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Ipomoea batatas strain:Kokei 14

ABSTRACT: Comprehensive transcriptomic analysis between adventitious roots and stems in sweet potato

PROVIDER: PRJDB5540 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR090230_1.fastq.gz	Fastqsanger.gz
	DRR090230_2.fastq.gz	Fastqsanger.gz
	DRR090231_1.fastq.gz	Fastqsanger.gz
	DRR090231_2.fastq.gz	Fastqsanger.gz
	DRR090232_1.fastq.gz	Fastqsanger.gz

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Ipomoea batatas strain:Kokei 14

Project description:Comprehensive transcriptomic analysis between adventitious roots and stems in sweet potato

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Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]

Project description:More than 3.5 million raw DGE tags were obtained in each library. The clean tags in each sample ranged from 3.35 to 3.63 million, and the distinct clean tags ranged from 93,593 to 139,389. The 21 bp DGE clean tags were mapped to sweet potato transcripts. Then, we compared 7 libraries pair-wisely so that 21 pairs of comparisons were implemented. Among these comparisons, we found that 4,721 to 12,151 transcripts had significant changes in expression, and the average number was 9,657. We also observed a large number of specifically expressed transcripts between each two libraries. The expression profiles of those genes involved in root development and carbohydrates accumulation were characterized. Moreover, other genes of interest, such as potentially abiotic stress tolerance and insect resistance, were also characterized. 7 samples are examined: young leaves, mature leaves, stems, fibrous roots, initial tuberous roots, expanding tuberous roots and harvest tuberous roots.

2012-02-18 | E-GEOD-35929 | biostudies-arrayexpress

Proteomics and proteogenomics analysis of sweet potato (Ipomoea batatas) leaf and root

Project description:Two complementary protein extraction methodologies coupled with an automated proteomic platform were employed to analyze tissue-specific proteomes and characterize biological and metabolic processes in sweet potato. A total of 74,255 peptides corresponding to 4,321 nonredundant proteins were successfully identified. Data were compared to predicted protein accessions for Ipomea species and mapped on the sweet potato transcriptome and haplotype-resolved genome. A proteogenomics analysis successfully mapped 12,902 peptides against the transcriptome or genome, representing 90.4% of the total 14,275 uniquely identified peptides, predicted 741 new protein-coding genes, and specified 2726 loci where annotations can be further improved. Overall, 39,916 peptides mapped to 3,143 unique proteins in leaves, and 34,339 peptides mapped to 2,928 unique proteins in roots; 32% and 27% unique identified proteins were leaves- and roots-specific, respectively.

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