Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships

BackgroundMiscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding. The whole genome transcriptomes of M. sinensis and M. sacchariflorus presented in this study may provide good resources to understand functional compositions of two important Miscanthus genomes and their evolutionary relationships.ResultsFor M. sinensis, a total of 457,891 and 512,950 expressed sequence tags (ESTs) were produced from leaf and rhizome tissues, respectively, which were assembled into 12,166 contigs and 89,648 singletons for leaf, and 13,170 contigs and 112,138 singletons for rhizome. For M. sacchariflorus, a total of 288,806 and 267,952 ESTs from leaf and rhizome tissues, respectively, were assembled into 8,732 contigs and 66,881 singletons for leaf, and 8,104 contigs and 63,212 singletons for rhizome. Based on the distributions of synonymous nucleotide substitution (Ks), sorghum and Miscanthus diverged about 6.2 million years ago (MYA), Saccharum and Miscanthus diverged 4.6 MYA, and M. sinensis and M. sacchariflorus diverged 1.5 MYA. The pairwise alignment of predicted protein sequences from sorghum-Miscanthus and two Miscanthus species found a total of 43,770 and 35,818 nsSNPs, respectively. The impacts of striking mutations found by nsSNPs were much lower between sorghum and Miscanthus than those between the two Miscanthus species, perhaps as a consequence of the much higher level of gene duplication in Miscanthus and resulting ability to buffer essential functions against disturbance.ConclusionsThe ESTs generated in the present study represent a significant addition to Miscanthus functional genomics resources, permitting us to discover some candidate genes associated with enhanced biomass production. Ks distributions based on orthologous ESTs may serve as a guideline for future research into the evolution of Miscanthus species as well as its close relatives sorghum and Saccharum.

• Publication year

  2014

• Venue

  BMC Plant Biology

• Publication date

  2014-05-18

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1186/1471-2229-14-134PMID 24884969PMCID 4046999
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The Gene Pool of Miscanthus Species and Its Improvement

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  2013cited by this paper
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  2012cited by this paper
• SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum

  2012influential reference
• A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

  2012cited by this paper
• Botanical and germinating characteristics of Miscanthus species native to Korea

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• High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis

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• Phytozome: a comparative platform for green plant genomics

  2011influential reference
• Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

  2010cited by this paper
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  2009cited by this paper
• The Sorghum bicolor genome and the diversification of grasses

  2009cited by this paper
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  2009cited by this paper
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• Comparing annual and perennial energy cropping systems with different management intensities

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  2007cited by this paper
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  2007cited by this paper
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  2006cited by this paper
• PHYLIP (Phylogeny Inference Package)

  2004cited by this paper
• GeneWise and Genomewise.

  2004cited by this paper
• The COG database: an updated version includes eukaryotes

  2003cited by this paper
• OrthoMCL: identification of ortholog groups for eukaryotic genomes.

  2003cited by this paper
• Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers

  2002cited by this paper
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  2002cited by this paper
• Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.

  1996cited by this paper
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994influential reference
• Germplasm Collection, Maintenance, and Use

  1987cited by this paper
• Sugarcane improvement through breeding

  1987cited by this paper
• BIOINFORMATICS APPLICATIONS NOTE

  year unknowncited by this paper
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• Lignocellulosic Feedstock Improvement for Biofuel Production Through Conventional Breeding and Biotechnology

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