The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
How to usefully compare homologous plant genes and chromosomes as DNA sequences
Open accessAbstract
Summary: There are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non‐coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text.
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
Brudno, M., Do, C. B., Cooper, G. M., Kim, M. F., Davydov, E., Program, N. C. S., Green, E. D., Sidow, A., & Batzoglou, S. (2003) · Genome Research · doi:10.1101/gr.926603 · Cited by 1,115
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development
Woolfe, A., Goodson, M., Goode, D. K., Snell, P., McEwen, G. K., Vavouri, T., Smith, S. F., North, P., Callaway, H., Kelly, K., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0030007 · Cited by 970
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern, B. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.211 · Cited by 678
Hardison, R. C. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0000058 · Cited by 252
Cited by
Evolution of Gene Duplication in Plants
Panchy, N., Lehti-Shiu, M., & Shiu, S.-H. (2016) · Plant Physiology · doi:10.1104/pp.16.00523 · Cited by 1,757
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J. H., Senin, P., Wang, W., Ly, B. V., Lewis, K. L. T., et al. (2008) · Nature · doi:10.1038/nature06856 · Cited by 1,084
Self-citationDe novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A., Qiu, Y., et al. (2021) · Science · doi:10.1126/science.abg5289 · Cited by 747
PGDD: a database of gene and genome duplication in plants
Lee, T.-H., Tang, H., Wang, X., & Paterson, A. H. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1104 · Cited by 593
SynMap2 and SynMap3D: web-based whole-genome synteny browsers
Haug-Baltzell, A., Stephens, S. A., Davey, S., Scheidegger, C. E., & Lyons, E. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx144 · Cited by 181
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Metadata
- Authors
- Lyons, E., & Freeling, M.
- Venue
- The Plant Journal
- Publisher
- Wiley
- Published
- 2008-02
- Volume
- 53
- Issue
- 4
- Pages
- 661-673
- ISSN
- 0960-7412 (ISSN-L)
- 1365-313X
- OpenAlex
- W2146384771
- Cited by
- 509
- References
- 6
- FWCI
- 5.21
- Type
- journal article
- Language
- en
- Open access
- bronze
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