scholarly journals The male and female gonad transcriptome of the edible sea urchin, Paracentrotus lividus: identification of sex-related and lipid biosynthesis genes

2021 ◽  
Author(s):  
André M. Machado ◽  
Sergio Fernández-Boo ◽  
Manuel Nande ◽  
Rui Pinto ◽  
Benjamin Costas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Transcriptome Assembly ◽  
Paracentrotus Lividus ◽  
Female Gonad ◽  
Male And Female ◽  
Gene Expression Analyses ◽  
Differential Gene ◽  
And Storage ◽  
Transcriptomic Resource

AbstractParacentrotus lividus is the most abundant, distributed and desirable echinoid species in Europe. Although, economically important, this species has scarce genomic resources available. Here, we produced and comprehensively characterized the male and female gonad transcriptome of P. lividus. The P. lividus transcriptome assembly has 53,865 transcripts, an N50 transcript length of 1,842 bp and an estimated gene completeness of 97.4% and 95.6% in Eukaryota and Metazoa BUSCO databases, respectively. Differential gene expression analyses yielded a total of 3371 and 3351 up regulated genes in P. lividus male and female gonad tissues, respectively. Additionally, we analysed and validated a catalogue of pivotal transcripts involved in sexual development and determination (206 transcripts) as well as in biosynthesis and storage of lipids (119 transcripts) in male and female specimens. This study provides a valuable transcriptomic resource and will contribute for the future conservation of the species as well as the exploitation in aquaculture settings.HighlightsAssembly of a reference transcriptome of Paracentrotus lividus gonads.Differential gene expression between males and female gonads of Paracentrotus lividus.Identification and validation of pivotal genes involved in biosynthesis and storage of lipids.

scholarly journals Why Pashmina Goat Produces Long Hair-fiber and Barbari doesn’t: A Differential Gene Expression Study

2021 ◽  
Author(s):  
Rashid Saif ◽  
Tania Mahmood ◽  
Aniqa Ejaz ◽  
Saeeda Zia
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Transcriptome Assembly ◽  
Hair Shaft ◽  
Hair Follicles ◽  
Differentially Expressed ◽  
Keratinocyte Differentiation ◽  
Dermal Papilla Cells ◽  
Differential Gene ◽  
Hair Fiber

The Pashmina and Barbari are two famous goat breeds found in the wide areas of the Indo-Pak region. Pashmina is famous for its long hair-fiber (Cashmere) production while Barbari is not-selected for this trait. So, the mRNA expression profiling in the skin samples of both breeds would be an attractive and judicious approach for detecting putative genes involved in this valued trait. Here, we performed differential gene expression analysis on publicly available RNA-Seq data from both breeds. Out of 44,617,994 filtered reads of Pashmina and 55,995,999 of Barbari which are 76.48% and 73.69% mapped to the ARS1 reference transcriptome assembly respectively. A pairwise comparison of both breeds resulted in 47,159 normalized expressed transcripts while 8,414 transcripts are differentially expressed above the significant threshold. Among these, 4,788 are upregulated in Pashmina while 3,626 transcripts are upregulated in Barbari. Fifty-nine transcripts harbor 57 genes including 32 LOC genes and 24 are annotated genes which were selected on the basis of TMM counts > 500. Genes with ectopic expressions other than uncharacterized and LOC symbol genes are Keratins (KRT) and Keratin Associated Proteins (KRTAPs), CystatinA&6, TCHH, SPRR4, PPIA, SLC25A4, S100A11, DMKN, LOR, ANXA2, PRR9 and SFN. All of these genes are likely to be involved in keratinocyte differentiation, sulfur matrix proteins, dermal papilla cells, hair follicles proliferation, hair curvature, wool fiber diameter, hair transition, hair shaft differentiation and its keratinization. These differentially expressed reported genes are critically valuable for enhancing the quality and quantity of the pashmina fiber and overall breed improvement. This study will also provide important information on hair follicle differentiation for further enrichment analyses and introducing this valued trait to other goat breeds as well.

Differential gene expression of cholinergic muscarinic receptor subtypes in male and female normal human urinary bladder

Urology ◽  
2002 ◽  
Vol 60 (4) ◽  
pp. 719-725 ◽  
Author(s):  
Sandra Sigala ◽  
Giuseppe Mirabella ◽  
Angelo Peroni ◽  
Giuseppe Pezzotti ◽  
Claudio Simeone ◽  
...  
Keyword(s):  
Gene Expression ◽  
Urinary Bladder ◽  
Muscarinic Receptor ◽  
Differential Gene Expression ◽  
Receptor Subtypes ◽  
Muscarinic Receptor Subtypes ◽  
Male And Female ◽  
Human Urinary Bladder ◽  
Normal Human ◽  
Differential Gene

scholarly journals De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech

PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184167 ◽  
Author(s):  
Markus Müller ◽  
Sarah Seifert ◽  
Torben Lübbe ◽  
Christoph Leuschner ◽  
Reiner Finkeldey
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
European Beech ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Differential Gene

scholarly journals A Comprehensive and Universal Method for Assessing the Performance of Differential Gene Expression Analyses

PLoS ONE ◽  
2010 ◽  
Vol 5 (9) ◽  
pp. e12657 ◽  
Author(s):  
Mikhail G. Dozmorov ◽  
Joel M. Guthridge ◽  
Robert E. Hurst ◽  
Igor M. Dozmorov
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Universal Method ◽  
Gene Expression Analyses ◽  
Differential Gene

scholarly journals Transcriptome Sequencing of Trichoderma Koningiopsis Strain Tk1 to Identify and Analyze Differential Gene Expression Patterns

2020 ◽  
Author(s):  
Mei Luo ◽  
Zhangyong Dong ◽  
Yongxin Shu ◽  
Mobing Chen
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Differential Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Antimicrobial Effect ◽  
Carbohydrate Active Enzymes ◽  
Differential Gene

Abstract Background: Trichoderma koningiopsis strain Tk1 shows good biocontrol potential. However, its biocontrol function may differ under different conditions. The objective of this study is to elucidate the biological and transcriptome differences of T. koningiopsis Tk1 under different media. Results: In this study, the mycelium weight and sporulation of T. koningiopsis Tk1 was found to differ in various media. Further, the Tk1 strain inhibited the growth of the pathogen Fusarium oxysporum in the three media tested. Fries3, PD, and PS were collected for RNA sequencing of Tk1 mycelia to identify the genes that are differentially expressed genes (DEGs) between Tk1 grown on different media. De novo transcriptome assembly resulted in identification of 14,208 unigenes. The differential gene expression pattern was more similar between the Fries3 and PS samples, whereas PD samples showed a different expression pattern. The DEGs were enriched in some metabolic and biosynthetic pathways. Additional analysis of the DEGs identified a set of carbohydrate-active enzymes that are upregulated or downregulated under different conditions.Conclusions: These results indicate that the Tk1 strain cultured in Fires3 and PS mediums can produce specific metabolic and carbohydrate-active enzymes to enhance their antimicrobial effect, providing a foundation for the subsequent mining of specific genes.

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