The tobacco genome sequence and its comparison with those of tomato and potato

Sierro, Nicolas; Battey, James N. D.; Ouadi, Sonia; Bakaher, Nicolas; Bovet, Lucien; Willig, Adrian; Goepfert, Simon; Peitsch, Manuel C.; Ivanov, Nikolai V.

doi:10.1038/ncomms4833

Cited by 510 publications

(428 citation statements)

References 60 publications

(90 reference statements)

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“…Texas Marker-1 (TM-1), which is widely used as a genetic standard 1,10 . We generated a genome sequence containing two-to about fourfold longer sequence scaffolds (N50 = 1,600 kb) than that produced for other allopolyploid species Brassica napus (N50 = 764 kb) 9 , Nicotiana tabacum sequencing of allotetraploid cotton (Gossypium hirsutum l. acc.…”

mentioning

confidence: 99%

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

et al. 2015

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mentioning

confidence: 99%

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

et al. 2015

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“…To obtain insight into the metabolic regulation of amino acids during protoxylem vessel element differentiation, we conducted RNA-seq analysis of VND7-VP16-GR BY-2 cells treated with DEX or mock for 0, 6, 12, 24, and 36 h. After the de novo assembly of sequence reads based on the tobacco reference genome (Sierro et al, 2014), we obtained 74,932 unique contigs from the mRNA-seq data for the VND7-VP16-GR BY-2 cells. Previous work reported the set of direct targets of Arabidopsis (Arabidopsis thaliana) VND6 and VND7 (Ohashi-Ito et al, 2010;Zhong et al, 2010;Yamaguchi et al, 2011); based on this, we first examined the expression patterns of genes homologous to the 63 VND7 direct target genes reported by Yamaguchi et al (2011).…”

Section: Transcriptome Analysis Of Vnd7-vp16-gr By-2 Cellsmentioning

confidence: 99%

Primary Metabolism during Biosynthesis of Secondary Wall Polymers of Protoxylem Vessel Elements

et al. 2016

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Xylem vessels, the water-conducting cells in vascular plants, undergo characteristic secondary wall deposition and programmed cell death. These processes are regulated by the VASCULAR-RELATED NAC-DOMAIN (VND) transcription factors. Here, to identify changes in metabolism that occur during protoxylem vessel element differentiation, we subjected tobacco (Nicotiana tabacum) BY-2 suspension culture cells carrying an inducible VND7 system to liquid chromatography-mass spectrometry-based wide-target metabolome analysis and transcriptome analysis. Time-course data for 128 metabolites showed dynamic changes in metabolites related to amino acid biosynthesis. The concentration of glyceraldehyde 3-phosphate, an important intermediate of the glycolysis pathway, immediately decreased in the initial stages of cell differentiation. As cell differentiation progressed, specific amino acids accumulated, including the shikimate-related amino acids and the translocatable nitrogen-rich amino acid arginine. Transcriptome data indicated that cell differentiation involved the active up-regulation of genes encoding the enzymes catalyzing fructose 6-phosphate biosynthesis from glyceraldehyde 3-phosphate, phosphoenolpyruvate biosynthesis from oxaloacetate, and phenylalanine biosynthesis, which includes shikimate pathway enzymes. Concomitantly, active changes in the amount of fructose 6-phosphate and phosphoenolpyruvate were detected during cell differentiation. Taken together, our results show that protoxylem vessel element differentiation is associated with changes in primary metabolism, which could facilitate the production of polysaccharides and lignin monomers and, thus, promote the formation of the secondary cell wall. Also, these metabolic shifts correlate with the active transcriptional regulation of specific enzyme genes. Therefore, our observations indicate that primary metabolism is actively regulated during protoxylem vessel element differentiation to alter the cell's metabolic activity for the biosynthesis of secondary wall polymers.

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“…Tobacco genome revealed its ancestral origin, familial and taxonomical relation with tomato and potato and different biochemical pathways involved in alkaloid biosynthesis. In addition, the study confirmed that disease resistance to different viruses in tobacco is caused by genomic deletion of the S-form eIF4E1 locus (Sierro et al, 2014). The findings are useful to screen the resistant genotypes to virus-caused diseases not only in tobacco but also in other plants while these data are used as the reference.…”

Section: * Ingeniero Agrónomomentioning

confidence: 55%

Genomic and transcriptomic approaches toward plant selection

Jazayeri¹,

Torres

2017

JSR

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Abstract-Omics era has opened a new window to biology. Genomics and transcriptomics are two well-known fields by which plant selection and breeding are fulfilled more easily and accurately. They provide useful information about genes, transcripts, their functions those are the principal data for other subsequent approaches. Reference genomes of various plants are available and facilitate genome-based studies. The complex of genomic, transcriptomic data and the findings from variant methods like QTLs (quantitative trait loci), SNPs (single nucleotide polymorphism), CNVs (copy number variant), resequencing, GBS (genome-by-sequencing) are extremely important for plant selection in terms of price and time. The new workflows are routinely using different approaches and mixing them based on the genomic/transcriptomic information in their subsequent steps. They, however, are validated during the whole process toward screening genotypes possessing agronomically important desired trait. SNP-Seq presented hereinafter is a new approach for analyzing plants toward selection and screening by SNP sequencing in various genotypes simultaneously. It can accelerate the cycle of plant selection from genotypes to phenotypes in a reverse engineering way.Keywords:-Genomics, Omics, Plant Selection, Plant Improvement, TranscriptomicsResumen-La era Omica ha abierto una nueva ventana a la biología. La genómica y la transcriptómica son dos campos conocidos, con los cuales, la selección y el mejoramiento de plantas se cumplen con mayor facilidad y precisión. Proporcionan informaciónútil sobre los genes, las transcripciones, sus funciones y sirven como datos primordiales para otros enfoques posteriores. Los genomas de referencia de varias plantas han sido secuenciados, y están disponibles, facilitando así el acceso a informaciónómica indispensable para llevar a cabo estudios basados en estos mismos genomas. El total de datos genómicos, transcriptómicos y los hallazgos de métodos variantes que van desde QTL (rasgo cuantitativo), PSN (polimorfismo de un solo nucleótido), NCV (número de copias variante), GBS (genoma por secuencia) son extremadamente importantes para la selección y el mejoramiento de plantas en términos de precio y tiempo. Los nuevos flujos de trabajo utilizan diferentes enfoques basados en la información genómica / transcriptómica en pasos posteriores mezclándolos y se validan durante todo el proceso para seleccionar genotipos que posean un rasgo deseado agronómicamente importante. SNP-Seq, que se presenta en este artículo, es un nuevo enfoque para analizar las plantas hacia la selección y la detección mediante secuenciación de SNP en varios genotipos simultáneamente. Este proceso puede acelerar el ciclo de selección de plantas desde los genotipos a los fenotipos en una forma de ingeniería inversa.

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The tobacco genome sequence and its comparison with those of tomato and potato

Cited by 510 publications

References 60 publications

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Primary Metabolism during Biosynthesis of Secondary Wall Polymers of Protoxylem Vessel Elements

Genomic and transcriptomic approaches toward plant selection

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