The Genomes of Oryza sativa: A History of Duplications

By Jun Yu, Jun Wang, Wei Lin, Songgang Li, Heng Li, Jun Zhou, Peixiang Ni, Wei Dong, Songnian Hu, Changqing Zeng and 106 more. PLoS Biology, 2005

942 citations recorded by the source corpus.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/26c7face7b93f4d38f522ad36c95641a1eca2e76

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Citations in the corpus

The genome of the cucumber, Cucumis sativus L. (2009, background): “Evidence indicates that rice underwent an ancient WG”
Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. (2009, background): “A japonica rice, Nipponbare (Reference 49 and references therein), carries a fractionated tetraploidy that predates the grass family (74, 89, 100, 103).”
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (2013, background): “Using the frequency distribution of 17-base oligomers in the usable sequencing reads to determine sequencing depth (19), we obtained an estimated genome size of 153 Mb (SI Appendix, Fig.”
Widespread genome duplications throughout the history of flowering plants. (2006, background): “Analysis of the rice genome also suggested ancient polyploidy in the early history of the grass family (Poaceae) (Paterson et al. 2004b; Yu et al. 2005).”
WEGO: a web tool for plotting GO annotations (2006, background): “WEGO has been applied in many important biological research studies, such as the comparative genomics study between the rice genome and the Arabidopsis genome (14,15) and the silkworm genome analysis (16).”
γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates (2009, methodology): “…γ -MYN in comparison with YN and MYN, we generated three groups of simulated sequences with the PAML package: (1) equal codon frequencies, (2) human frequencies (based on human protein-coding genes from the ENSEMBL data-base) [37] and (3) rice frequencies (based on rice protein-coding genes) [38].”
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads (2013, methodology): “Lastly, we generate contigs in the manner of SOAPdenovo2.”