ArticlePloS one2015
De Novo Assembly and Annotation of the Chinese Chive (Allium tuberosum Rottler ex Spr.) Transcriptome Using the Illumina Platform.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 34 citations in OpenAlex.
- Genetic diversity and association analysis between agronomic traits and EST-SSR markers in Chinese chive (Frontiers in plant science · 2026Article
- A multi-omic characterization of the physiological responses to salt stress in Scenedesmus obliquus UTEX393.Communications biology · 2025Article
- Integrated metabolomics and transcriptomics analysis reveals the potential mechanism by which Methyl jasmonate enhances the pungent flavor of soilless-cultivated Chinese chives (Allium tuberosum).BMC plant biology · 2025Article
- Construction of a core collection and SNP fingerprinting database for Chinese chive (Frontiers in plant science · 2025Article
- LC-MS/MS Method Minimizing Matrix Effect for the Analysis of Bifenthrin and Butachlor in Chinese Chives and Its Application for Residual Study.Foods (Basel, Switzerland) · 2023Article
- Turning Garlic into a Modern Crop: State of the Art and Perspectives.Plants (Basel, Switzerland) · 2023Review
- Biosynthesis and Metabolism of Garlic Odor Compounds in Cultivated Chinese Chives (International journal of molecular sciences · 2022Article
- Jasmonates in plant growth and development and elicitation of secondary metabolites: An updated overview.Frontiers in plant science · 2022Review
- Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling.Scientific reports · 2021Article
- Transcriptome analysis and genetic diversity ofMitochondrial DNA. Part B, Resources · 2021Article
- De novo transcriptome analysis of stressed blood clam (Anadara broughtonii) and identification of genes associated with hemoglobin.Genes & genomics · 2020Article
- Omics approaches inPeerJ · 2020Article
- Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L.Scientific reports · 2018Article
- Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium.BMC genomics · 2017Article
- Therapeutic Role of Functional Components in Alliums for Preventive Chronic Disease in Human Being.Evidence-based complementary and alternative medicine : eCAM · 2017Review
- The Amaryllidaceae alkaloids: biosynthesis and methods for enzyme discovery.Phytochemistry reviews : proceedings of the Phytochemical Society of Europe · 2016Article
- De novo assembly and characterization of the Welsh onion (Allium fistulosum L.) transcriptome using Illumina technology.Molecular genetics and genomics : MGG · 2016Article
- De Novo Transcriptome Assembly and Annotation of the Leaves and Callus of Cyclocarya Paliurus (Bata1) Iljinskaja.PloS one · 2016Article
- Identification of an NAC Transcription Factor Family by Deep Transcriptome Sequencing in Onion (Allium cepa L.).PloS one · 2016Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chinese chive (A. tuberosum Rottler ex Spr.) is one of the most widely cultivated Allium species in China. However, minimal transcriptomic and genomic data are available to reveal its evolution and genetic diversity. In this study, de novo transcriptome sequencing was performed to produce large transcript sequences using an Illumina HiSeq 2000 instrument. We produced 51,968,882 high-quality clean reads and assembled them into 150,154 contigs. A total of 60,031 unigenes with an average length of 631 bp were identified. Of these, 36,523 unigenes were homologous to existing database sequences, 35,648 unigenes were annotated in the NCBI non-redundant (Nr) sequence database, and 23,509 unigenes were annotated in the Swiss-Prot database. A total of 26,798 unigenes were assigned to 57 Gene Ontology (GO) terms, and 13,378 unigenes were assigned to Cluster of Orthologous Group categories. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, we mapped 21,361 unigenes onto 128 pathways. Furthermore, 2,125 sequences containing simple sequence repeats (SSRs) were identified. This new dataset provides the most comprehensive resource currently available for gene expression, gene discovery, and future genomic research on Chinese chive. The sequence resources developed in this study can be used to develop molecular markers that will facilitate further genetic research on Chinese chive and related species.
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