ArticleBMC genomics2010
De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas).
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 237 papers, 1 of them a synthesis that pooled it.
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Who cites it
237 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives.Plant communications · 2022Pooled it
- Genome-wide identification of the ATL gene family and their expression analysis in sweetpotato and its two diploid relatives.BMC plant biology · 2026Article
- Unravelling the molecular mechanism underlying drought stress tolerance in Dinanath (Pennisetum pedicellatum Trin.) grass via integrated transcriptomic and metabolomic analyses.BMC plant biology · 2024Article
- De novo transcriptome assembly, annotation and SSR mining data of Hellula undalis (Fabr.) (Lepidoptera: Pyralidae), the cabbage webworm.Journal, genetic engineering & biotechnology · 2024Article
- Discovering the regulators of heat stress tolerance inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Genetic diversity and population structure analysis of 418 tomato cultivars based on single nucleotide polymorphism markers.Frontiers in plant science · 2024Article
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- Characterisation of theBiodiversity data journal · 2024Article
- Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz.Scientific reports · 2023Article
- Transcriptome profiling reveals the genes involved in tuberous root expansion in Pueraria (Pueraria montana var. thomsonii).BMC plant biology · 2023Article
- An Overview of Molecular Basis and Genetic Modification of Floral Organs Genes: Impact of Next-Generation Sequencing.Molecular biotechnology · 2023Review
- Construction of SNP fingerprint and population genetic analysis of honeysuckle germplasm resources in China.Frontiers in plant science · 2023Article
- Development of simple sequence repeat markers for sugarcane from data mining of expressed sequence tags.Frontiers in plant science · 2023Article
- Transcriptomic analysis reveals mechanisms for the different drought tolerance of sweet potatoes.Frontiers in plant science · 2023Article
- Transcriptome sequencing and DEG analysis in different developmental stages of floral buds induced by potassium chlorate inPlant biotechnology (Tokyo, Japan) · 2022Article
- Exogenous Betaine Enhances the Protrusion Vigor of Rice Seeds under Heat Stress by Regulating Plant Hormone Signal Transduction and Its Interaction Network.Antioxidants (Basel, Switzerland) · 2022Article
- Transcriptomic analysis of tuberous root in two sweet potato varieties reveals the important genes and regulatory pathways in tuberous root development.BMC genomics · 2022Article
- De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.).Scientific reports · 2021Article
- Transcriptome analysis reveals the importance of exogenous nutrition in regulating antioxidant defenses during the mouth-opening stage in oviparous fish.Fish physiology and biochemistry · 2021Article
- Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato.Plants (Basel, Switzerland) · 2021Article
177 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
backgroundThe tuberous root of sweet potato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweet potato root for gene discovery and molecular marker development.
resultsIn this study, more than 59 million sequencing reads were generated using Illumina paired-end sequencing technology. De novo assembly yielded 56,516 unigenes with an average length of 581 bp. Based on sequence similarity search with known proteins, a total of 35,051 (62.02%) genes were identified. Out of these annotated unigenes, 5,046 and 11,983 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 17,598 (31.14%) unigenes were mapped to 124 KEGG pathways, and 11,056 were assigned to metabolic pathways, which were well represented by carbohydrate metabolism and biosynthesis of secondary metabolite. In addition, 4,114 cDNA SSRs (cSSRs) were identified as potential molecular markers in our unigenes. One hundred pairs of PCR primers were designed and used for validation of the amplification and assessment of the polymorphism in genomic DNA pools. The result revealed that 92 primer pairs were successfully amplified in initial screening tests.
conclusionThis study generated a substantial fraction of sweet potato transcript sequences, which can be used to discover novel genes associated with tuberous root formation and development and will also make it possible to construct high density microarrays for further characterization of gene expression profiles during these processes. Thousands of cSSR markers identified in the present study can enrich molecular markers and will facilitate marker-assisted selection in sweet potato breeding. Overall, these sequences and markers will provide valuable resources for the sweet potato community. Additionally, these results also suggested that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for gene discovery and molecular marker development for non-model species, especially those with large and complex genome.
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