Comparative transcriptome sequencing analysis and functional identification of a NAM-2-like gene in jute (Corchorus capsularis L.)

The saccharification of sweetpotato storage roots is a common phenomenon in the cooking process, which determines the edible quality of table use sweetpotato. In the present study, two high saccharified sweetpotato cultivars (Y25, Z13) and one low saccharified cultivar (X27) in two growth periods (S1, S2) were selected as materials to reveal the molecular mechanism of sweetpotato saccharification treated at high temperature by transcriptome sequencing and non-targeted metabolome determination. The results showed that the comprehensive taste score, sweetness, maltose content and starch change of X27 after steaming were significantly lower than those of Y25 and Z13. Through transcriptome sequencing analysis, 1918 and 1520 differentially expressed genes were obtained in the two periods of S1 and S2, respectively. Some saccharification-related transcription factors including MYB families, WRKY families, bHLH families and inhibitors were screened. Metabolic analysis showed that 162 differentially abundant metabolites related to carbohydrate metabolism were significantly enriched in starch and sucrose capitalization pathways. The correlation analysis between transcriptome and metabolome confirmed that the starch and sucrose metabolic pathways were significantly co-annotated, indicating that it is a vitally important metabolic pathway in the process of sweetpotato saccharification. The data obtained in this study can provide valuable resources for follow-up research on sweetpotato saccharification and will provide new insights and theoretical basis for table use sweetpotato breeding in the future.

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Single-cell transcriptome sequencing analysis reveals gynaecomastia to breast cancer transition

The Breast ◽

10.1016/s0960-9776(21)00109-0 ◽

2021 ◽

Vol 56 ◽

pp. S26

Author(s):

H. Sun ◽

C. Yang ◽

Z. Wang ◽

L. Shi ◽

T. Xia ◽

...

Keyword(s):

Breast Cancer ◽

Single Cell ◽

Transcriptome Sequencing ◽

Sequencing Analysis ◽

Cell Transcriptome ◽

Single Cell Transcriptome

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

BMC Genomics ◽

10.1186/1471-2164-15-1026 ◽

2014 ◽

Vol 15 (1) ◽

pp. 1026 ◽

Cited By ~ 63

Author(s):

Liyu Huang ◽

Fan Zhang ◽

Wensheng Wang ◽

Yongli Zhou ◽

...

Keyword(s):

Drought Stress ◽

Transcriptome Sequencing ◽

Introgression Line ◽

Comparative Transcriptome

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A combined small RNA and transcriptome sequencing analysis reveal regulatory roles of miRNAs during anther development of Upland cotton carrying cytoplasmic male sterile Gossypium harknessii (D2) cytoplasm

BMC Plant Biology ◽

10.1186/s12870-018-1446-7 ◽

2018 ◽

Vol 18 (1) ◽

Cited By ~ 6

Author(s):

Bingbing Zhang ◽

Xuexian Zhang ◽

Guoyuan Liu ◽

Liping Guo ◽

Tingxiang Qi ◽

...

Keyword(s):

Small Rna ◽

Upland Cotton ◽

Transcriptome Sequencing ◽

Anther Development ◽

Sequencing Analysis ◽

Male Sterile ◽

Cytoplasmic Male Sterile

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Studies on trans-sutural distraction osteogenesis-related genes based on transcriptome sequencing

10.1101/2020.04.11.037085 ◽

2020 ◽

Author(s):

Baicheng Wang ◽

Hongyu Xue ◽

Haizhou Tong ◽

Peiyang Zhang ◽

Mei Wang ◽

...

Keyword(s):

Cell Cycle ◽

Distraction Osteogenesis ◽

Transcriptome Sequencing ◽

Molecular Mechanisms ◽

Sequencing Analysis ◽

Sprague Dawley ◽

Down Regulation ◽

Important Approach ◽

Immune Pathways ◽

Experimental Group

AbstractTrans-sutural distraction osteogenesis (TSDO) is an important approach to improve mid-face hypoplasia. In recent years, many studies have been carried out on physical mechanisms of TSDO; however, it’s specific cytological and molecular mechanisms are still unclear. In this study, we performed transcriptome sequencing analysis in Sprague Dawley rats at 1 and 2 weeks after suture osteogenesis and compared RNA expression levels between experimental and control groups. At one week, enrichment pathways were mainly up-regulated in muscle- and bone-related pathways. By contrast, pathways of the immune system showed a state of inhibition and down-regulation, especially for B cells; the main immune pathways showed significant down-regulation. However, two weeks later, the experimental group showed positive up-regulation of the pathways related to DNA synthesis and replication, cell cycle, and chromosome replication. At the same time, the immune pathways that were down-regulated in the first week were up-regulated in the second week. In other words, the up-regulated muscle- and bone-related pathways show opposite trends. The expression of bone- and myogenesis-related transcriptome was up-regulated and the immune-related pathways were down-regulated in the experimental group at 1 week. At 2 weeks, the pathways related to bone- and muscle were down-regulated, while those related to cell cycle regulation and DNA replication were up-regulated. These results suggest that musculoskeletal-related molecules may play an important role during suture osteogenesis at 1 week, and immune regulation may be involved in this process; however, at 2 weeks, molecules related to cell proliferation and replication may be a major role.

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

Frontiers in Sustainable Food Systems ◽

10.3389/fsufs.2021.639841 ◽

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.

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

Archives Animal Breeding ◽

10.5194/aab-63-303-2020 ◽

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.

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