scholarly journals Transcriptome analysis reveals the genetic basis underlying the development of skin appendages and immunity in hedgehog (Atelerix albiventris)

2020 ◽  
Author(s):  
Hui-Ming Li ◽  
Bi-Ze Yang ◽  
Xiu-Juan Zhang ◽  
Hai-Ying Jiang ◽  
Lin-Miao Li ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Immune Genes ◽  
Hair Type ◽  
Keratin Filament

AbstractThe expression of hair features is an evolutionary adaptation resulting from interactions between many organisms and their environment. Elucidation of the mechanisms that underlie the expression of such traits is a topic in evolutionary biology research. Therefore, we assessed the de novo transcriptome of Atelerix albiventris at three developmental stages and compared gene expression profiles between abdomen hair and dorsal spine tissues. We identified 328,576 unigenes in our transcriptome, among which 3,598 were differentially expressed between hair- and spine-type tissues. Dorsal and abdomen skin tissues 5 days after birth were compared and the resulting differentially expressed genes were mainly enriched in keratin filament, epithelium cell differentiation, and epidermis development based on GO enrichment analysis, and tight junction, p53, and cell cycle signaling pathways based on KEGG enrichment analysis. Expression variations of MBP8, SFN, Wnt10, KRT1, and KRT2 may be the main factors regulating hair and spine differentiation for the hedgehog. Strikingly, DEGs in hair-type tissues were also significantly enriched in immune-related terms and pathways with hair-type tissues exhibiting more upregulated immune genes than spine-type tissues. Thus, we propose that spine development was an adaptation that provided protection against injuries or stress and reduced hedgehog vulnerability to infection.

scholarly journals Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Juan Ma ◽  
Rongyan Wang ◽  
Xiuhua Li ◽  
Bo Gao ◽  
Shulong Chen
Keyword(s):  
Sweet Potato ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Average Length ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cylas Formicarius ◽  
Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

scholarly journals Comparative RNA-Seq Analysis of High- and Low-Oil Yellow Horn During Embryonic Development

2018 ◽  
Vol 19 (10) ◽  
pp. 3071 ◽  
Author(s):  
Li Wang ◽  
Chengjiang Ruan ◽  
Lingyue Liu ◽  
Wei Du ◽  
Aomin Bao
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Acyl Carrier Protein ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Oil Accumulation ◽  
Carboxylase Activity

Yellow horn (Xanthoceras sorbifolium Bunge) is an endemic oil-rich shrub that has been widely cultivated in northern China for bioactive oil production. However, little is known regarding the molecular mechanisms that contribute to oil content in yellow horn. Herein, we measured the oil contents of high- and low-oil yellow horn embryo tissues at four developmental stages and investigated the global gene expression profiles through RNA-seq. The results found that at 40, 54, 68, and 81 days after anthesis, a total of 762, 664, 599, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil lines. Gene ontology (GO) enrichment analysis revealed some critical GO terms related to oil accumulation, including acyl-[acyl-carrier-protein] desaturase activity, pyruvate kinase activity, acetyl-CoA carboxylase activity, and seed oil body biogenesis. The identified differentially expressed genes also included several transcription factors, such as, AP2-EREBP family members, B3 domain proteins and C2C2-Dof proteins. Several genes involved in fatty acid (FA) biosynthesis, glycolysis/gluconeogenesis, and pyruvate metabolism were also up-regulated in the high-oil line at different developmental stages. Our findings indicate that the higher oil accumulation in high-oil yellow horn could be mostly driven by increased FA biosynthesis and carbon supply, i.e. a source effect.

scholarly journals Evolutionary transition in accessible chromatin landscapes during vertebrate embryogenesis

2018 ◽  
Author(s):  
Masahiro Uesaka ◽  
Shigeru Kuratani ◽  
Hiroyuki Takeda ◽  
Naoki Irie
Keyword(s):  
Evolutionary Biology ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Molecular Evidence ◽  
Regulatory Regions ◽  
Evolutionary Origins ◽  
A Genome ◽  
Hourglass Model ◽  
Accessible Chromatin

The relationship between development and evolution is a central topic in evolutionary biology1,2. Recent transcriptome-based studies support the developmental hourglass model, which predicts that the animal embryogenetic program is most strongly conserved at mid-embryonic stages3-9. This model does not necessarily contradict the classical hypothesis10,11 that animal development recapitulates its evolutionary history after the mid-embryonic stages2,12. However, to date there is no molecular evidence supporting the hypothesis that gene-expression profiles that are more evolutionarily derived appear sequentially in late development. Here, by estimating activated genomic regions and their evolutionary origins, we show that the recapitulative pattern appears during late embryonic stages. We made a genome-wide assessment of accessible chromatin regions throughout embryogenesis in three vertebrate species (mouse, chicken, and medaka) and determined the phylogenetic range at which these regions were shared. In all three species, sequential activation of putative regulatory regions that were more derived occurred later in embryogenesis, whereas ancestral ones tended to be activated early. Our results clarify the chronologic changes in accessible chromatin landscapes and reveal a phylogenetic hierarchy in the evolutionary origins of putative regulatory regions that parallels developmental stages of activation. This relationship may explain, at least in part, the background for morphological observations of recapitulative events during embryogenesis.

scholarly journals De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

scholarly journals Identification of mRNA and Long Non-Coding RNA Expression Profiles in Developing Yorkshire Pig Spleens

2021 ◽  
Author(s):  
Xinjian Li ◽  
Xuelei Han ◽  
Caixia Sun ◽  
Gaiying Li ◽  
Kejun Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Economic Loss ◽  
Differentially Expressed ◽  
Farm Animals ◽  
Lncrna Expression ◽  
Lncrna Transcript

Abstract Background: Epidemic diseases cause great economic loss in pig farms each year, some of which are characterized mainly in spleen. Yorkshire pig is the most popular used first dam in the commercial pork production system. But the mRNA and lncRNA expression networks in developing Yorkshire pig spleens remain obscure. Results: Here, we profiled the systematic characters of mRNA and lncRNA repertoires in three groups of spleens from nine Yorkshire pigs, each three aged at 7 days, 90 days and 180 days. By using a precise mRNA and lncRNA identification pipeline, we identified 19,647 genes and 219 known and 3,219 putative lncRNA transcripts, 1,729 genes and 64 lncRNAs therein were found to express differentially in three groups. Gene expression characteristics of genes and lncRNAs were found to be basically fixed before 90 days after birth. Enrichment analysis of differentially expressed genes and potential target genes of differentially expressed lncRNAs both displayed crucial roles of up-regulation in immune activation and hematopoiesis and down-regulation in cell replication and division in 90 and 180 days compared to 7 days. The unregulated terms and their significance levels in 90 and 180 days both showed an extremely high degree of consistency. ENSSSCT00000001325 was the only lncRNA transcript that existed in three groups. CDK1, PCNA and PLK were detected to be hub genes that varied with age. BNIP3L, IL5, CD38 and TGFβ1 were found to be common top regulators from 7 to 90 and 180 days while ERAP1, NLRC5 and IL2RG were top regulators from 90 to 180 days.Conclusions: This study provided the first mRNA and lncRNA expression profiles in Yorkshire spleens at three developmental stages. We established gene expression modules and networks in the spleen of pigs from immune system initiation to adulthood. Our results are helpful for the study of transcriptome and functional genomics of spleen tissue in farm animals.

scholarly journals Integrative DNA Methylation and Gene Expression Analysis Reveals Candidate Biomarkers Associated with Dichotomized Response to Chemoimmunotherapy in Diffuse Large B-Cell Lymphoma

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 22-22
Author(s):  
Ellen K. Kendall ◽  
Manishkumar S. Patel ◽  
Sarah Ondrejka ◽  
Agrima Mian ◽  
Yazeed Sawalha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Research Funding ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
B Cell Lymphoma ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Gene Sets

Background: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. While 60% of DLBCL patients achieve complete remission with frontline therapy, relapsed/refractory (R/R) DLBCL patients have a poor prognosis with median overall survival below one year, necessitating investigation into the biological principles that distinguish cured from R/R DLBCL. Recent analyses have identified unfavorable molecular signatures when accounting for gene expression, copy number alterations and mutational profiles in R/R DLBCL. However, an integrative analysis of the relationship between epigenetic and transcriptomic changes has yet to be described. In this study, we compared baseline methylation and gene expression profiles of DLBCL patients with dichotomized clinical outcomes. Methods: Diagnostic DLBCL biopsies were obtained from two patient cohorts: patients who relapsed or were refractory following chemoimmunotherapy ("R/R"), and patients who entered durable clinical remission following therapy ("cured"). The median age for R/R and cured cohorts were 62 (range 35-86) years vs. 64 (range 28-83) years (P= 0.27). High-intermediate or high IPI scores were present in 14 vs. 6 patients (P= 0.08) in the R/R and cured cohorts, respectively. All patients were treated with frontline R-CHOP or R-EPOCH. DNA and RNA were extracted simultaneously from formalin-fixed, paraffin embedded biopsy samples. An Illumina 850k Methylation Array was used to identify DNA methylation levels in 29 R/R patients and 20 cured patients. RNA sequencing was performed on 9 R/R patients and 7 cured patients at diagnosis using Illumina HiSeq4000. Differentially methylated probes were identified using the DMRcate package, and differentially expressed genes were identified using the DESeq2 package. Gene set enrichment analysis was performed using canonical pathway gene sets from MSigDB. Results: At the time of diagnosis, we found significant epigenetic and transcriptomic differences between cured and R/R patients. Comparing cured to R/R samples, there were 8,159 differentially methylated probes (FDR<0.05). Differentially methylated regions between R/R and cured cohorts overlap with genes previously identified as mutation hotspots in DLBCL. Upon comparing transcriptomic profiles between R/R and cured, 267 genes were found to be differentially expressed (Log2FC>|1| and FDR<0.05). Gene set enrichment analysis revealed gene sets related to cell cycle, membrane trafficking, Rho and Rab family GTPase function, and transcriptional regulation were upregulated in the R/R samples. Gene sets related to innate immune signaling, Type I and II interferon signaling, fatty acid and carbohydrate metabolism were upregulated in the cured samples. To identify genes likely to be regulated by specific changes in methylation, we selected genes that were both differentially expressed and differentially methylated between the R/R and cured cohorts. In the R/R samples, 13 genes (ARMC5, ARRDC1, C12orf57, CCSER1, D2HGDH, DUOX2, FAM189B, FKBP2, KLF5, MFSD10, NEK8, NT5C, and WDR18) were significantly hypermethylated and underexpressed when compared to cured specimens, suggesting that epigenetic silencing of these genes is associated with lack of response to chemoimmunotherapy. In contrast, 12 genes (ATP2B1, C15orf41, FAM102B, FAM3C, FHOD3, FYTTD1, GPR180, KIAA1841, LRMP, MEF2A, RRAS2, and TPD52) were significantly hypermethylated and underexpressed in cured patients, suggesting that epigenetic silencing of these genes is favorable for treatment response. Many of these epigenetically modified genes have been previously implicated in cancer biology, including roles in NOTCH signaling, chromosomal instability, and biomarkers of prognosis. Conclusions: This is the first integrative epigenetic and transcriptomic analysis of diagnostic biopsies from cured and R/R DLBCL patients following chemoimmunotherapy. At the time of diagnosis, both the methylation and gene expression profiles significantly differ between patients that enter durable remission as opposed to those who are R/R to therapy. Soon, the hypomethylating agent CC-486 (i.e. oral azacitidine) will be explored in combination with mini-R-CHOP for older DLBCL patients in whom DNA methylation is likely increased. These data support the use of hypomethylating agents to potentially restore sensitivity of DLBCL to chemoimmunotherapy. Disclosures Hsi: Eli Lilly: Research Funding; Abbvie: Research Funding; Miltenyi: Consultancy, Honoraria; Seattle Genetics: Consultancy, Honoraria; CytomX: Consultancy, Honoraria. Hill:Celgene: Consultancy, Honoraria, Research Funding; BMS: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria; Kite, a Gilead Company: Consultancy, Honoraria, Research Funding; AstraZenica: Consultancy, Honoraria, Research Funding; Pharmacyclics: Consultancy, Honoraria, Research Funding; Takeda: Research Funding; Beigene: Consultancy, Honoraria, Research Funding; Genentech: Consultancy, Honoraria, Research Funding; Abbvie: Consultancy, Honoraria, Research Funding; Karyopharm: Consultancy, Honoraria, Research Funding.

scholarly journals Dysfunctional network and mutation genes of hypertrophic cardiomyopathy

2020 ◽  
Author(s):  
Yunwen Cui ◽  
Cheng Liu ◽  
Jian Luo ◽  
Jie Liang
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Differential Analysis ◽  
Ppi Network ◽  
Roc Curve Analysis ◽  
Study Gene Expression

Abstract Background Hypertrophic cardiomyopathy (HCM) is a group of heterogeneous diseases that affect the myocardium. It is also a common familial disease. The symptoms are not common and easy to find. Methods In this study, gene expression profiles of 37 samples (GSE130036) were downloaded from GEO database. Differential analysis was used to identify the related dysregulated genes in patients with HCM. Enrichment analysis identified the biological function and signal pathway of these differentially expressed genes. Then, we build PPI network and verify it in GSE36961 dataset. Finally, the gene of single nuclear variants (SNVs) in HCM samples was screened by means of maftools. Results Herein, we obtained 920 differentially expressed genes, and found that these genes are mainly related to metabolic related signaling pathways. 187 interacting genes were identified by PPI network analysis, and the expression trends of C1QB, F13A1, CD163, FCN3, PLA2G2A and CHRDL2 were verified by another dataset. ROC curve analysis showed that they had certain clinical diagnostic ability, and they were the potential key dysfunctional genes of HCM. In addition, we found that PRMT5 mutation was the most frequent in HCM samples, which may affect the pathogenesis of HCM. Conclusions Therefore, the key genes and enrichment results identified by our analysis may provide a reference for the occurrence and development mechanism of HCM. In addition, mutations in PRMT5 may be a useful therapeutic and diagnostic target for HCM.

Comparative Transcriptomes Analysis of Taenia pisiformis at Different Development Stages

2018 ◽  
Author(s):  
Lin Chen ◽  
Yu Jing ◽  
Jing Xu ◽  
Wei Wang ◽  
Lily Ji ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Target Genes ◽  
Developmental Stages ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Bioinformatic Tools ◽  
Sequence Similarity Analysis ◽  
Two Stages

To understand the characteristics of the transcriptional group of Taenia pisiformis at different developmental stages, and to lay the foundation for the screening of vaccine antigens and drug target genes, the transcriptomes of adult and larva of T. pisiformis were assembled and analyzed using bioinformatic tools. A total of 36,951 unigenes with a mean length of 950bp were formed, among which 12,665, 8,188, 7,577, and 6,293 unigenes have been annotated respectively by sequence similarity analysis with four databases (NR, Swiss-Prot, KOG, and KEGG). It should be noted there are 5,662 unigenes that share good similarity with the four databases and get a relatively perfect functional annotation. Besides, a total of 10,247 differentially expressed genes were screened. To be specific, 6,910 unigenes were up-regulated in the larva stage while 3,337 were down-regulated in the adult stage. To sum up, this study sequenced and analyzed the transcriptomes of the larval and adult stages of T. pisiformis. The results of differentially expressed genes in these two stages could provide basis for functional genomics, immunology and gene expression profiles of T. pisiformis.

scholarly journals Identification and Verification of Core Genes in Colorectal Cancer

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Houxi Xu ◽  
Yuzhu Ma ◽  
Jinzhi Zhang ◽  
Jialin Gu ◽  
Xinyue Jing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Malignant Neoplasm ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Core Genes

Colorectal cancer, a malignant neoplasm that occurs in the colorectal mucosa, is one of the most common types of gastrointestinal cancer. Colorectal cancer has been studied extensively, but the molecular mechanisms of this malignancy have not been characterized. This study identified and verified core genes associated with colorectal cancer using integrated bioinformatics analysis. Three gene expression profiles (GSE15781, GSE110223, and GSE110224) were downloaded from the Gene Expression Omnibus (GEO) databases. A total of 87 common differentially expressed genes (DEGs) among GSE15781, GSE110223, and GSE110224 were identified, including 19 upregulated genes and 68 downregulated genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed for common DEGs using clusterProfiler. These common DEGs were significantly involved in cancer-associated functions and signaling pathways. Then, we constructed protein-protein interaction networks of these common DEGs using Cytoscape software, which resulted in the identification of the following 10 core genes: SST, PYY, CXCL1, CXCL8, CXCL3, ZG16, AQP8, CLCA4, MS4A12, and GUCA2A. Analysis using qRT-PCR has shown that SST, CXCL8, and MS4A12 were significant differentially expressed between colorectal cancer tissues and normal colorectal tissues (P<0.05). Gene Expression Profiling Interactive Analysis (GEPIA) overall survival (OS) has shown that low expressions of AQP8, ZG16, CXCL3, and CXCL8 may predict poor survival outcome in colorectal cancer. In conclusion, the core genes identified in this study contributed to the understanding of the molecular mechanisms involved in colorectal cancer development and may be targets for early diagnosis, prevention, and treatment of colorectal cancer.

scholarly journals Gene Expression Profiles and microRNA Regulation Networks in Tiller Primordia, Stem Tips, and Young Spikes of Wheat Guomai 301

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 686 ◽  
Author(s):  
Li ◽  
Jiao ◽  
He ◽  
Sun ◽  
Xu ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Triticum Aestivum L ◽  
Differentially Expressed ◽  
High Yield ◽  
Differentially Expressed Mirnas ◽  
Key Events ◽  
Post Transcriptional Regulation

Tillering and spike differentiation are two key events for wheat (Triticum aestivum L.). A study on the transcriptomes and microRNA group profiles of wheat at the two key developmental stages will bring insight into the molecular regulation mechanisms. Guomai 301 is a representative excellent new high yield wheat cultivar in the Henan province in China. The transcriptomes and microRNA (miRNA) groups of tiller primordia (TPs), stem tips (STs), and young spikes (YSs) in Guomai 301 were compared to each other. A total of 1741 tillering specifically expressed and 281 early spikes differentiating specifically expressed differentially expressed genes (DEGs) were identified. Six major expression profile clusters of tissue-specific DEGs for the three tissues were classified by gene co-expression analysis using K-means cluster. The ribosome (ko03010), photosynthesis-antenna proteins (ko00196), and plant hormone signal transduction (ko04075) were the main metabolic pathways in TPs, STs, and YSs, respectively. Similarly, 67 TP specifically expressed and 19 YS specifically expressed differentially expressed miRNAs were identified, 65 of them were novel. The roles of 3 well known miRNAs, tae-miR156, tae-miR164, and tae-miR167a, in post-transcriptional regulation were similar to that of other researches. There were 651 significant negative miRNA–mRNA interaction pairs in TPs and YSs, involving 63 differentially expressed miRNAs (fold change > 4) and 416 differentially expressed mRNAs. Among them 12 key known miRNAs and 16 novel miRNAs were further analyzed, and miRNA–mRNA regulatory networks during tillering and early spike differentiating were established.

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