The DOI matches its Crossref record; 62 of the 62 references it cites were found in a registry or an index.
A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era
Open accessAbstract
Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for clade-specific homology inference and analysis have increased in pangenomic era. We proposed a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops such as wheat, barley, and rye. We then built Triticeae-GeneTribe (http://wheat.cau.edu.cn/TGT/) as a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2 as a combined result of genome translocation, duplication, and polyploidization and gene loss events. Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources.
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12628 · Cited by 4,823
Emms, D. M., & Kelly, S. (2015) · Genome Biology · doi:10.1186/s13059-015-0721-2 · Cited by 3,408
AmiGO: online access to ontology and annotation data
Carbon, S., Ireland, A., Mungall, C. J., Shu, S., Marshall, B., Lewis, S., Hub, T. A., & the Web Presence Working Group (2009) · Bioinformatics · doi:10.1093/bioinformatics/btn615 · Cited by 1,952
Synteny and Collinearity in Plant Genomes
Tang, H., Bowers, J. E., Wang, X., Ming, R., Alam, M., & Paterson, A. H. (2008) · Science · doi:10.1126/science.1153917 · Cited by 1,612
The Wheat VRN2 Gene Is a Flowering Repressor Down-Regulated by Vernalization
Yan, L., Loukoianov, A., Blechl, A., Tranquilli, G., Ramakrishna, W., SanMiguel, P., Bennetzen, J. L., Echenique, V., & Dubcovsky, J. (2004) · Science · doi:10.1126/science.1094305 · Cited by 1,159
Berardini, T. Z., Reiser, L., Li, D., Mezheritsky, Y., Muller, R., Strait, E., & Huala, E. (2015) · genesis · doi:10.1002/dvg.22877 · Cited by 1,143
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Chen, C., Jost, M., Outram, M. A., Friendship, D., Chen, J., Wang, A., Periyannan, S., Bartoš, J., Holušová, K., Doležel, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41021-2 · Cited by 38
Metadata
- Authors
- Chen, Y., Song, W., Xie, X., Wang, Z., Guan, P., Peng, H., Jiao, Y., Ni, Z., Sun, Q., & Guo, W.
- Venue
- Molecular Plant
- Publisher
- Elsevier BV
- Published
- 2020-12
- Volume
- 13
- Issue
- 12
- Pages
- 1694-1708
- ISSN
- 1674-2052 (ISSN-L)
- OpenAlex
- W3089071526
- Cited by
- 287
- References
- 62
- FWCI
- 16.94
- Type
- journal article
- Language
- en
- Open access
- bronze
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- The paper
- Chen, Y., Song, W., Xie, X., Wang, Z., Guan, P., Peng, H., Jiao, Y., Ni, Z., Sun, Q., & Guo, W. (2020). A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era. Molecular Plant. https://doi.org/10.1016/j.molp.2020.09.019
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