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

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.

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Identification and characterization of three new molecular markers associated with spawning date in coho salmon (Oncorhynchus kisutch)

Aquaculture ◽

10.1016/j.aquaculture.2007.07.022 ◽

2007 ◽

Vol 272 ◽

pp. S240 ◽

Cited By ~ 2

Author(s):

C. Araneda ◽

N.F. Díaz ◽

G. Gómez ◽

P. Iturra

Keyword(s):

Molecular Markers ◽

Coho Salmon ◽

Oncorhynchus Kisutch ◽

Identification And Characterization

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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

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Assessment of Genetic Diversity of Rheum species (Endangered Medicinal Herb of Indian Himalayan Region) using Molecular Markers

Research Journal of Biotechnology ◽

10.25303/1611rjbt147154 ◽

2021 ◽

Vol 16 (11) ◽

pp. 147-154

Author(s):

Anjali Uniyal ◽

Akhilesh Kumar ◽

Sweta Upadhyay ◽

Vijay Kumar ◽

Sanjay Gupta

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Fragment Length Polymorphism ◽

Dna Polymorphisms ◽

Inter Simple Sequence Repeats ◽

Pharmaceutical Industries ◽

Endangered Medicinal Herb ◽

Identification And Characterization ◽

Simple Sequence

The Rheum species are important medicinal plants that are facing extinction due to their unplanned development and overexploitation by pharmaceutical industries. DNA polymorphisms are not prone to environmental modifications, thus they are widely used for the identification and characterization of plants. The use of different molecular markers has enabled the researchers for the valuation of genetic variability and diversity in its natural zone of distribution. The conventional approach may take several years to yield this information. For the estimation of molecular and genetic variations in geographical zone of distribution, various molecular markers technique are available like RAPD (Randomly Amplified Polymorphic DNA), RFLP (Restriction fragment length polymorphism), ISSR (Inter-Simple Sequence Repeats), SSR and AFLP. The uses of different molecular markers for the study of genetic diversity have been discussed in the review.

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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.)

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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.

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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

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

Genetica ◽

10.1007/s10709-020-00087-2 ◽

2020 ◽

Vol 148 (2) ◽

pp. 55-68

Author(s):

Yaya Zou ◽

Huaping Tang ◽

Ting Li ◽

Min Sun ◽

Xiangru Qu ◽

...

Keyword(s):

Rna Seq ◽

Endosperm Mutant ◽

Identification And Characterization

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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.

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