The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
Open accessAbstract
Genetic differences between Arabidopsis thaliana accessions underlie the plant’s extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana, especially the MAGIC genetic reference population descended from these accessions. The genomes and transcriptomes of 18 natural Arabidopsis thaliana strains have been compared with that of Col-0, the most widely used A. thaliana wild type that was sequenced as part of the Arabidopsis Genome Initiative. The comparison has been used to create a comprehensive overview of genetic variability in this classic 'laboratory' plant. Each individual genome was compared with every other individual genome in a 'many-to-many' approach, which maximizes the capture of gene variations.
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Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
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Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
Atwell, S., Huang, Y. S., Vilhjálmsson, B. J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A. M., Hu, T. T., et al. (2010) · Nature · doi:10.1038/nature08800 · Cited by 1,780
Mouse genomic variation and its effect on phenotypes and gene regulation.
Keane, T. M., Goodstadt, L., Danecek, P., White, M. A., Wong, K., Yalcin, B., Heger, A., Agam, A., Slater, G., Goodson, M., et al. (2011) · Nature · doi:10.1038/nature10413 · Cited by 1,580
Self-citationRNA‐Seq Read Alignments with PALMapper
Jean, G., Kahles, A., Sreedharan, V. T., Bona, F. D., & Rätsch, G. (2010) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1106s32 · Cited by 59
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Metadata
- Authors
- Gan, X., Stegle, O., Behr, J., Steffen, J. G., Drewe, P., Hildebrand, K. L., Lyngsoe, R., Schultheiss, S. J., Osborne, E. J., Sreedharan, V. T., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E. J., Harberd, N. P., Kemen, E., Toomajian, C., Kover, P. X., Clark, R. M., Rätsch, G., & Mott, R.
- Venue
- Nature
- Published
- 2011-08-28
- Volume
- 477
- Issue
- 7365
- Pages
- 419-423
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2166469005
- Cited by
- 643
- References
- 7
- FWCI
- 23.86
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Gan, X., Stegle, O., Behr, J., Steffen, J. G., Drewe, P., Hildebrand, K. L., Lyngsoe, R., Schultheiss, S. J., Osborne, E. J., Sreedharan, V. T., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E. J., Harberd, N. P., Kemen, E., Toomajian, C., . . . Mott, R. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. https://doi.org/10.1038/nature10414
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