The DOI matches its Crossref record; 135 of the 135 references it cites were found in a registry or an index.
A super pan-genomic landscape of rice
Open accessAbstract
Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.
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Cited by
NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads
Hu, J., Wang, Z., Sun, Z., Hu, B., Ayoola, A. O., Liang, F., Li, J., Sandoval, J. R., Cooper, D. N., Ye, K., et al. (2024) · Genome Biology · doi:10.1186/s13059-024-03252-4 · Cited by 431
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Metadata
- Authors
- Shang, L., Li, X., He, H., Yuan, Q., Song, Y., Wei, Z., Lin, H., Hu, M., Zhao, F., Zhang, C., Li, Y., Gao, H., Wang, T., Liu, X., Zhang, H., Zhang, Y., Cao, S., Yu, X., Zhang, B., Zhang, Y., Tan, Y., Qin, M., Ai, C., Yang, Y., Zhang, B., Hu, Z., Wang, H., Lv, Y., Wang, Y., Ma, J., Wang, Q., Lu, H., Wu, Z., Liu, S., Sun, Z., Zhang, H., Guo, L., Li, Z., Zhou, Y., Li, J., Zhu, Z., Xiong, G., Ruan, J., & Qian, Q.
- Venue
- Cell Research
- Published
- 2022-07-12
- Volume
- 32
- Issue
- 10
- Pages
- 878-896
- ISSN
- 1001-0602 (ISSN-L)
- 1748-7838
- OpenAlex
- W4285093403
- Cited by
- 369
- References
- 135
- FWCI
- 40.93
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Shang, L., Li, X., He, H., Yuan, Q., Song, Y., Wei, Z., Lin, H., Hu, M., Zhao, F., Zhang, C., Li, Y., Gao, H., Wang, T., Liu, X., Zhang, H., Zhang, Y., Cao, S., Yu, X., Zhang, B., . . . Qian, Q. (2022). A super pan-genomic landscape of rice. Cell Research. https://doi.org/10.1038/s41422-022-00685-z
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