Comparison of differential expression genes in ovaries and testes of Pearlscale angelfish Centropyge vrolikii based on RNA-Seq analysis

2021 ◽  
Vol 47 (5) ◽  
pp. 1565-1583
Author(s):  
Zhaowei Zhong ◽  
Lulu Ao ◽  
Yilei Wang ◽  
Shuhong Wang ◽  
Liping Zhao ◽  
...  
Keyword(s):  
Differential Expression ◽  
Rna Seq ◽  
Differential Expression Genes

scholarly journals Transcriptome analysis of flower color reveals the correlation between SNP and differential expression genes in Phalaenopsis

2021 ◽  
Author(s):  
Yu Ding ◽  
Ding-Hai Yang ◽  
Ma-Yin Wang ◽  
Dai-Cheng Hao ◽  
Wei-Shi Li ◽  
...  
Keyword(s):  
Differential Expression ◽  
Economic Value ◽  
Flower Color ◽  
Rna Seq ◽  
Transcription Level ◽  
Color Formation ◽  
Pathway Enrichment ◽  
Differential Expression Genes ◽  
Important Position ◽  
Transcriptome Level

Abstract Background Phalaenopsis is an important ornamental plant, which occupies an important position in the world flower market and has great economic value due to its rich and diverse flower colors. In order to investigate the flower color formation of Phalaenopsis at transcription level, the flower color formation involved genes were identified from RNA-seq in this study.Results White and purple petals of Phalaenopsis were collected in this study, and results were focused on two aspects: (1) the differential expression genes (DEGs) between white and purple flower color; and (2) association between SNP mutations and DEGs in transcriptome level. Results indicated that a total of 1,175 DEGs were identified, and the up- and down-regulation genes were 718 and 457, respectively. Gene Ontology (GO) and pathway enrichment showed that the biosynthesis of secondary metabolites pathway was key responsible for color formation and twelve crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase and E1.11.17) from them involved in the regulation of flower color in Phalaenopsis. Conclusion This study firstly reported that the SNP mutations strongly associated with DEGs in color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.

scholarly journals Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii)

2019 ◽  
Author(s):  
Xiujuan Zhang ◽  
Jiabin Zhou ◽  
Linmiao Li ◽  
Wenzhong Huang ◽  
Hafiz Ishfaq Ahmad ◽  
...  
Keyword(s):  
Differential Expression ◽  
Average Length ◽  
Full Length ◽  
Rna Seq ◽  
Genetic Characteristics ◽  
Kegg Pathways ◽  
Amur Sturgeon ◽  
Differential Expression Genes ◽  
Transcription Data ◽  
Development And Evolution

Abstract Background Sturgeons (Acipenseriformes) are polyploid chondrostean fish that constitute an important model species for studying development and evolution in vertebrates. To better understand the mechanisms of reproduction regulation in sturgeon, this study combined PacBio isoform sequencing (Iso-Seq) with Illumina short-read RNA-seq methods to discover full-length genes involved in early gametogenesis of the Amur sturgeon, Acipenser schrenckii .Results A total of 50.04 G subread bases were generated from two SMRT cells, and herein 164,618 nonredundant full-length transcripts (unigenes) were produced with an average length of 2,782 bp from gonad tissues (three testes and four ovaries) from seven 3-year-old A. schrenckii individuals. The number of ovary-specific expressed unigenes was greater than those of testis (19,716 vs. 3,028), and functional assignment indicated that 6 of 14 annotated KEGG pathways were directly ovary-related and had abundant transcripts and differential expression genes. Importantly, 60 early gametogenesis-related genes (involving 755 unigenes) were successfully identified, and exactly 50 percent (30/60) of those showed differential expression in testes and ovaries. The Amh and Gsdf with testis-biased expression, and Foxl2 and Cyp19a with ovary-biased expression strongly suggested the important regulatory roles in spermatogenesis and oogenesis of A. schrenckii , respectively. We also found the four novel Sox9 transcript variants, which increase the numbers of regulatory genes and imply function complexity of early gametogenesis. Finally, a total of 236,672 AS events (involving 36,522 unigenes) were detected, and 10,556 putative long noncoding RNAs (lncRNAs) and 4,339 predicted transcript factors (TFs) were also respectively identified, which all significantly associated with the early gametogenesis of A. schrenckii .Conclusions Overall, our results provide new genetic resources of full-length transcription data and information as a genomic-level reference for sturgeon. Crucially, we explored the comprehensive genetic characteristics that differ between the testes and ovaries of A. schrenckii in the early gametogenesis stage. These provide candidate genes and theoretical basis for further the mechanisms of reproduction regulation of sturgeon.

Screening, cloning and sequence analysis of the differential expression genes in Longissimus dorsi of Yanbian Yellow Cattle

2011 ◽  
Vol 33 (11) ◽  
pp. 1219-1224 ◽  
Author(s):  
Wan-Nian TIAN ◽  
Shou-Fa ZHANG ◽  
Xiang-Zi LI ◽  
Qing-Shan GAO ◽  
Xin JIN ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Differential Expression ◽  
Longissimus Dorsi ◽  
Yellow Cattle ◽  
Differential Expression Genes

scholarly journals Best practices on the differential expression analysis of multi-species RNA-seq

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Matthew Chung ◽  
Vincent M. Bruno ◽  
David A. Rasko ◽  
Christina A. Cuomo ◽  
José F. Muñoz ◽  
...  
Keyword(s):  
Best Practices ◽  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Single Species ◽  
Rna Seq ◽  
Species Analysis ◽  
Differential Gene ◽  
Multiple Species ◽  
Downstream Analysis

AbstractAdvances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.

scholarly journals High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Weitong Cui ◽  
Huaru Xue ◽  
Lei Wei ◽  
Jinghua Jin ◽  
Xuewen Tian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Small Sample ◽  
Differentially Expressed ◽  
Cancer Type ◽  
Rna Seq ◽  
Sample Sizes ◽  
Large Sample ◽  
Expression Levels ◽  
Gene Expression Levels

Abstract Background RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible. Results Our findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially expressed under different conditions. Poor reproducibility of DE results is mainly caused by high variation of gene expression levels for the same gene in different samples. Even though biological variation may account for much of the high variation of gene expression levels, the effect of outlier count data also needs to be treated seriously, as outlier data severely interfere with DE analysis. Conclusions High heterogeneity exists not only in tumor tissue samples of each cancer type studied, but also in normal samples. High heterogeneity leads to poor reproducibility of DEGs, undermining generalization of differential expression results. Therefore, it is necessary to use large sample sizes (at least 10 if possible) in RNA-Seq experimental designs to reduce the impact of biological variability and DE results should be interpreted cautiously unless soundly validated.

scholarly journals How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

RNA ◽  
2016 ◽  
Vol 22 (6) ◽  
pp. 839-851 ◽  
Author(s):  
Nicholas J. Schurch ◽  
Pietá Schofield ◽  
Marek Gierliński ◽  
Christian Cole ◽  
Alexander Sherstnev ◽  
...  
Keyword(s):  
Differential Expression ◽  
Rna Seq
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