scholarly journals Transcriptome Profiling Reveals Key Genes In Regulation Of The Tepal Trichome Development In Lilium Pumilum D.C.

2021 ◽  
Author(s):  
Yin Xin ◽  
Wenqiang Pan ◽  
Xi Chen ◽  
Yixin Liu ◽  
Mingfang Zhang ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Alkali Resistance ◽  
Rna Seq ◽  
Abiotic And Biotic Stress ◽  
Wild Type ◽  
Quantitative Real Time Pcr ◽  
Crop Breeding ◽  
Economic Trait ◽  
Specialized Structure ◽  
Lilium Davidii

Abstract Trichome is a specialized structure found on the surface of the plant with important function in survival against abiotic and biotic stress. It is also an important economic trait in crop breeding. Extensive research has investigated the foliar trichome in model plants (Arabidopsis and tomato). However, the developmental mechanism of tepal trichome remains elusive. Lilium pumilum is an edible ornamental bulb and a good breeding parent possessing cold and salt-alkali resistance. Here, we found a natural mutant of Lilium pumilum grown on a highland whose tepals are covered by trichomes. Our data indicate that trichomes of this mutant are multicellular and branchless. Notably, stomata are also developed on the tepal of the mutant as well, suggesting there may be a correlated between trichome and stomata regulation. Furthermore, we isolated 27 differentially expressed genes (DEGs) by comparing the transcriptome profiling between the natural mutant and the wild type. These twenty-seven genes belong to four groups: epidermal cell cycle and division, trichome morphogenesis, stress response, and transcription factors. Quantitative real-time PCR in Lilium pumilum (natural mutant and the wild type) and other lily species (Lilium leichtlinii var. maximowiczii/ trichome; Lilium davidii var. willmottiael, trichomeless) confirmed the validation of RNA-seq data and identified several trichome-related genes.

scholarly journals Putative transmembrane transporter modulates higher-level aggression in Drosophila

2017 ◽  
Vol 114 (9) ◽  
pp. 2373-2378 ◽  
Author(s):  
Budhaditya Chowdhury ◽  
Yick-Bun Chan ◽  
Edward A. Kravitz
Keyword(s):  
Causal Effect ◽  
Nerve Terminals ◽  
Rna Seq ◽  
Wild Type ◽  
Temperature Dependent ◽  
Number Of Genes ◽  
Interesting Family ◽  
Solute Carrier ◽  
Transmembrane Transporter ◽  
Selection Of

By selection of winners of dyadic fights for 35 generations, we have generated a hyperaggressive Bully line of flies that almost always win fights against the parental wild-type Canton-S stock. Maintenance of the Bully phenotype is temperature dependent during development, with the phenotype lost when flies are reared at 19 °C. No similar effect is seen with the parent line. This difference allowed us to carry out RNA-seq experiments and identify a limited number of genes that are differentially expressed by twofold or greater in the Bullies; one of these was a putative transmembrane transporter, CG13646, which showed consistent and reproducible twofold down-regulation in Bullies. We examined the causal effect of this gene on the phenotype with a mutant line for CG13646, and with an RNAi approach. In all cases, reduction in expression of CG13646 by approximately half led to a hyperaggressive phenotype partially resembling that seen in the Bully flies. This gene is a member of a very interesting family of solute carrier proteins (SLCs), some of which have been suggested as being involved in glutamine/glutamate and GABA cycles of metabolism in excitatory and inhibitory nerve terminals in mammalian systems.

scholarly journals Overexpression of OsABCG48 Lowers Cadmium in Rice (Oryza sativa L.)

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 918
Author(s):  
Xingzhe Cai ◽  
Meng Wang ◽  
Yucong Jiang ◽  
Changhu Wang ◽  
David W. Ow
Keyword(s):  
Oryza Sativa L ◽  
Cost Effective ◽  
Health Issues ◽  
Rna Seq ◽  
Wild Type ◽  
Genetic Changes ◽  
Cd Accumulation ◽  
Lateral Root Development ◽  
Atp Binding Cassette Transporter ◽  
Cost Effective Approach

Cadmium pollution threatens food safety and security by causing health issues and reducing farmland availability. Engineering genetic changes in crop plants to lower Cd accumulation can be a cost-effective approach to address this problem. Previously, we reported that a rice line, 2B, which expresses a truncated version of OsO3L2 had reduced Cd accumulation throughout the plant, including in seed. However, downstream events caused by expression of this gene were not known. In this study, RNA-seq was used to identify differentially expressed genes between the wild type and 2B rice with or without Cd treatment, leading to the study of an ABC transporter gene, OsABCG48 (ATP-Binding Cassette transporter G family member 48). Heterologous expression of OsABCG48 conferred tolerance to Cd in Schizosaccharomyces pombe, Arabidopsis and rice. Moreover, overexpressing OsABCG48 in rice lowered root Cd accumulation that was associated with more extensive lateral root development. These data suggest that OsABCG48 might have applications for engineering low-Cd rice.

scholarly journals Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia

2021 ◽  
Vol 22 (5) ◽  
pp. 2683
Author(s):  
Princess D. Rodriguez ◽  
Hana Paculova ◽  
Sophie Kogut ◽  
Jessica Heath ◽  
Hilde Schjerven ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
B Cell ◽  
Molecular Mechanisms ◽  
Lymphoblastic Leukemia ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Technological Developments ◽  
Cell Acute Lymphoblastic Leukemia

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

scholarly journals Characterization of neuroendocrine tumors in heterozygous mutant MENX rats: a novel model of invasive medullary thyroid carcinoma

2018 ◽  
Vol 25 (2) ◽  
pp. 145-162 ◽  
Author(s):  
Sara Molatore ◽  
Andrea Kügler ◽  
Martin Irmler ◽  
Tobias Wiedemann ◽  
Frauke Neff ◽  
...  
Keyword(s):  
Neuroendocrine Tumors ◽  
Early Stage ◽  
Pituitary Tumors ◽  
Transcriptome Profiling ◽  
Thyroid Neoplasms ◽  
Recessive Trait ◽  
Wild Type ◽  
Incurable Cancer ◽  
Medullary Thyroid ◽  
Adrenal Pheochromocytoma

Rats affected by the MENX syndrome spontaneously develop multiple neuroendocrine tumors (NETs) including adrenal, pituitary and thyroid gland neoplasms. MENX was initially reported to be inherited as a recessive trait and affected rats were found to be homozygous for the predisposingCdkn1bmutation encoding p27. We here report that heterozygous MENX-mutant rats (p27+/mut) develop the same spectrum of NETs seen in the homozygous (p27mut/mut) animals but with slower progression. Consequently, p27+/mut rats have a significantly shorter lifespan compared with their wild-type (p27+/+) littermates. In the tumors of p27+/mut rats, the wild-typeCdkn1ballele is neither lost nor silenced, implying that p27 is haploinsufficient for tumor suppression in this model. Transcriptome profiling of rat adrenal (pheochromocytoma) and pituitary tumors having different p27 dosages revealed a tissue-specific, dose-dependent effect of p27 on gene expression. In p27+/mut rats, thyroid neoplasms progress to invasive and metastatic medullary thyroid carcinomas (MTCs) accompanied by increased calcitonin levels, as in humans. Comparison of expression signatures of late-stage vs early-stage MTCs from p27+/mut rats identified genes potentially involved in tumor aggressiveness. The expression of a subset of these genes was evaluated in human MTCs and found to be associated with aggressive RET-M918T-positive tumors. Altogether, p27 haploinsufficiency in MENX rats uncovered a novel, representative model of invasive and metastatic MTC exploitable for translational studies of this often aggressive and incurable cancer.

scholarly journals Erratum: Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

2014 ◽  
Vol 32 (11) ◽  
pp. 1166-1166 ◽  
Author(s):  
Sheng Li ◽  
Scott W Tighe ◽  
Charles M Nicolet ◽  
Deborah Grove ◽  
Shawn Levy ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Combined Metabolome and Transcriptome Profiling Reveal Optimal Harvest Strategy Model Based on Different Production Purposes in Olive

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 360
Author(s):  
Guodong Rao ◽  
Jianguo Zhang ◽  
Xiaoxia Liu ◽  
Xue Li ◽  
Chenhe Wang
Keyword(s):  
Gene Expression ◽  
Olive Oil ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Minor Components ◽  
Harvest Time ◽  
Rna Seq ◽  
Optimal Harvest ◽  
Harvest Strategy ◽  
Different Color

Olive oil has been favored as high-quality edible oil because it contains balanced fatty acids (FAs) and high levels of minor components. The contents of FAs and minor components are variable in olive fruits of different color at harvest time, which render it difficult to determine the optimal harvest strategy for olive oil producing. Here, we combined metabolome, Pacbio Iso-seq, and Illumina RNA-seq transcriptome to investigate the association between metabolites and gene expression of olive fruits at harvest time. A total of 34 FAs, 12 minor components, and 181 other metabolites (including organic acids, polyols, amino acids, and sugars) were identified in this study. Moreover, we proposed optimal olive harvesting strategy models based on different production purposes. In addition, we used the combined Pacbio Iso-seq and Illumina RNA-seq gene expression data to identify genes related to the biosynthetic pathways of hydroxytyrosol and oleuropein. These data lay the foundation for future investigations of olive fruit metabolism and gene expression patterns, and provide a method to obtain olive harvesting strategies for different production purposes.

scholarly journals RNA-Seq transcriptome profiling of mouse oocytes after in vitro maturation and/or vitrification

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lei Gao ◽  
Gongxue Jia ◽  
Ai Li ◽  
Haojia Ma ◽  
Zhengyuan Huang ◽  
...  
Keyword(s):  
In Vitro Maturation ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Mouse Oocytes

scholarly journals Transcriptomic Profiling of Fruits from Pepper (Capsicum annuum L.), Variety Padrón (Mild Hot), at Two Ripening States

2021 ◽  
Vol 3 (1) ◽  
pp. 16
Author(s):  
Salvador González-Gordo ◽  
José M. Palma ◽  
Francisco J. Corpas
Keyword(s):  
Capsicum Annuum ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Functional Categories ◽  
Transcriptomic Profiling ◽  
Local Conditions ◽  
Capsicum Annuum L ◽  
Climacteric Fruit ◽  
Genetic Level ◽  
Genus Capsicum

Pepper (Capsicum annuum L.) fruits are one of the most consumed vegetables worldwide. This produce has a great agro-economical relevance, since it is extensively cultivated. These fruits are characterized by their high content of vitamins C and A [1]. Capsicum annuum has many varieties, whose fruits differ in size, shape, color, and pungency, this last characteristic being due to the presence, in different degrees, of capsaicinoids and alkaloids, which are exclusive to the genus Capsicum [2]. The present study focuses on the transcriptomic profiling of an autochthonous Spanish variety called “Padrón” (mild hot) [3]. Pepper “Padrón” plants were grown in farms under the local conditions (42°44′05″ N 8°37′42″ W), and fruits at both green and red ripe ripening stages were collected. The transcriptome profiling was carried out in both types of fruits by RNA sequencing (RNA-seq) using the NextSeq550 system (Illumina®) [4,5]. RNA-seq analysis revealed that the expression of more than half of the 17,499 identified transcripts was modulated during ripening. Comparing to green fruits, 5626 and 5241 genes were up- and down-regulated, respectively, in red fruits. These differentially expressed genes (DEGs) have been analyzed to determine the functional categories that orchestrate the ripening process at the genetic level of this non-climacteric fruit.

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