The Sorghum bicolor genome and the diversification of grasses

Abstract

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

“…The accuracy rate is very high at 99.99995%, and a relatively high proportion of the errors (two-thirds) are small insertions or deletions (indels). The accuracy rate is similar to those obtained with WGS Sanger approaches 5,36 and is higher than those reported for most NGS-based assemblies. The estimated residual within-genome heterozygosity for the Oropetium genome is very low at 0.087%, which probably contributed to the high contiguity of the assembly.…”

“…A pan-cereal whole-genome duplication (WGD) event, called rho, occurred before the diversification of grasses 5,19 . There appear to have been no further WGDs in the selected grass genomes, including Oropetium, since the shared rho event 4,5 .Genome alignments between Oropetium and selected grass genomes are mostly one-to-one after exclusion of the alignments derived from the shared genome duplication events (Extended Data Fig. 3a-e).…”

“…Despite its compact size, the Oropetium genome has a typical number of predicted protein coding genes at 28,446. A pan-cereal whole-genome duplication (WGD) event, called rho, occurred before the diversification of grasses 5,19 . There appear to have been no further WGDs in the selected grass genomes, including Oropetium, since the shared rho event 4,5 .…”

“…The largest genome assemblies, such as maize (2,300 megabases (Mb)) 7 , barley (5,100 Mb) 8 and wheat (hexaploid, 17,000 Mb) 9 are highly fragmented as a result of the inability of current sequencing technologies to span complex repeat regions. Near-finished reference genomes are available for rice 4 , Sorghum 5 and Brachypodium 10 , but more high-quality grass genomes are needed for comparative genomics and gene discovery. Here we present the 'near-complete' draft genome of the grass Oropetium thomaeum, the first high-quality reference genome from the Chloridoideae subfamily.…”

The tomato genome: implications for plant breeding, genomics and evolution

“…As many as 20 plant genomes have been sequenced and assembled in the last two years [6-25]. Genome sequences of plants belonging to different groups, such as two plants from the early land plant clades (a moss Physcomitrella patens and a spikemoss Selaginella moellendorffii ) and numerous economically important monocots (Box 1), such as rice, maize, sorghum, and so on, have now been decoded [4,5,25-28] (Figure 1). Eudicots (Box 1), the largest group in flowering plants, are composed of two major clades, the Eurosids and Euasterids.…”