The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense
Open accessAbstract
Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete1–4. Here we report reference-grade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3–79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes1,3, these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadense to G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement. The improved genome assemblies of allotetraploid cotton species Gossypium hirsutum and Gossypium barbadense provide insights into cotton evolution and inform the construction of introgression lines used to identify loci associated with fiber quality.
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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
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
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
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
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Servant, N., Varoquaux, N., Lajoie, B. R., Viara, E., Chen, C.-J., Vert, J.-P., Heard, E., Dekker, J., & Barillot, E. (2015) · Genome Biology · doi:10.1186/s13059-015-0831-x · Cited by 2,565
Fast algorithms for large-scale genome alignment and comparison
Delcher, A. L. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2478 · Cited by 1,036
Cited by
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
Ranallo-Benavidez, T. R., Jaron, K. S., & Schatz, M. C. (2020) · Nature Communications · doi:10.1038/s41467-020-14998-3 · Cited by 2,759
Pan-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
TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
Monat, C., Padmarasu, S., Lux, T., Wicker, T., Gundlach, H., Himmelbach, A., Ens, J., Li, C., Muehlbauer, G. J., Schulman, A. H., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1899-5 · Cited by 251
Kirungu, J. N., Magwanga, R. O., Lu, P., Cai, X., Zhou, Z., Wang, X., Peng, R., Wang, K., & Liu, F. (2019) · BMC Genetics · doi:10.1186/s12863-019-0756-6 · Cited by 76
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Metadata
- Authors
- Wang, M., Tu, L., Yuan, D., Zhu, D., Shen, C., Li, J., Liu, F., Pei, L., Wang, P., Zhao, G., Ye, Z., Huang, H., Yan, F., Ma, Y., Zhang, L., Liu, M., You, J., Yang, Y., Liu, Z., Huang, F., Li, B., Qiu, P., Zhang, Q., Zhu, L., Jin, S., Yang, X., Min, L., Li, G., Chen, L.-L., Zheng, H., Lindsey, K., Lin, Z., Udall, J. A., & Zhang, X.
- Venue
- Nature Genetics
- Published
- 2018-12-03
- Volume
- 51
- Issue
- 2
- Pages
- 224-229
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2902012935
- Cited by
- 775
- References
- 6
- FWCI
- 71.21
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Wang, M., Tu, L., Yuan, D., Zhu, D., Shen, C., Li, J., Liu, F., Pei, L., Wang, P., Zhao, G., Ye, Z., Huang, H., Yan, F., Ma, Y., Zhang, L., Liu, M., You, J., Yang, Y., Liu, Z., . . . Zhang, X. (2019). Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature Genetics. https://doi.org/10.1038/s41588-018-0282-x
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