Genome-wide transcriptome analysis of genes involved in flavonoid biosynthesis between red and white strains of Magnolia sprengeri pamp

The short-chain dehydrogenases/reductases (SDR) superfamily is involved in multiple physiological processes. In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases. Overall, the number of SDR genes in animals increased with whole genome duplication (WGD), suggesting the expansion of SDRs during evolution, especially in 3R-WGD and polyploidization of teleosts. Phylogenetic analysis indicated that vertebrates SDRs were clustered into five categories: classical, extended, undefined, atypical, and complex. Moreover, tandem duplication of hpgd-a, rdh8b and dhrs13 was observed in teleosts analyzed. Additionally, tandem duplications of dhrs11-a, dhrs7a, hsd11b1b, and cbr1-a were observed in all cichlids analyzed, and tandem duplication of rdh10-b was observed in tilapiines. Transcriptome analysis of adult fish revealed that 93 SDRs were expressed in more than one tissue and 5 in one tissue only. Transcriptome analysis of gonads from different developmental stages showed that expression of 17 SDRs were sexually dimorphic with 11 higher in ovary and 6 higher in testis. The sexually dimorphic expressions of these SDRs were confirmed by in situ hybridization (ISH) and qPCR, indicating their possible roles in steroidogenesis and gonadal differentiation. Taken together, the identification and the expression data obtained in this study contribute to a better understanding of SDR superfamily evolution and functions in teleosts.

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Genome-wide transcriptome analysis of microspore abortion initiation in radish (Raphanus sativus L.)

Gene ◽

10.1016/j.gene.2021.145753 ◽

2021 ◽

pp. 145753

Author(s):

Chen Liu ◽

Weimin Fu ◽

Wenling Xu ◽

Xianxian Liu ◽

Shufen Wang

Keyword(s):

Transcriptome Analysis ◽

Raphanus Sativus ◽

Genome Wide ◽

Raphanus Sativus L

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Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Genes ◽

10.3390/genes12030341 ◽

2021 ◽

Vol 12 (3) ◽

pp. 341

Author(s):

Lei Zhang ◽

Haoyun Sun ◽

Tao Xu ◽

Tianye Shi ◽

Zongyun Li ◽

...

Keyword(s):

Transcriptome Analysis ◽

Morphological Analysis ◽

Molecular Mechanisms ◽

Flavonoid Biosynthesis ◽

Phenotypic Characterization ◽

Comparative Transcriptome ◽

Hub Genes ◽

Breeding Programs ◽

Comparative Transcriptome Analysis ◽

Key Pathways

Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars.

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Genome-wide transcriptome analysis of Arabidopsis response to sulfur dioxide fumigation

Molecular Genetics and Genomics ◽

10.1007/s00438-014-0870-0 ◽

2014 ◽

Vol 289 (5) ◽

pp. 989-999 ◽

Cited By ~ 12

Author(s):

Jun Zhao ◽

Huilan Yi

Keyword(s):

Sulfur Dioxide ◽

Transcriptome Analysis ◽

Genome Wide

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Genome-wide association study and transcriptome analysis discover new genes for bacterial leaf blight resistance in rice (Oryza sativa L.)

BMC Plant Biology ◽

10.1186/s12870-021-03041-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xinyue Shu ◽

Aijun Wang ◽

Bo Jiang ◽

Yuqi Jiang ◽

Xing Xiang ◽

...

Keyword(s):

Oryza Sativa ◽

Association Study ◽

Transcriptome Analysis ◽

Genome Wide Association Study ◽

Leaf Blight ◽

Genome Wide Association ◽

Bacterial Leaf Blight ◽

Significant Differential Expression ◽

Genome Wide ◽

A Genome

Abstract Background Rice (Oryza sativa) bacterial leaf blight (BLB), caused by the hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases affecting the production of rice worldwide. The development and use of resistant rice varieties or genes is currently the most effective strategy to control BLB. Results Here, we used 259 rice accessions, which are genotyped with 2 888 332 high-confidence single nucleotide polymorphisms (SNPs). Combining resistance variation data of 259 rice lines for two Xoo races observed in 2 years, we conducted a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) conferring plant resistance against BLB. The expression levels of genes, which contains in GWAS results were also identified between the resistant and susceptible rice lines by transcriptome analysis at four time points after pathogen inoculation. From that 109 candidate resistance genes showing significant differential expression between resistant and susceptible rice lines were uncovered. Furthermore, the haplotype block structure analysis predicted 58 candidate genes for BLB resistance based on Chr. 7_707158 with a minimum P-value (–log 10 P = 9.72). Among them, two NLR protein-encoding genes, LOC_Os07g02560 and LOC_Os07g02570, exhibited significantly high expression in the resistant line, but had low expression in the susceptible line of rice. Conclusions Together, our results reveal novel BLB resistance gene resources, and provide important genetic basis for BLB resistance breeding of rice crops.

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Genome-wide transcriptome analysis of hydrogen production in the cyanobacterium Synechocystis: Towards the identification of new players

International Journal of Hydrogen Energy ◽

10.1016/j.ijhydene.2012.11.118 ◽

2013 ◽

Vol 38 (4) ◽

pp. 1866-1872 ◽

Cited By ~ 8

Author(s):

Christophe Leplat ◽

Raphaël Champeimont ◽

Panatda Saenkham ◽

Corinne Cassier-Chauvat ◽

Aude Jean-Christophe ◽

...

Keyword(s):

Hydrogen Production ◽

Transcriptome Analysis ◽

Genome Wide

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Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans

BMC Genomics ◽

10.1186/s12864-021-07439-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yong Shi ◽

Heng Xia ◽

Xiaoting Cheng ◽

Libin Zhang

Keyword(s):

Secondary Metabolites ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Flavonoid Biosynthesis ◽

Integrated Network ◽

Osmanthus Fragrans ◽

Flavonoid Synthesis ◽

Genome Wide

AbstractBackgroundOsmanthus fragransis an important economical plant containing multiple secondary metabolites including flavonoids and anthocyanins. During the past years, the roles of miRNAs in regulating the biosynthesis of secondary metabolites in plants have been widely investigated. However, few studies on miRNA expression profiles and the potential roles in regulating flavonoid biosynthesis have been reported inO. fragrans.ResultsIn this study, we used high-throughput sequencing technology to analyze the expression profiles of miRNAs in leaf and flower tissues ofO. fragrans. As a result, 106 conserved miRNAs distributed in 47 families and 88 novel miRNAs were identified. Further analysis showed there were 133 miRNAs differentially expressed in leaves and flowers. Additionally, the potential target genes of miRNAs as well as the related metabolic pathways were predicted. In the end, flavonoid content was measured in flower and leaf tissues and potential role of miR858 in regulating flavonoid synthesis was illustrated inO. fragrans.ConclusionsThis study not only provided the genome-wide miRNA profiles in the flower and leaf tissue ofO. fragrans, but also investigated the potential regulatory role of miR858a in flavonoid synthesis inO. fragrans. The results specifically indicated the connection of miRNAs to the regulation of secondary metabolite biosynthesis in non-model economical plant.

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