The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
The draft genome of sweet orange (Citrus sinensis)
Open accessAbstract
Oranges are an important nutritional source for human health and have immense economic value. Here we present a comprehensive analysis of the draft genome of sweet orange (Citrus sinensis). The assembled sequence covers 87.3% of the estimated orange genome, which is relatively compact, as 20% is composed of repetitive elements. We predicted 29,445 protein-coding genes, half of which are in the heterozygous state. With additional sequencing of two more citrus species and comparative analyses of seven citrus genomes, we present evidence to suggest that sweet orange originated from a backcross hybrid between pummelo and mandarin. Focused analysis on genes involved in vitamin C metabolism showed that GalUR, encoding the rate-limiting enzyme of the galacturonate pathway, is significantly upregulated in orange fruit, and the recent expansion of this gene family may provide a genomic basis. This draft genome represents a valuable resource for understanding and improving many important citrus traits in the future.
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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
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
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
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
Cited by
Genomics of the origin and evolution of Citrus
Wu, G. A., Terol, J., Ibanez, V., López-García, A., Pérez-Román, E., Borredá, C., Domingo, C., Tadeo, F. R., Carbonell-Caballero, J., Alonso, R., et al. (2018) · Nature · doi:10.1038/nature25447 · Cited by 892
Self-citationGenome sequencing and population genomics in non-model organisms
Ellegren, H. (2014) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2013.09.008 · Cited by 759
Peng, A., Chen, S., Lei, T., Xu, L., He, Y., Wu, L., Yao, L., & Zou, X. (2017) · Plant Biotechnology Journal · doi:10.1111/pbi.12733 · Cited by 731
PLAZA 3.0: an access point for plant comparative genomics
Proost, S., Van Bel, M., Vaneechoutte, D., Van de Peer, Y., Inzé, D., Mueller-Roeber, B., & Vandepoele, K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku986 · Cited by 317
Zhang, Y., Xu, J., Riera, N., Jin, T., Li, J., & Wang, N. (2017) · Microbiome · doi:10.1186/s40168-017-0304-4 · Cited by 257
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Metadata
- Authors
- Xu, Q., Chen, L.-L., Ruan, X., Chen, D., Zhu, A., Chen, C., Bertrand, D., Jiao, W.-B., Hao, B.-H., Lyon, M. P., Chen, J., Gao, S., Xing, F., Lan, H., Chang, J.-W., Ge, X., Lei, Y., Hu, Q., Miao, Y., Wang, L., Xiao, S., Biswas, M. K., Zeng, W., Guo, F., Cao, H., Yang, X., Xu, X.-W., Cheng, Y.-J., Xu, J., Liu, J.-H., Luo, O. J., Tang, Z., Guo, W.-W., Kuang, H., Zhang, H.-Y., Roose, M. L., Nagarajan, N., Deng, X.-X., & Ruan, Y.
- Venue
- Nature Genetics
- Published
- 2012-11-25
- Volume
- 45
- Issue
- 1
- Pages
- 59-66
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W1985557598
- Cited by
- 1,005
- References
- 7
- FWCI
- 65.36
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Xu, Q., Chen, L.-L., Ruan, X., Chen, D., Zhu, A., Chen, C., Bertrand, D., Jiao, W.-B., Hao, B.-H., Lyon, M. P., Chen, J., Gao, S., Xing, F., Lan, H., Chang, J.-W., Ge, X., Lei, Y., Hu, Q., Miao, Y., . . . Ruan, Y. (2013). The draft genome of sweet orange (Citrus sinensis). Nature Genetics. https://doi.org/10.1038/ng.2472
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