The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes
Open accessAbstract
Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.
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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.021 · Cited by 819
De 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
Self-citationPan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
Qin, P., Lu, H., Du, H., Wang, H., Chen, W., Chen, Z., He, Q., Ou, S., Zhang, H., Li, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.046 · Cited by 578
Self-citationThe population genetics of structural variants in grapevine domestication
Zhou, Y., Minio, A., Massonnet, M., Solares, E., Lv, Y., Beridze, T., Cantu, D., & Gaut, B. S. (2019) · Nature Plants · doi:10.1038/s41477-019-0507-8 · Cited by 339
Self-citationA complete telomere-to-telomere assembly of the maize genome
Chen, J., Wang, Z., Tan, K., Huang, W., Shi, J., Li, T., Hu, J., Wang, K., Wang, C., Xin, B., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01419-6 · Cited by 323
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Metadata
- Authors
- Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., Liu, H., Ma, X., Jiao, Y., Wang, B., Wei, X., Stein, J. C., Glaubitz, J. C., Lu, F., Yu, G., Liang, C., Fengler, K., Li, B., Rafalski, A., Schnable, P. S., Ware, D. H., Buckler, E. S., & Lai, J.
- Venue
- Nature Genetics
- Published
- 2018-07-30
- Volume
- 50
- Issue
- 9
- Pages
- 1289-1295
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2884730312
- Cited by
- 400
- References
- 7
- FWCI
- 48.55
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., Liu, H., Ma, X., Jiao, Y., Wang, B., Wei, X., Stein, J. C., Glaubitz, J. C., Lu, F., Yu, G., . . . Lai, J. (2018). Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature Genetics. https://doi.org/10.1038/s41588-018-0182-0
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