Identification and characterization of mRNAs and lncRNAs of a barley shrunken endosperm mutant using RNA-seq

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

Download Full-text

Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots

BMC Genomics ◽

10.1186/s12864-018-5205-9 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 10

Author(s):

Omika Thakur ◽

Gursharn Singh Randhawa

Keyword(s):

Molecular Markers ◽

Cyamopsis Tetragonoloba ◽

Rna Seq ◽

Identification And Characterization

Download Full-text

The identification and characterization of novel transcripts from RNA-seq data

Briefings in Bioinformatics ◽

10.1093/bib/bbv067 ◽

2015 ◽

Vol 17 (4) ◽

pp. 678-685 ◽

Cited By ~ 20

Author(s):

Tyler Weirick ◽

Giuseppe Militello ◽

Raphael Müller ◽

David John ◽

Stefanie Dimmeler ◽

...

Keyword(s):

Rna Seq ◽

Novel Transcripts ◽

Identification And Characterization

Download Full-text

OMIC-04. IDENTIFICATION AND CHARACTERIZATION OF CIRCULATING RNAS (CODING AND NONCODING) AND METABOLITES IN CEREBROSPINAL FLUID IN MEDULLOBLASTOMA PATIENTS

Neuro-Oncology ◽

10.1093/neuonc/noab090.151 ◽

2021 ◽

Vol 23 (Supplement_1) ◽

pp. i37-i37

Author(s):

Bongyong Lee ◽

Stacie Stapleton ◽

Rudramani Pokhrel ◽

Chetan Bettegowda ◽

George Jallo ◽

...

Keyword(s):

Cerebrospinal Fluid ◽

Brain Tumor ◽

Metabolic Pathways ◽

Tumor Tissue ◽

Tumor Type ◽

Molecular Signatures ◽

Rna Seq ◽

Neuro Imaging ◽

Identification And Characterization

Abstract Medulloblastoma (MB) is the most common malignant brain tumor in children, and monitoring patients for treatment response and recurrence can be challenging with available current technologies in neuro-imaging and performing a biopsy to confirm response or recurrence carries risks, whereas cerebrospinal fluid (CSF) can be obtained with a little invasiveness. MB has altered cellular metabolism due to changes in gene expression, therefore, we hypothesized that any changes in MB cells lead to changes in cell-free transcripts and metabolites in CSF. To test this, we applied RNA-sequencing and mass spectrometry to analyze transcripts and metabolites including lipid in CSF from patients with different sub-groups of MB tumors (i.e., WNT, SHH, G3/4, G4, and unknown) and compared them to non-cancerous CSF. Tumor and sub-group specific transcriptomic and metabolic signatures were shown by unsupervised hierarchical clustering facilitating tumor type differentiation. By comparison with previously published tumor tissue RNA-seq data, we were able to identify a group of upregulated molecular signatures in both tumor tissue and CSF. We also identified a group of lipids that differentiate each MB sub-group from normal CSF, and Pathway analysis confirmed alterations in multiple metabolic pathways. Finally, we attempted to integrate RNA-seq data with lipidomics data, and results depict that the combinatorial analysis of CSF RNAs and metabolites can be useful in diagnosing and monitoring patients with MB tumors. (This research was conducted using samples made available by The Children’s Brain Tumor Network.)

Download Full-text

Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

10.1101/482208 ◽

2018 ◽

Cited By ~ 1

Author(s):

Elsie C. Jacobson ◽

Ralph S. Grand ◽

Jo K. Perry ◽

Mark H. Vickers ◽

Ada L. Olins ◽

...

Keyword(s):

Cell Line ◽

Cell Lines ◽

Myeloid Leukemia ◽

Large Scale ◽

Rna Seq ◽

Structural Variants ◽

The Stability ◽

Different Sources ◽

Identification And Characterization

AbstractCancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter- and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used Hi-C and RNA-seq to identify and compare large SVs in HL-60 and HL-60/S4 cell lines. Comparisons with previously published karyotypes identified novel SVs in both cell lines. Hi-C was used to characterize the known expansion centered on the MYC locus. The MYC expansion was integrated into known locations in HL-60/S4, and a novel location (chr4) in HL-60. The HL-60 cell line has more within-line structural variation than the HL-60/S4 derivative cell line. Collectively we demonstrate the usefulness of Hi-C and with RNA-seq data for the identification and characterization of SVs.

Download Full-text

Identification and characterization of circular RNA in lactating mammary glands from two breeds of sheep with different milk production profiles using RNA-Seq

Genomics ◽

10.1016/j.ygeno.2019.12.014 ◽

2020 ◽

Vol 112 (3) ◽

pp. 2186-2193 ◽

Cited By ~ 9

Author(s):

Zhiyun Hao ◽

Huitong Zhou ◽

Jon G.H. Hickford ◽

Hua Gong ◽

Jiqing Wang ◽

...

Keyword(s):

Milk Production ◽

Circular Rna ◽

Mammary Glands ◽

Rna Seq ◽

Identification And Characterization

Download Full-text

Identification and Characterization of Circular RNA as a Novel Regulator and Biomarker in Preterm Birth

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2020.566984 ◽

2020 ◽

Vol 8 ◽

Author(s):

Yuxin Ran ◽

Nanlin Yin ◽

Dongni Huang ◽

Yangyu Zhao ◽

Jing Yang ◽

...

Keyword(s):

Preterm Birth ◽

Roc Analysis ◽

Underlying Mechanism ◽

Circular Rna ◽

Diagnosis And Treatment ◽

Rna Seq ◽

Discrimination Ability ◽

First Time ◽

Identification And Characterization

Preterm birth (PTB), as the leading cause of neonatal death, is a severe threat to maternal–fetal health. The diagnosis and treatment of PTB are difficult as its underlying mechanism still unknown. Circular RNA (circRNA) is an emerging molecule that plays an essential role in the pathological processes of various diseases. However, it is still unclear whether circRNAs are abnormal or involves in the PTB pathology. In this study, we analyzed RNA-seq data of peripheral blood from preterm and term pregnant women and verified with microarray data. There were 211 circRNA expression disorders in PTB, of which 68 increased and 143 decreased. Bioinformatics analysis revealed that the top 20 circRNAs competitively bind 68 miRNAs, thereby regulating 622 mRNAs mainly related to immunity, inflammation, and nerve activity, which may ultimately contribute to the occurrence of PTB. Moreover, 6 regulatory pairs, including hsa-MORC3_0001–hsa-miR-1248–CHRM2 were the core parts of this mechanism network, which might be therapeutic targets for PTB. Besides, ROC analysis indicated that hsa-ANKFY1_0025, hsa-FAM13B_0019, and hsa-NUSAP1_0010 (AUC = 0.7138, 0.9589, 1.000) have an excellent discrimination ability for PTB. Taken together, we explored for the first time the circRNA expression profile of PTB, and preliminarily analyzed its regulatory mechanism and predictive value for PTB, thus bringing new light to the diagnosis and treatment of PTB.

Download Full-text

Genome-Wide Analysis, Evolutionary History and Response of ALMT Family to Phosphate Starvation in Brassica napus

International Journal of Molecular Sciences ◽

10.3390/ijms22094625 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4625

Author(s):

Ismail Din ◽

Ihteram Ullah ◽

Wei Wang ◽

Hao Zhang ◽

Lei Shi

Keyword(s):

Brassica Napus ◽

Gene Family ◽

P Availability ◽

Rna Seq ◽

Soil P ◽

Genome Wide ◽

Low Phosphorus ◽

Leaf Tissues ◽

Identification And Characterization

Low phosphorus (P) availability is one of the major constraints to plant growth, particularly in acidic soils. A possible mechanism for enhancing the use of sparsely soluble P forms is the secretion of malate in plants by the aluminum-activated malate transporter (ALMT) gene family. Despite its significance in plant biology, the identification of the ALMT gene family in oilseed rape (Brassica napus; B. napus), an allotetraploid crop, is unveiled. Herein, we performed genome-wide identification and characterization of ALMTs in B. napus, determined their gene expression in different tissues and monitored transcriptional regulation of BnaALMTs in the roots and leaves at both a sufficient and a deficient P supply. Thirty-nine BnaALMT genes were identified and were clustered into five branches in the phylogenetic tree based on protein sequences. Collinearity analysis revealed that most of the BnaALMT genes shared syntenic relationships among BnaALMT members in B. napus, which suggested that whole-genome duplication (polyploidy) played a major driving force for BnaALMTs evolution in addition to segmental duplication. RNA-seq analyses showed that most BnaALMT genes were preferentially expressed in root and leaf tissues. Among them, the expression of BnaC08g13520D, BnaC08g15170D, BnaC08g15180D, BnaC08g13490D, BnaC08g13500D, BnaA08g26960D, BnaC05g14120D, BnaA06g12560D, BnaC05g20630D, BnaA07g02630D, BnaA04g15700D were significantly up-regulated in B. napus roots and leaf at a P deficient supply. The current study analyzes the evolution and the expression of the ALMT family in B. napus, which will help in further research on their role in the enhancement of soil P availability by secretion of organic acids.

Download Full-text

Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

PeerJ ◽

10.7717/peerj.3747 ◽

2017 ◽

Vol 5 ◽

pp. e3747 ◽

Cited By ~ 20

Author(s):

Weilong Kong ◽

Shaozong Yang ◽

Yulu Wang ◽

Mohammed Bendahmane ◽

Xiaopeng Fu

Keyword(s):

Sugar Beet ◽

Beta Vulgaris ◽

Growth And Development ◽

Phylogenetic Analyses ◽

Rna Seq ◽

Reference Base ◽

Genome Wide ◽

Aquaporin Gene ◽

Identification And Characterization

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.

Download Full-text

A Mutation in CsHY2 Encoding a Phytochromobilin (PΦB) Synthase Leads to an Elongated Hypocotyl 1(elh1) Phenotype in Cucumber (Cucumis sativus L.)

10.21203/rs.3.rs-182705/v1 ◽

2021 ◽

Author(s):

Liangliang Hu ◽

Peng Liu ◽

Zhuoshuai Jin ◽

Jing Sun ◽

Yiqun Weng ◽

...

Keyword(s):

Cell Elongation ◽

Ectopic Expression ◽

Rna Seq ◽

Wild Type ◽

Hypocotyl Growth ◽

Hypocotyl Length ◽

Critical Determinant ◽

Cucumis Sativus L ◽

Identification And Characterization

Abstract Hypocotyl length is a critical determinant in establishing high quality seedlings for successful cucumber production, but knowledge on the molecular regulation of hypocotyl growth in cucumber is very limited. Here we reported identification and characterization of a cucumber elongated hypocotyl 1 (elh1) mutant. We found that the longer hypocotyl in elh1 was due to longitudinal growth of hypocotyl cells. With fine mapping, the elh1 locus was delimited to a 20.9-kb region containing three annotated genes; only one polymorphism was identified in this region between two parental lines, which was a non-synonymous SNP (G28153633A) in the third exon of CsHY2 (CsGy1G030000) that encodes a phytochromobilin (PΦB) synthase. Uniqueness of the mutant allele at CsHY2 was verified in 515 cucumber lines. Ectopic expression of CsHY2 in Arabidopsis hy2-1 mutant led to reduced hypocotyl length. The PΦB protein was targeted to chloroplasts. The expression levels of CsHY2 and five phytochrome genes, CsPHYA1, CsPHYA2, CsPHYB, CsPHYC and CsPHYE were all significantly down-regulated while several cell elongation related genes were up-regulated in elh1 mutant compared to wild type cucumber, which are correlated with dynamic hypocotyl elongation in the mutant. RNA-seq analysis in the WT and mutant revealed differentially expressed genes involved in porphyrin and chlorophyll metabolisms, cell elongation, and plant hormone signal transduction pathways. This is the first report to characterize and clone the CsHY2 gene in cucumber. This work reveals the important of CsHY2 in regulating hypocotyl length and extends our understanding of the roles of CsHY2 in cucumber.

Download Full-text