The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)
Open accessAbstract
Unlike most plants, date palms are either male or female. Assembly of a draft date palm genome, the first for a member of the order Arecales, reveals loci linked to gender and provides markers for improving traits such as fruit quality and ripening time. Date palm is one of the most economically important woody crops cultivated in the Middle East and North Africa and is a good candidate for improving agricultural yields in arid environments. Nonetheless, long generation times (5–8 years) and dioecy (separate male and female trees) have complicated its cultivation and genetic analysis. To address these issues, we assembled a draft genome for a Khalas variety female date palm, the first publicly available resource of its type for a member of the order Arecales. The ∼380 Mb sequence, spanning mainly gene-rich regions, includes >25,000 gene models and is predicted to cover ∼90% of genes and ∼60% of the genome. Sequencing of eight other cultivars, including females of the Deglet Noor and Medjool varieties and their backcrossed males, identified >3.5 million polymorphic sites, including >10,000 genic copy number variations. A small subset of these polymorphisms can distinguish multiple varieties. We identified a region of the genome linked to gender and found evidence that date palm employs an XY system of gender inheritance.
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Cites
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
<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
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180
Self-citationCNV-seq, a new method to detect copy number variation using high-throughput sequencing
Xie, C., & Tammi, M. T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-80 · Cited by 582
Assessing the gene space in draft genomes
Parra, G., Bradnam, K., Ning, Z., Keane, T., & Korf, I. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn916 · Cited by 395
Cited by
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
Kajitani, R., Toshimoto, K., Noguchi, H., Toyoda, A., Ogura, Y., Okuno, M., Yabana, M., Harada, M., Nagayasu, E., Maruyama, H., et al. (2014) · Genome Research · doi:10.1101/gr.170720.113 · Cited by 1,017
Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3943 · Cited by 513
Self-citationThe genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads
Wang, Z., Hobson, N., Galindo, L., Zhu, S., Shi, D., McDill, J., Yang, L., Hawkins, S., Neutelings, G., Datla, R., et al. (2012) · The Plant Journal · doi:10.1111/j.1365-313x.2012.05093.x · Cited by 448
The water lily genome and the early evolution of flowering plants
Zhang, L., Chen, F., Zhang, X., Li, Z., Zhao, Y., Lohaus, R., Chang, X., Dong, W., Ho, S. Y. W., Liu, X., et al. (2020) · Nature · doi:10.1038/s41586-019-1852-5 · Cited by 429
Self-citationA draft genome sequence of the pulse crop chickpea (Cicer arietinum L.)
Jain, M., Misra, G., Patel, R. K., Priya, P., Jhanwar, S., Khan, A. W., Shah, N., Singh, V. K., Garg, R., Jeena, G., et al. (2013) · The Plant Journal · doi:10.1111/tpj.12173 · Cited by 406
Metadata
- Authors
- Al-Dous, E. K., George, B., Al-Mahmoud, M. E., Al-Jaber, M. Y., Wang, H., Salameh, Y. M., Al-Azwani, E. K., Chaluvadi, S., Pontaroli, A. C., DeBarry, J., Arondel, V., Ohlrogge, J., Saie, I. J., Suliman-Elmeer, K. M., Bennetzen, J. L., Kruegger, R. R., & Malek, J. A.
- Venue
- Nature Biotechnology
- Published
- 2011-05-29
- Volume
- 29
- Issue
- 6
- Pages
- 521-527
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2167034214
- Cited by
- 405
- References
- 7
- FWCI
- 39.60
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Al-Dous, E. K., George, B., Al-Mahmoud, M. E., Al-Jaber, M. Y., Wang, H., Salameh, Y. M., Al-Azwani, E. K., Chaluvadi, S., Pontaroli, A. C., DeBarry, J., Arondel, V., Ohlrogge, J., Saie, I. J., Suliman-Elmeer, K. M., Bennetzen, J. L., Kruegger, R. R., & Malek, J. A. (2011). De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nature Biotechnology. https://doi.org/10.1038/nbt.1860
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