,856), ‘Genetic information processing’ (5,267), and ‘Environmental information processing’ (1,517). Over 700 putative targets were categorized as belonging to the ‘Plant Hormone Signal Transduction pathway’. 26,230 target genes exhibited Gene Ontology (GO) terms: 23,092 genes were categorized into the ‘Cellular component’, 23,501 into the ‘Molecular function’, and 22,939 into the ’Biological process’. Conclusion Our results indicate that miRNAs and siRNAs in yellow lupine may influence the development of flowers and, consequently, their fate by repressing their target genes, particularly those associated with the homeostasis of phytohormones, mainly auxins.

scholarly journals Integrated Analysis of Small RNA, Transcriptome and Degradome Sequencing Provides New Insights into Floral Development and Abscission in Yellow Lupine (Lupinus luteus L.)

2019 ◽  
Vol 20 (20) ◽  
pp. 5122 ◽  
Author(s):  
Paulina Glazińska ◽  
Milena Kulasek ◽  
Wojciech Glinkowski ◽  
Waldemar Wojciechowski ◽  
Jan Kosiński
Keyword(s):  
Small Rna ◽  
Floral Development ◽  
Crop Improvement ◽  
Lupinus Luteus ◽  
Economic Losses ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Legume Crop ◽  
Yellow Lupine

The floral development in an important legume crop yellow lupine (Lupinus luteus L., Taper cv.) is often affected by the abscission of flowers leading to significant economic losses. Small non-coding RNAs (sncRNAs), which have a proven effect on almost all developmental processes in other plants, might be of key players in a complex net of molecular interactions regulating flower development and abscission. This study represents the first comprehensive sncRNA identification and analysis of small RNA, transcriptome and degradome sequencing data in lupine flowers to elucidate their role in the regulation of lupine generative development. As shedding in lupine primarily concerns flowers formed at the upper part of the inflorescence, we analyzed samples from extreme parts of raceme separately and conducted an additional analysis of pedicels from abscising and non-abscising flowers where abscission zone forms. A total of 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development 59 miRNAs displayed differential expression (DE) and 46 DE miRNAs were found while comparing the upper and lower flowers. Identified tasiR-ARFs were DE in developing flowers and were strongly expressed in flower pedicels. The DEmiR-targeted genes were preferentially enriched in the functional categories related to carbohydrate metabolism and plant hormone transduction pathways. This study not only contributes to the current understanding of how lupine flowers develop or undergo abscission but also holds potential for research aimed at crop improvement.

scholarly journals Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the MiR156, MiR5488 and MiR399 Are Involved in the Regulation of Male Sterility in PTGMS Rice

2021 ◽  
Vol 22 (5) ◽  
pp. 2260
Author(s):  
Yujun Sun ◽  
Xinguo Xiong ◽  
Qian Wang ◽  
Lan Zhu ◽  
Lei Wang ◽  
...  
Keyword(s):  
Male Sterility ◽  
Small Rna ◽  
Male Fertility ◽  
Target Genes ◽  
Hybrid Rice ◽  
Basic Material ◽  
Integrated Analysis ◽  
Male Sterile ◽  
Degradome Sequencing ◽  
Ptgms Rice

A photoperiod- and thermo-sensitive genic male sterile (PTGMS) line is the basic material for two-hybrid rice and is an important genetic breeding resource. Peiai64S (PA64S) is an important germplasm resource of PTGMS rice, and it has been applied to two-line hybrid rice systems in China. Pollen fertility in PA64S is regulated by the temperature and photoperiod, but the mechanism of the fertility transition is unclear. In this study, we obtained the male fertile plant PA64S(F) and the male sterile plant PA64S(S) by controlling different temperatures under long light conditions and used the male fertile and sterile plants to investigate the role of microRNAs (miRNAs) in regulating male fertility in rice. We performed the small RNA library sequencing of anthers from PA64S(S) and PA64S(F). A total of 196 miRNAs were identified—166 known miRNAs among 27 miRNA families and 30 novel miRNAs. In the transcriptome analysis, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes revealed significant enrichment in the synthesis and metabolism of fatty acids and some secondary metabolism pathways such as fatty acid metabolism and phenylalanine metabolism. With a comprehensive analysis of miRNA, transcriptome, and degradome sequencing, we identified that 13 pairs of miRNA/target genes regulated male fertility in rice by responding to temperature change, among which the miR156, miR5488, and miR399 affect the male fertility of PA64S by influencing SPLs, the lignin synthesis of anther walls, and the flavonoid metabolism pathway. The results provide a new understanding of PTGMS rice, which will help us better understand the potential regulatory mechanisms of male sterility in the future.

scholarly journals Small RNAs and their targets are associated with the transgenerational effects of water-deficit stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Haipei Liu ◽  
Amanda J. Able ◽  
Jason A. Able
Keyword(s):  
Durum Wheat ◽  
Water Deficit ◽  
Small Rna ◽  
Wheat Yield ◽  
Water Deficit Stress ◽  
Integrated Analysis ◽  
Sequencing Analysis ◽  
Biological Interactions ◽  
Transgenerational Effects ◽  
Nutrient Metabolism

AbstractWater-deficit stress negatively affects wheat yield and quality. Abiotic stress on parental plants during reproduction may have transgenerational effects on progeny. Here we investigated the transgenerational influence of pre-anthesis water-deficit stress by detailed analysis of the yield components, grain quality traits, and physiological traits in durum wheat. Next-generation sequencing analysis profiled the small RNA-omics, mRNA transcriptomics, and mRNA degradomics in first generation progeny. Parental water-deficit stress had positive impacts on the progeny for traits including harvest index and protein content in the less stress-tolerant variety. Small RNA-seq identified 1739 conserved and 774 novel microRNAs (miRNAs). Transcriptome-seq characterised the expression of 66,559 genes while degradome-seq profiled the miRNA-guided mRNA cleavage dynamics. Differentially expressed miRNAs and genes were identified, with significant regulatory patterns subject to trans- and inter-generational stress. Integrated analysis using three omics platforms revealed significant biological interactions between stress-responsive miRNA and targets, with transgenerational stress tolerance potentially contributed via pathways such as hormone signalling and nutrient metabolism. Our study provides the first confirmation of the transgenerational effects of water-deficit stress in durum wheat. New insights gained at the molecular level indicate that key miRNA-mRNA modules are candidates for transgenerational stress improvement.

Small RNA, transcriptome, and degradome sequencing to identify salinity stress responsive miRNAs and target genes in Dunaliella salina

2018 ◽  
Vol 31 (2) ◽  
pp. 1175-1183 ◽  
Author(s):  
Xiangnan Gao ◽  
Yuting Cong ◽  
Jinrong Yue ◽  
Zhenyu Xing ◽  
Yuan Wang ◽  
...  
Keyword(s):  
Salinity Stress ◽  
Small Rna ◽  
Dunaliella Salina ◽  
Target Genes ◽  
Degradome Sequencing

21 CHARACTERIZATION OF THE micro-RNA TRANSCRIPTOME IN LUNG TISSUES OF CLONED CALVES SUFFERING FROM RESPIRATORY DISTRESS SYNDROME

2015 ◽  
Vol 27 (1) ◽  
pp. 103
Author(s):  
Y. Liu ◽  
Y. Zhang ◽  
H.-S. Hao ◽  
W.-H. Du ◽  
H.-B. Zhu ◽  
...  
Keyword(s):  
Respiratory Distress Syndrome ◽  
Western Blot ◽  
Respiratory Distress ◽  
Small Rna ◽  
Distress Syndrome ◽  
Normal Lung ◽  
Regulation Of Transcription ◽  
Primary Role ◽  
Healthy Individuals ◽  
Micro Rnas

Developmental deficiency leads to low survival rates of newborns, especially in cloned animals. Alveoli collapse leading to respiratory failure is one of the major causes of death in newborn cloned calves. The present study provides an insight into the expression pattern of micro-RNAs (miRNAs) in lung tissues and their role in the respiratory distress syndrome (RDS) in the cloned calves. Short RNA high-throughput sequencing and bioinformatic analysis from small RNA libraries created from collapsed lung tissues from 4 newborn cloned calves with RDS and normal lung tissues from 4 age-matched healthy individuals were implemented. Lung tissues were collected by dissection from newborns that died due to RDS and from healthy individuals on the first day after birth. RNA samples from the lung tissues were processed to generate small RNA libraries that were further used for deep sequencing. Expression profiles of surfactant-associated protein B (SPB), surfactant-associate protein C (SPC), and their key transcription regulator thyroid transcription factor-1 (TTF-1), which are responsible for stabilising alveolar surface, reducing surface tension, and thus preventing alveoli collapse, were verified through real-time RT-PCR, Western blot, and immunohistochemistry (IHC). Differentially expressed (DE) miRNAs were quantified by edgeR (empirical analysis of digital gene expression data in R), and their target genes were predicted by both TargetScan and miRanda software. Only miRNAs with P values <0.05 were considered statistically significant (Fisher exact test). Sequence analysis revealed the presence of 1592 and 1777 miRNAs in the RDS and healthy groups, respectively. A total of 326 miRNAs were DE between the two groups according to our criteria, of which 179 miRNAs were up-regulated and 147 were down-regulated in the RDS group. Gene ontological analysis showed that the DE miRNAs had a primary role in DNA-dependent regulation of transcription, cytoplasm biosynthesis, and nucleotide binding. Eleven miRNAs (bta-miR-186, bta-miR-2284x_R+1, bta-miR-24–3p_R-2, bta-miR-424–3p, bta-miR-592_L-1, bta-miR-660, bta-miR-150_R-1, bta-miR-2478_L-2, bta-miR-450b_R-1, bta-miR-134_L+2R-2 and bta-miR-326_R+1) were DE between the 2 groups and were predicted to target SPB, SPC, and TTF-1, respectively. Among these DE miRNAs, 5 miRNAs (bta-miR-134_L+2R-2, bta-miR-424–3p, bta-miR-660, bta-miR-2478_L-2, bta-miR-450b_R-1) were up-regulated in the RDS group. Western blot and IHC confirmed the down-regulation of SPB, SPC, and TTF-1 at the protein level in RDS group. This increase in abundance of miRNAs targeting key regulatory genes in lung of newborn cloned calves may take part in the dysregulation of alveolus development leading to alveoli collapse and RDS. The assay for target gene verification and analysis of gene transcription profile are under study.Y. Liu and Y. Zhang contributed equally to this work. This project was supported by the National Natural Science Foundation of China (No. 31301977) and the National Nonprofit Institute Research Grant (No. 2011cj-11).

Sign in / Sign up

Export Citation Format

Share Document