Comparative Analysis of <i>Miscanthus</i> and <i>Saccharum</i> Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates

Kim, Changsoo; Wang, Xiyin; Lee, Tae‐Ho; Jakob, Katrin; Lee, Geung–Joo; Paterson, Andrew H.

doi:10.1105/tpc.114.125583

Cited by 73 publications

(83 citation statements)

References 71 publications

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“…13b). Putative peaks at higher K S values might represent more ancient WGD events in the monocot lineage that might have been shared by orchids or their ancestors 29,30 ( Supplementary Fig. 13b).…”

Section: Genome Evolutionmentioning

confidence: 99%

The genome sequence of the orchid Phalaenopsis equestris

et al. 2014

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Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers

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Section: Genome Evolutionmentioning

confidence: 99%

The genome sequence of the orchid Phalaenopsis equestris

et al. 2014

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“…This problem is confounded in the Saccharum lineage, where there was an ancestral genome duplication (in common with Miscanthus) (Kim et al, 2014) with a subsequent alloploid hybridization event with S. spontaneum, which led to modern sugarcane lineages. This means that even in balanced regions of the genome and only for low or single copy number genes there could be up to four copies of each gene (multi-copy genes could have far higher copy numbers).…”

Section: Advantages and Drawbacks Of Plastid-based Phylogeniesmentioning

confidence: 96%

Complete chloroplast genomes of Saccharum spontaneum, Saccharum officinarum and Miscanthus floridulus (Panicoideae: Andropogoneae) reveal the plastid view on sugarcane origins

Evans

Joshi

2016

Systematics and Biodiversity

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Sugarcane (Saccharum hybrid cultivar) ranks among the world's top 10 food crops and annually provides 60À70% of the sugar produced worldwide. Despite its economic importance there has been no large-scale systematics study of genus Saccharum and the existing model of sugarcane origins has remained largely unchallenged for almost 50 years. For the first time, we have assembled the complete plastid genomes of Miscanthus floridulus (first report for this genus), Saccharum spontaneum and Saccharum officinarum allowing us to elucidate the phylogenetic origins of Saccharum s.s. species. We demonstrate that Saccharum s.s. is divided into four species, with S. spontaneum diverging from the remainder of the genus about 1.5 million years ago and S. robustum diverging 750,000 years ago. Two separate lineages, one leading to S. officinarum and the other leading to modern hybrid cultivars diverged from S. robustum 640,000 years ago. These findings overturn all previous hypotheses on sugarcane origins, demonstrating that sugarcane's antecedents could not have arisen by human action. All modern cultivars share a common Polynesian origin, whereas Old World canes, S. barberi and S. sinense, cluster as a distinct S. officinarum lineage. This makes modern cultivars a distinct species of genus Saccharum, and we formally propose the name Saccharum cultum for the ancestor of all lineages currently classified as Saccharum hybrid cultivars.

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“…MYA (Kim et al, 2014a) and Saccharum underwent lineage-specific autotetraploidization (Kim et al, 2014b). Another interesting point inferred by a series of the comparative approaches is the evolution of basal chromosome numbers of the Andropogoneae.…”

Section: Comparative Genomics Approaches For Larger-genome Speciesmentioning

confidence: 99%

“…3 indicates the basal chromosome numbers of various accessions in S. officinarum, S. robustum, and S. spontaneum which are representatives of Saccharum spp. The data was originally collected by Irvine (1999) and reformatted by Kim et al (2014b). As conventional cultivars with a large amount of sugar production, the genomes of S. officinarum and S. robustum remain quite fixed to x = 10 as shown in Fig.…”

Section: Inmentioning

confidence: 99%

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Perspectives on the genomics research of important crops in the tribe Andropogoneae: Focusing on the Saccharum complex

Choi¹,

Chung²,

Kim³

2016

Korean Journal of Agricultural Science

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Climate changes are shifting the perception of C4 photosynthetic crops due to their superior adaptability to harsh conditions. The tribe Andropogoneae includes some economically important grasses, such as Zea mays, Sorghum bicolor, Miscanthus spp., and Saccharum spp., representing C4 photosynthetic grasses. Although the Andropogoneae grasses diverged fairly recently, their genomic structures are remarkably different from each other. As previously reported, the family Poaceae shares the pan-cereal duplication event occurring ca. 65 MYA. Since this event, Sorghum bicolor has never experienced any additional duplication event. However, some lineage-specific duplication events were reported in Z. mays and Saccharum spp., and, more recently, it was revealed that a shared allotetraploidization event occurred before the divergence between Miscanthus and Saccharum (but after the divergence from S. bicolor), which provided important clues to those two species having large genome sizes with complicated ploidy numbers. The complex genomic structures of sugarcane and Miscanthus (defined as the Saccharum complex along with some other taxa) have had a limiting effect on the use of their molecular information in breeding programs. For the last decade, genomics-associated technologies have become an important tool for molecular crop breeding (genomics-assisted breeding, GAB), but it has not been directly applied to sugarcane and Miscanthus due to their complicated genome structures. As genomics research advances, molecular breeding of those crops can take advantage of technical improvements at a reasonable cost through comparative genomic approaches. Active genomic research of non-model species using closely related model species will facilitate the improvement of those crops in the future.

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Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates

Cited by 73 publications

References 71 publications

The genome sequence of the orchid Phalaenopsis equestris

The genome sequence of the orchid Phalaenopsis equestris

Complete chloroplast genomes of Saccharum spontaneum, Saccharum officinarum and Miscanthus floridulus (Panicoideae: Andropogoneae) reveal the plastid view on sugarcane origins

Perspectives on the genomics research of important crops in the tribe Andropogoneae: Focusing on the Saccharum complex

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