ArticlePloS one2012
A genome-wide survey of switchgrass genome structure and organization.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass.BMC genomics · 2024Article
- Host genomic influence on bacterial composition in the switchgrass rhizosphere.Molecular ecology · 2022Article
- Genotyping-by-Sequencing and QTL Mapping of Biomass Yield in Two Switchgrass FFrontiers in plant science · 2022Article
- Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L.BMC plant biology · 2021Article
- Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation.Plant, cell & environment · 2021Article
- Influence of PGPB Inoculation onPlants (Basel, Switzerland) · 2019Article
- Development and validation of whole genome-wide and genic microsatellite markers in oil palm (Elaeis guineensis Jacq.): First microsatellite database (OpSatdb).Scientific reports · 2019Article
- Partitioning Apomixis Components to Understand and Utilize Gametophytic Apomixis.Frontiers in plant science · 2019Review
- Extensive Genetic Diversity is Present within North American Switchgrass Germplasm.The plant genome · 2018Article
- siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass.Biotechnology for biofuels · 2018Article
- Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass.Plant cell reports · 2017Article
- Sweet sorghum as biofuel feedstock: recent advances and available resources.Biotechnology for biofuels · 2017Review
- Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species.BMC genomics · 2016Article
- Article
- Field Guide to Plant Model Systems.Cell · 2016Review
- Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution.Scientific reports · 2016Article
- Comparative cell-specific transcriptomics reveals differentiation of C4 photosynthesis pathways in switchgrass and other C4 lineages.Journal of experimental botany · 2016Article
- Genome-wide mining, characterization, and development of microsatellite markers in gossypium species.Scientific reports · 2015Article
- Article
- Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.The Plant journal : for cell and molecular biology · 2014Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The perennial grass, switchgrass (Panicum virgatum L.), is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated) and 110 kb (BstYI-generated). A total of 330,297 high quality BAC-end sequences (BES) were generated, accounting for 263.2 Mbp (16.4%) of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs). Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.