scholarly journals Comparative Transcriptome and WGCNA RevealKey Genes Involved in Lignocellulose Degradation in Sarcomyxa Edulis

2022 ◽  
Author(s):  
Chao Duan ◽  
Feng-Hua Tian ◽  
Lan Yao ◽  
Jian-Hua Lv ◽  
Chuan-Wen Jia ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Developmental Process ◽  
Molecular Genetic ◽  
Extracellular Enzyme ◽  
Lignocellulose Degradation ◽  
Transcriptome Data ◽  
Comparative Transcriptome ◽  
Cold Stimulation ◽  
Genetic Mechanisms ◽  
Key Genes

Abstract In order to explore the molecular mechanism of Sarcomyxa edulis response to lignocelluloses degradation, the developmental transcriptomes was analyzed for six stages covering the whole developmental process, including mycelium growing to half bag (B1), mycelium in cold stimulation after full bag (B2), mycelium in primordia appearing (B3), primordia (B4), mycelium at the harvest stage (B5) and mature fruiting body (B6). A total of 6 samples were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, we constructed a co-expression network of weighted genes associated with extracellular enzyme physiological traits by WGCNA, and obtained 19 gene co-expression modules closely related to lignocelluloses degradation. In addition, a number of key genes involved in lignocelluloses degradation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of Sarcomyxa edulis lignocelluloses degradation.

scholarly journals Analysis of key genes of jasmonic acid mediated signal pathway for defense against insect damages by comparative transcriptome sequencing

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Fengshan Yang ◽  
Yuliang Zhang ◽  
Qixing Huang ◽  
Guohua Yin ◽  
Kayla K. Pennerman ◽  
...  
Keyword(s):  
Jasmonic Acid ◽  
Transcriptome Sequencing ◽  
Signal Pathway ◽  
Comparative Transcriptome ◽  
Key Genes

scholarly journals Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jifang Zhang ◽  
Jian Zhao ◽  
Qunyun Tan ◽  
Xiaojun Qiu ◽  
Shiyong Mei
Keyword(s):  
Transcription Factors ◽  
Raphanus Sativus ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Comparative Transcriptome ◽  
Structural Genes ◽  
Key Genes ◽  
Transcript Profiles ◽  
Species Specific ◽  
Anthocyanin Biosynthetic Genes

AbstractRadish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.

scholarly journals Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 1026 ◽  
Author(s):  
Liyu Huang ◽  
Fan Zhang ◽  
Fan Zhang ◽  
Wensheng Wang ◽  
Yongli Zhou ◽  
...  
Keyword(s):  
Drought Stress ◽  
Transcriptome Sequencing ◽  
Introgression Line ◽  
Comparative Transcriptome

scholarly journals RNA Sequencing Analysis of Metopolophium dirhodum (Walker) (Hemiptera: Aphididae) Reveals the Mechanism Underlying Insecticide Resistance

2021 ◽  
Vol 5 ◽  
Author(s):  
Haifeng Gao ◽  
Xun Zhu ◽  
Guangkuo Li ◽  
Enliang Liu ◽  
Yuyang Shen ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Transcriptome Sequencing ◽  
Western China ◽  
Sequencing Analysis ◽  
Transcriptome Data ◽  
Metopolophium Dirhodum ◽  
Gene Characterization ◽  
Agricultural Regions ◽  
Phloem Feeding ◽  
Aphid Development

Xinjiang (XJ) and Ningxia (NX) provinces are important agricultural regions in western China. Aphids are one kind of the most devastating pests in both the provinces. Aphids are typical phloem-feeding insects distributed worldwide and can severely damage crops. In this study, two representative Metopolophium dirhodum (Walker) (Hemiptera: Aphididae) populations were collected from the typical agricultural regions of XJ and NX, respectively for a high-throughput transcriptome sequencing analysis. A total of 5,265 differentially expressed genes (DEGs) were identified. The functional annotation of DEGs and the identification of enriched pathways indicated many of the DEGs are involved in processes related to energy metabolism, development, and insecticide resistance. Furthermore, an investigation of insecticide toxicity revealed the NX population is more resistant to insecticide treatments than the XJ population. Thus, the transcriptome data generated in present study can be used for functional gene characterization relevant to aphid development, metabolism, environmental adaptation, and insecticide resistance.

scholarly journals Comparative transcriptome and histomorphology analysis of testis tissues from mulard and Pekin ducks

2020 ◽  
Vol 63 (2) ◽  
pp. 303-313
Author(s):  
Li Li ◽  
Linli Zhang ◽  
Zhenghong Zhang ◽  
Nemat O. Keyhani ◽  
Qingwu Xin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Candidate Genes ◽  
Transcriptome Sequencing ◽  
Differentially Expressed ◽  
Pekin Duck ◽  
Comparative Transcriptome ◽  
Qrt Pcr ◽  
Pekin Ducks ◽  
Testis Tissue

Abstract. Testicular transcriptomes were analyzed to characterize the differentially expressed genes between mulard and Pekin ducks, which will help establish gene expression datasets to assist in further determination of the mechanisms of genetic sterility in mulard ducks. Paraffin sections were made to compare the developmental differences in testis tissue between mulard and Pekin ducks. Comparative transcriptome sequencing of testis tissues was performed, and the expression of candidate genes was verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). In mulard ducks, spermatogonia and spermatocytes were arranged in a disordered manner, and no mature sperm were observed in the testis tissue. However, different stages of development of sperm were observed in seminiferous tubules in the testis tissue of Pekin ducks. A total of 43.84 Gb of clean reads were assembled into 193 535 UniGenes. Of these, 2131 transcripts exhibited differential expression (false discover rate <0.001 and fold change ≥2), including 997 upregulated and 1134 downregulated transcripts in mulard ducks as compared to those in Pekin duck testis tissues. Several upregulated genes were related to reproductive functions, including ryanodine receptor 2 (RYR2), calmodulin (CALM), argininosuccinate synthase and delta-1-pyrroline-5-carboxylate synthetase ALDH18A1 (P5CS). Downregulated transcripts included the testis-specific serine/threonine-protein kinase 3, aquaporin-7 (AQP7) and glycerol kinase GlpK (GK). The 10 related transcripts involved in the developmental biological process were identified by GO (Gene Ontology) annotation. The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways indicated that peroxisome proliferator-activated receptors (PPARs) and calcium signaling pathways were significantly (P<0.001) associated with normal testis physiology. The differential expression of select genes implicated in reproductive processes was verified by qRT-PCR, which was consistent with the expression trend of transcriptome sequencing (RNA-seq). Differentially expressed candidate genes RYR2, CALM, P5CS, AQP7 and GK were identified by transcriptional analysis in mulard and Pekin duck testes. These were important for the normal development of the male duck reproductive system. These data provide a framework for the further exploration of the molecular and genetic mechanisms of sterility in mulard ducks. Highlights. The mulard duck is an intergeneric sterile hybrid offspring resulting from mating between Muscovy and Pekin ducks. The transcriptomes of testis tissue from mulard and Pekin ducks were systematically characterized, and differentially expressed genes were screened, in order to gain insights into potential gonad gene expression mechanisms contributing to genetic sterility in mulard ducks.

scholarly journals Comparative transcriptome analysis of mule uncovered several heterosis-related genes for improving muscular endurance and cognition

2019 ◽  
Author(s):  
Shan Gao
Keyword(s):  
Alternative Splicing ◽  
Molecular Genetic ◽  
Hybrid Vigor ◽  
Neuronal System ◽  
Future Studies ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms ◽  
Productive Traits ◽  
Genome Wide Gene Expression

AbstractHeterosis has been widely exploited in animal and plant breeding to enhance the productive traits of hybrid progeny of two breeds or two species. Although, there were multiple models for explaining the hybrid vigor, such as dominance and over-dominance hypothesis, its underlying molecular genetic mechanisms remain equivocal. The aim of this study is through comparing the different expression genes (DEGs) and different alternative splicing (DAS) genes to explore the mechanism of heterosis. Here, we performed a genome-wide gene expression and alternative splicing analysis of two heterotic crosses between donkey and horse in three tissues. The results showed that the DAS genes influenced the heterosis-related phenotypes in a unique than DEGs and about 10% DEGs are DAS genes. In addition, over 69.7% DEGs and 87.2% DAS genes showed over-dominance or dominance, respectively. Furthermore, the “Muscle Contraction” and “Neuronal System” pathways were significantly enriched both for the DEGs and DAS genes in muscle. TNNC2 and RYR1 genes may contribute to mule’s great endurance while GRIA2 and GRIN1 genes may be related with mule’s cognition. Together, these DEGs and DAS genes provide the candidates for future studies of the genetic and molecular mechanism of heterosis in mule.

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