scholarly journals Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 631
Author(s):  
Zhicheng Sun ◽  
Fangrui Lou ◽  
Yuan Zhang ◽  
Na Song
Keyword(s):  
Signal Transduction ◽  
Salinity Stress ◽  
De Novo ◽  
Enrichment Analysis ◽  
Gill Tissue ◽  
Control Group ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Kegg Pathways ◽  
Pathways Analysis

Acanthogobius ommaturus is a euryhaline fish widely distributed in coastal, bay and estuarine areas, showing a strong tolerance to salinity. In order to understand the mechanism of adaptation to salinity stress, RNA-seq was used to compare the transcriptome responses of Acanthogobius ommaturus to the changes of salinity. Four salinity gradients, 0 psu, 15 psu (control), 30 psu and 45 psu were set to conduct the experiment. In total, 131,225 unigenes were obtained from the gill tissue of A. ommaturus using the Illumina HiSeq 2000 platform (San Diego, USA). Compared with the gene expression profile of the control group, 572 differentially expressed genes (DEGs) were screened, with 150 at 0 psu, 170 at 30 psu, and 252 at 45 psu. Additionally, among these DEGs, Gene Ontology (GO) analysis indicated that binding, metabolic processes and cellular processes were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis detected 3, 5 and 8 pathways related to signal transduction, metabolism, digestive and endocrine systems at 0 psu, 30 psu and 45 psu, respectively. Based on GO enrichment analysis and manual literature searches, the results of the present study indicated that A. ommaturus mainly responded to energy metabolism, ion transport and signal transduction to resist the damage caused by salinity stress. Eight DEGs were randomly selected for further validation by quantitative real-time PCR (qRT-PCR) and the results were consistent with the RNA-seq data.

scholarly journals RNA seq analyses of chicken reveals biological pathways involved in acclimation into different geographical locations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Himansu Kumar ◽  
Hyojun Choo ◽  
Asankadyr U. Iskender ◽  
Krishnamoorthy Srikanth ◽  
Hana Kim ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Climatic Conditions ◽  
Rna Seq ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Commercial Chicken ◽  
Pathways Analysis ◽  
Ppar Signaling ◽  
Transcriptome Expression

Abstract Transcriptome expression reflects genetic response in diverse conditions. In this study, RNA sequencing was utilized to profile multiple tissues such as liver, breast, caecum, and gizzard of Korean commercial chicken raised in Korea and Kyrgyzstan. We analyzed ten samples per tissue from each location to identify candidate genes which are involved in the adaptation of Korean commercial chicken to Kyrgyzstan. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, we found 315, 196, 167 and 198 genes in liver, breast, cecum, and gizzard respectively as differentially expressed between the two locations. GO enrichment analysis showed that these genes were highly enriched for cellular and metabolic processes, catalytic activity, and biological regulations. Similarly, KEGG pathways analysis indicated metabolic, PPAR signaling, FoxO, glycolysis/gluconeogenesis, biosynthesis, MAPK signaling, CAMs, citrate cycles pathways were differentially enriched. Enriched genes like TSKU, VTG1, SGK, CDK2 etc. in these pathways might be involved in acclimation of organisms into diverse climatic conditions. The qRT-PCR result also corroborated the RNA-Seq findings with R2 of 0.76, 0.80, 0.81, and 0.93 for liver, breast, caecum, and gizzard respectively. Our findings can improve the understanding of environmental acclimation process in chicken.

scholarly journals Functional Annotation of Transcripts Obtained from Fall-Grown Tall Fescue as Influenced by Endophyte Infection

2021 ◽  
Author(s):  
Md. Shofiqul Islam ◽  
Nick Krom ◽  
Taegun Kwon ◽  
Guifen Li ◽  
Malay Saha
Keyword(s):  
Tall Fescue ◽  
De Novo ◽  
Primary Source ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Fungal Endophyte ◽  
Freezing Stress ◽  
Biotic Stresses ◽  
Kegg Pathways ◽  
Pathways Analysis

Abstract Tall fescue is one of the primary source of forage for livestock. It grows well in the marginal soils of the temperate zones. It hosts a fungal endophyte (Epichloë coenophiala), which helps the plants to tolerate abiotic and biotic stresses. The genetics and biology underlying mechanism of freezing stress tolerance of tall fescue is still unknown, due to its complex genetic background and outbreeding modes of pollination, limited genomic, and transcriptomic resources. The aim of this study was to identify differentially expressed genes (DEGs) in two tissues between novel endophyte-positive (E+) and endophyte-free (E-) tall fescue genotypes at three diurnal time points; in the morning (-3.0 to 0.5°C), afternoon (11 to 12°C), and evening (12 − 10°C) in the field environment, by exploring the transcriptional landscape via RNA sequencing. For the first time, we generated 226,054 and 224,376 transcripts from E + and E- Texoma MaxQ II tall fescue, respectively by de novo assembly. The upregulated transcripts were detected fewer than the downregulated ones in both tissues (S: 803 up and 878 down; L: 783 up and 846 down) under the freezing temperatures in the morning. By Gene Ontology enrichment analysis, 10 GO terms were found only under the freezing stress in the morning. Metabolic pathway and biosynthesis of secondary metabolites genes showed lowest number of DEGs under morning freezing stress and highest number in evening cold condition by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis. The DEGs expressed under morning stress condition and the nine candidate genes that we identified using GO analysis, might be the possible route underlying cold tolerance in tall fescue.

scholarly journals Comprehensive Analysis of Differences of N6-Methyladenosine of Lncrnas Between Atrazine-Inducedand Normal Xenopus Laevis Testis

2021 ◽  
Author(s):  
Xuejie Qi ◽  
Xiao Geng ◽  
Juan Zhang ◽  
Ling Li ◽  
Qiang Jia ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Rna Stability ◽  
Enrichment Analysis ◽  
Control Group ◽  
Pathway Enrichment Analysis ◽  
Amphibian Species ◽  
Illumina Hiseq ◽  
Kegg Pathways ◽  
Non Coding Rna ◽  
First Time

Abstract Background: Increasing evidence suggested N6-methyladenosine (m6A) plays an important role in RNA stability, degradation, splicing and translation. M6A is found in different RNA including long non-coding RNA (lncRNA) which has been found possess significant biological functions. Our previous study examined the m6A profile of mRNAs in testis tissues of Xenopus laevis (X. laevis) with and without treatment with 100 µg/L atrazine (AZ). The result revealed that m6A is a highly conserved modification across the species. Methods: In this study, we apply previous approach to further investigate m6A modification profile of lncRNAs and predict the potential mechanism. In brief, m6A was sequenced by MeRIP sequencing using the latest Illumina HiSeq sequencer. Pathway enrichment analysis was used to maps genes to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Results: The results showed that m6A of lncRNAs enriched around intergenic region in testes of X. laevis. We further investigated the differential expression of lncRNAs m6A in testes of AZ-exposed compared with that in animals from control group. The results indicated that up to 198 differentially methylated m6A sites were detected within 188 lncRNAs, in which 89 sites were significantly up-regulated and 109 sites were significantly down-regulated. Data from Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that AZ-affected lncRNAs m6A sites were mainly involved in 10 pathways in which 3 mutual pathways were found in the result of differentially m6A-methylated mRNAs. Conclusions: These findings suggest that differentially m6A-methylated lncRNAs and these 3 pathways may act on regulatory roles in abnormal testis development of AZ-exposed X. laevis. This study for the first time provide insights into the profile of lncRNAs m6A modifications in amphibian species.

scholarly journals RNA-seq and Analysis of Argyrosomus japonicus Under Different Salinities

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhujun Li ◽  
Tianxiang Gao ◽  
Zhiqiang Han
Keyword(s):  
Enrichment Analysis ◽  
Gill Tissue ◽  
Control Group ◽  
Rna Seq ◽  
Pathway Enrichment ◽  
Salinity Changes ◽  
Physiological Processes ◽  
Complex Process ◽  
Low Salt ◽  
Key Genes

Salinity variation affects the physiological processes of fish. This study analyzed the transcriptome of the gill tissue of Argyrosomus japonicus to determine the significantly differentially expressed genes (DEGs) of A. japonicus under salinity changes. Transcriptome analysis of nine samples yielded 55.873 Gb of clean data, 64,912 transcripts, and 29,567 unigenes, and 83.62% of the transcripts and 81.89% of the unigenes were annotated. Compared with the control group, the high- and low-salt groups showed 1,731 and 695 DEGs, respectively. Gene Ontology enrichment analysis revealed that the DEGs were significantly enriched in transportation, metabolism, and stress response. Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that the DEGs were significantly enriched in some signaling pathways. Several key genes (KRT1, KRT2, ATP1A, LDH, PFN, ACTB_G1, TUBB, GZMB, MHC2, CCL19, EPX, ANXA5, ACBP, EHF, BHMT, COL1A, and RHOA) were related to salinity adaptation. When environmental salinity fluctuated, genes related to stress, immunity, ion transport, and metabolism became more sensitive. These results suggest that the adaptation of A. japonicus under salinity changes is a complex process that involves multiple genes acting together.

scholarly journals De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Development Processes ◽  
The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

scholarly journals RNA Sequencing (RNA-Seq) Based Transcriptome Analysis in Immune Response of Holstein Cattle to Killed Vaccine against Bovine Viral Diarrhea Virus Type I

Animals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 344 ◽  
Author(s):  
Bryan Irvine Lopez ◽  
Kier Gumangan Santiago ◽  
Donghui Lee ◽  
Seungmin Ha ◽  
Kangseok Seo
Keyword(s):  
Immune Response ◽  
Enrichment Analysis ◽  
Receptor Interaction ◽  
Type I ◽  
Rna Seq ◽  
Diarrhea Virus ◽  
Viral Diarrhea ◽  
Kegg Pathways ◽  
Viral Diarrhea Virus

Immune response of 107 vaccinated Holstein cattle was initially obtained prior to the ELISA test. Five cattle with high and low bovine viral diarrhea virus (BVDV) type I antibody were identified as the final experimental animals. Blood samples from these animals were then utilized to determine significant differentially expressed genes (DEGs) using the RNA-seq transcriptome analysis and enrichment analysis. Our analysis identified 261 DEGs in cattle identified as experimental animals. Functional enrichment analysis in gene ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed the DEGs potentially induced by the inactivated BVDV type I vaccine, and might be responsible for the host immune responses. Our findings suggested that inactivated vaccine induced upregulation of genes involved in different GO annotations, including antigen processing and presentation of peptide antigen (via MHC class I), immune response, and positive regulation of interferon-gamma production. The observed downregulation of other genes involved in immune response might be due to inhibition of toll-like receptors (TLRs) by the upregulation of the Bcl-3 gene. Meanwhile, the result of KEGG pathways revealed that the majority of DEGs were upregulated and enriched to different pathways, including cytokine-cytokine receptor interaction, platelet activation, extracellular matrix (ECM) receptor interaction, hematopoietic cell lineage, and ATP-binding cassette (ABC) transporters. These significant pathways supported our initial findings and are known to play a vital role in shaping adaptive immunity against BVDV type 1. In addition, type 1 diabetes mellitus pathways tended to be significantly enriched. Thus, further studies are needed to investigate the prevalence of type 1 diabetes mellitus in cattle vaccinated with inactivated and live BVDV vaccine.

scholarly journals Transcriptomic and Lipidomic Analysis of Lipids in Forsythia suspensa

2021 ◽  
Vol 12 ◽  
Author(s):  
Bei Wu ◽  
Yinping Li ◽  
Wenjia Zhao ◽  
Zhiqiang Meng ◽  
Wen Ji ◽  
...  
Keyword(s):  
De Novo ◽  
Growth Stages ◽  
Rna Seq ◽  
Dynamic Regulation ◽  
Kegg Pathways ◽  
Reference Information ◽  
Forsythia Suspensa ◽  
First Time ◽  
Differential Genes ◽  
Lipid Components

Forsythiae Fructus (Lianqiao in Chinese) is widely used in traditional Chinese medicine. The lipid components in Forsythiae Fructus are the basis of plant growth and active metabolism. Samples were collected at two growth stages for a comprehensive study. Transcriptome and lipidomics were performed by using the RNA-seq and UPLC-Q-TOF-MS techniques separately. For the first time, it was reported that there were 5802 lipid components in Lianqiao comprised of 31.7% glycerolipids, 16.57% phospholipids, 13.18% sphingolipids, and 10.54% fatty acids. Lipid components such as terpenes and flavonoids have pharmacological activity, but their content was low. Among these lipids which were isolated from Forsythiae Fructus, 139 showed significant differences from the May and July harvest periods. The lipids of natural products are mainly concentrated in pregnenolones and polyvinyl lipids. RNA-Seq analysis revealed 92,294 unigenes, and 1533 of these were differentially expressed. There were 551 differential genes enriched in 119 KEGG pathways. The de novo synthesis pathways of terpenoids and flavonoids were explored. Combined with the results of lipidomics and transcriptomics, it is hypothesized that in the synthesis of abscisic acid, a terpenoid, may be under the dynamic regulation of genes EC: 1.1.1.288, EC: 1.14.14.137 and EC: 1.13.11.51 in balanced state. In the synthesis of gibberellin, GA20-oxidase (GA20ox, EC: 1.14.11.12), and GA3-oxidase (GA3ox, EC: 1.14.11.15) catalyze the production of active GAs, and EC: 1.14.11.13 is the metabolic enzymes of active GAs. In the synthesis of flavonoids, MF (multifunctional), PAL (phenylalanine ammonia-lyase), CHS (chalcone synthase), ANS (anthocyanidin synthase), FLS (flavonol synthase) are all key enzymes. The results of the present study provide valuable reference information for further research on the metabolic pathways of the secondary metabolites of Forsythia suspensa.

scholarly journals RNA-Seq-Based Analysis of Cortisol-Induced Differential Gene Expression Associated with Piscirickettsia salmonis Infection in Rainbow Trout (Oncorhynchus mykiss) Myotubes

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2399
Author(s):  
Rodrigo Zuloaga ◽  
Phillip Dettleff ◽  
Macarena Bastias-Molina ◽  
Claudio Meneses ◽  
Claudia Altamirano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Rainbow Trout ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Transcriptomic Response ◽  
Bacterial Gene ◽  
Intensive Farming ◽  
Piscirickettsia Salmonis

Salmonid rickettsial septicemia (SRS) is the major infectious disease of the Chilean salmonid aquaculture industry caused by Piscirickettsia salmonis. Intensive farming conditions generate stress and increased susceptibility to diseases, being skeletal muscle mainly affected. However, the interplay between pathogen infection and stress in muscle is poorly understood. In this study, we perform an RNA-seq analysis on rainbow trout myotubes that are pretreated for 3 h with cortisol (100 ng/mL) and then infected with P. salmonis strain LF-89 for 8 h (MOI 50). Twelve libraries are constructed from RNA samples (n = 3 per group) and sequenced on Illumina HiSeq 4000. A total of 704,979,454 high-quality reads are obtained, with 70.25% mapped against the reference genome. In silico DETs include 175 total genes—124 are upregulated and 51 are downregulated. GO enrichment analysis reveals highly impacted biological processes related to apoptosis, negative regulation of cell proliferation, and innate immune response. These results are validated by RT-qPCR of nine candidate transcripts. Furthermore, cortisol pretreatment significantly stimulated bacterial gene expression of ahpC and 23s compared to infection. In conclusion, for the first time, we describe a transcriptomic response of trout myotubes infected with P. salmonis by inducing apoptosis, downregulating cell proliferation, and intrinsic immune-like response that is differentially regulated by cortisol.

scholarly journals Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Fahad Al-Qurainy ◽  
Aref Alshameri ◽  
Abdel-Rhman Gaafar ◽  
Salim Khan ◽  
Mohammad Nadeem ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Transcriptome Assembly ◽  
Average Frequency ◽  
Cyamopsis Tetragonoloba ◽  
Metabolic Pathway Analysis ◽  
Illumina Hiseq ◽  
Forage Crop ◽  
Kegg Pathways ◽  
Advanced Analysis

The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat, drought, and mild salinity. A complete image on its genic architecture will promote our understanding about gene expression networks and different tolerance mechanisms at the molecular level. Therefore, whole mRNA sequence approach on the Guar plant was conducted to provide a snapshot of the mRNA information in the cell under salinity, heat, and drought stresses to be integrated with previous transcriptomic studies. RNA-Seq technology was employed to perform a 2×100 paired-end sequencing using an Illumina HiSeq 2500 platform for the transcriptome of leaves of C. tetragonoloba under normal, heat, drought, and salinity conditions. Trinity was used to achieve a de novo assembly followed by gene annotation, functional classification, metabolic pathway analysis, and identification of SSR markers. A total of 218.2 million paired-end raw reads (~44 Gbp) were generated. Of those, 193.5M paired-end reads of high quality were used to reconstruct a total of 161,058 transcripts (~266 Mbp) with N50 of 2552 bp and 61,508 putative genes. There were 6463 proteins having >90% full-length coverage against the Swiss-Prot database and 94% complete orthologs against Embryophyta. Approximately, 62.87% of transcripts were blasted, 50.46% mapped, and 43.50% annotated. A total of 4715 InterProScan families, 3441 domains, 74 repeats, and 490 sites were detected. Biological processes, molecular functions, and cellular components comprised 64.12%, 25.42%, and 10.4%, respectively. The transcriptome was associated with 985 enzymes and 156 KEGG pathways. A total of 27,066 SSRs were gained with an average frequency of one SSR/9.825 kb in the assembled transcripts. This resulting data will be helpful for the advanced analysis of Guar to multi-stress tolerance.

scholarly journals De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)

2020 ◽  
Author(s):  
Ying Li ◽  
Chunxia Zhang ◽  
Kebin Yang ◽  
Jingjing Shi ◽  
Yulong Ding ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Flowering Time ◽  
De Novo ◽  
Extreme Environments ◽  
Tibet Plateau ◽  
Kegg Pathways ◽  
Growing Period ◽  
Time Control ◽  
Illumina Deep Sequencing ◽  
Flowering Time Control

Abstract Background: Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2,000 ~ 3,800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results: Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9,296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions: F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.

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