IC4R004-Genome-2013-23481403

Project Title

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution

The genus Oryza, consisting of 24 species along an evolutionary gradient of B15 million years, is an ideal model for studying plant genome evolution10–12. The evolutionary signatures of Oryza genome evolution vary among different loci6,13,14, suggesting the demand for whole-genome comparisons of these Oryza species. The wild rice Oryza brachyantha is defined as F genome type and placed on the basal lineage in Oryza15 (Supplementary Note S1 and Supplementary Fig. S1). It contains a different set of repeat sequences compared with rice or other Oryza genomes16,17. Its compact genome and unique phylogenetic position put O. brachyantha more close to the ancestral state of the Oryza genomes10 (Supplementary Note S1 and Supplementary Figs S1 and S2). Thus, comparisons of the O.brachyantha and rice genomes will provide us a unique opportunity to explore the genomic changes and the underlying mechanisms of Oryza genome evolution.

The researchers used a whole-genome shotgun approach combined with the bacterial artificial chromosome (BAC)-based physical map to assemble B261 Mb of the O. brachyantha genome. O.brachyantha has a compact genome composed of less than 30% of repeat elements. The researchers annotated 32,038 gene models in O.brachyantha, which is much lower than in rice18, implying a massive amplification of gene families in the domesticated rice genome. The researchers showed that both tandem gene duplications and gene transpositions had contributed to the burst of gene families in the rice genome. These duplicated sequences might have impacts on the erosion of synteny and accumulation of transposable elements in the heterochromatic regions.

The researchers used a whole-genome shotgun sequencing approach to generate 31 Gb of the raw sequence of O. brachyantha using the Illumina GA II platform (Supplementary Table S1). The genome was initially assembled using SOAPdenovo19, and the length of the sequence scaffold was further increased by integrating BAC-end sequences generated by Sanger technology20 (Supplementary Methods). The final assembled sequence was 261 Mb with a scaffold N50 size of 1.6 Mb (Supplementary Table S2). The ordering of the scaffolds along each chromosome was accomplished by integration with the BAC-based physical map20. The scaffolds were eventually merged into 36 large sequence blocks covering 96% of the sequenced genome (Fig. 1). These sequence blocks were anchored onto each chromosome by a cytogenetic approach (Supplementary Fig. S3), resulting in 12 pseudomolecules representing the 12 chromosomes of O. brachyantha.

Figure 1. Alignment of 36 sequence blocks of O. brachyantha to rice chromosomes

Approximately 29.2% of the O. brachyantha genome is composed of transposable elements (Supplementary Table S3), consistent with their genome sizes. The Mutator-like element is the most abundant transposon family, accounting for 7.5% (18.3 Mb versus 13.4 Mb in rice18) of the O. brachyantha genome and more than 25% of the DNA transposons in O. brachyantha. Retrotransposons,mostly long-terminal repeat (LTR) retrotransposons, comprise B10% of the O. brachyantha genome. A total of 184 LTR retrotransposon families have been discovered, including 75 Ty1-copia, 55 Ty3-gypsy and 54 unclassified families. It is interesting to note that 40 families are present in the form of solo LTRs or fragments. The transposable elements are unevenly distributed on each chromosome with retrotransposons concentrated in pericentromeric or heterochromatic regions (Fig. 2 and Supplementary Fig. S4).

Figure 2 . Distributions of genomic features in O. brachyantha and O. sativa on chromosome 4.

Figure 4.Venn diagram showing the distribution of gene families between O. brachyantha, O. sativa and Sorghum bicolor.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
Institute of Plant Breeding,Genetics and Genomics, University of Georgia, Athens, Georgia 30602, USA.
Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute,University of Arizona, Tucson, Arizona 85721, USA.
Department of Genetics and Cell Biology, Nankai University, Tianjin 300071, China.
Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
Department of Biology, University of Copenhagen, Ole Maaløes Vej 5 DK-2200 Copenhagen N, Denmark.
King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Kingdom of Saudi Arabia.

Jun Wang(email: wangj@genomics.org.cn) & Mingsheng Chen (email: mschen@genetics.ac.cn) & Rod A.Wing (email:rwing@Ag.arizona.edu).