Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond
Open accessAbstract
The sudden availability of DNA sequencing technologies that rapidly produce vast amounts of sequence information has triggered a paradigm shift in genomics, enabling massively parallel surveying of complex nucleic acid populations. The diversity of applications to which these technologies have already been applied demonstrates the immense range of cellular processes and properties that can now be studied at the single-base resolution. These include genome resequencing and polymorphism discovery, mutation mapping, DNA methylation, histone modifications, transcriptome sequencing, gene discovery, alternative splicing identification, small RNA profiling, DNA-protein, and possibly even protein-protein interactions. Thus, these deep sequencing technologies offer plant biologists unprecedented opportunities to increase the understanding of the functions and dynamics of plant cells and populations.
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High-throughput sequencing strategies can be adapted to generate transcriptome data, either by aligning cDNA to an assembled genome or through de novo assembly.
“high-throughput sequencing strategies can be adapted to generate transcriptome data, either by aligning cDNA sequence data to an assembled genome or through de novo transcriptome assembly [111,112]”
From Biofuels from algae: Challenges and potential (2010) · cites this paper as [112]
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- Authors
- Lister, R., Gregory, B. D., & Ecker, J. R.
- Affiliations
- Salk Institute for Biological Studies (US)
- Corresponding author
- Ecker, Joseph R
- Venue
- Current Opinion in Plant Biology
- Publisher
- Elsevier BV
- Published
- 2009-04
- Volume
- 12
- Issue
- 2
- Pages
- 107-118
- ISSN
- 1369-5266 (ISSN-L)
- PMC
- PMC2723731
- OpenAlex
- W2067360806
- Cited by
- 274
- References
- 88
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 3 · 2023: 2 · 2022: 5 · 2021: 7 · 2020: 5 · 2019: 8 · 2018: 13 · 2017: 16 · 2016: 13 · 2015: 17 · 2014: 30 · 2013: 29 · 2012: 29
- FWCI
- 3.16
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Current Opinion in Plant Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- UWA Profiles and Research Repository (UWA) (submittedVersion)
- Funders
- Damon Runyon Cancer Research Foundation
- Mary K. Chapman Foundation
- National Institute of Environmental Health Sciences (U01ES017166)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- next-generation sequencing, DNA sequencing technologies, genome resequencing, mutation mapping, DNA methylation, histone modifications, transcriptome sequencing, gene discovery, alternative splicing, small RNA profiling, protein-DNA interactions, plant genomics
- MeSH terms
- Polymorphism, Genetic, Sequence Analysis, DNA, Genome, Plant, RNA, Plant, DNA Methylation, Gene Expression Profiling
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