ArticlePloS one2013
De novo assembly and characterization of the Barnyardgrass (Echinochloa crus-galli) transcriptome using next-generation pyrosequencing.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 70 citations in OpenAlex.
- Weed biology and management in the multi-omics era: Progress and perspectives.Plant communications · 2024Review
- Transcriptomic analysis of Amaranthus retroflex resistant to PPO-inhibitory herbicides.PloS one · 2023Article
- Improvement of millets in the post-genomic era.Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Review
- Transcriptome analysis identified the mechanism of synergy between sethoxydim herbicide and a mycoherbicide on green foxtail.Scientific reports · 2020Article
- Barnyard Millet for Food and Nutritional Security: Current Status and Future Research Direction.Frontiers in genetics · 2020Review
- Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.).BMC plant biology · 2018Article
- Changes in the proteome of the problem weed blackgrass correlating with multiple-herbicide resistance.The Plant journal : for cell and molecular biology · 2018Article
- RNA-Seq transcriptome analysis of Amaranthus palmeri with differential tolerance to glufosinate herbicide.PloS one · 2018Article
- De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages.BMC genomics · 2017Article
- Transcriptome Profiling to Identify Genes Involved in Mesosulfuron-Methyl Resistance inFrontiers in plant science · 2017Article
- Data for iTRAQ-based quantitative proteomics analysis of different biotypes inData in brief · 2016Article
- Target-site and non-target-site based resistance to the herbicide tribenuron-methyl in flixweed (Descurainia sophia L.).BMC genomics · 2016Article
- Transcriptome Profiling of Buffalograss Challenged with the Leaf Spot Pathogen Curvularia inaequalis.Frontiers in plant science · 2016Article
- Article
- RNA-Seq transcriptome analysis of maize inbred carrying nicosulfuron-tolerant and nicosulfuron-susceptible alleles.International journal of molecular sciences · 2015Article
- RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance.Plant molecular biology · 2015Article
- Uncovering the differential molecular basis of adaptive diversity in three Echinochloa leaf transcriptomes.PloS one · 2015Article
- Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution.Frontiers in plant science · 2015Review
- Rice transcriptome analysis to identify possible herbicide quinclorac detoxification genes.Frontiers in genetics · 2015Article
- Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBarnyardgrass (Echinochloa crus-galli) is an important weed that is a menace to rice cultivation and production. Rapid evolution of herbicide resistance in this weed makes it one of the most difficult to manage using herbicides. Since genome-wide sequence data for barnyardgrass is limited, we sequenced the transcriptomes of susceptible and resistant barnyardgrass biotypes using the 454 GS-FLX platform.
results454 pyrosequencing generated 371,281 raw reads with an average length of 341.8 bp, which made a total length of 126.89 Mb (SRX160526). De novo assembly produced 10,142 contigs (∼5.92 Mb) with an average length of 583 bp and 68,940 singletons (∼22.13 Mb) with an average length of 321 bp. About 244,653 GO term assignments to the biological process, cellular component and molecular function categories were obtained. A total of 6,092 contigs and singletons with 2,515 enzyme commission numbers were assigned to 151 predicted KEGG metabolic pathways. Digital abundance analysis using Illumina sequencing identified 78,124 transcripts among susceptible, resistant, herbicide-treated susceptible and herbicide-treated resistant barnyardgrass biotypes. From these analyses, eight herbicide target-site gene groups and four non-target-site gene groups were identified in the resistant biotype. These could be potential candidate genes involved in the herbicide resistance of barnyardgrass and could be used for further functional genomics research. C4 photosynthesis genes including RbcS, RbcL, NADP-me and MDH with complete CDS were identified using PCR and RACE technology.
conclusionsThis is the first large-scale transcriptome sequencing of E. crus-galli performed using the 454 GS-FLX platform. Potential candidate genes involved in the evolution of herbicide resistance were identified from the assembled sequences. This transcriptome data may serve as a reference for further gene expression and functional genomics studies, and will facilitate the study of herbicide resistance at the molecular level in this species as well as other weeds.
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