Abstract
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.
Highlights
Miscanthus is a promising biomass crop for temperate regions
The genome-wide coverage of unigenes based on the size of the haploid genome of M. sinensis and M. sacchariflorus [12] was about 1.5% and 1.1%, respectively, while the estimated coverage of coding sequences in sorghum was 5.5% [6]
A total of 34,355 (MSI) and 35,177 (MSA) unigenes have significant similarities to sorghum gene models (34,496 in total) [6] based on blast search (e < 10−5), indicating that the number of Miscanthus Expressed sequence tag (EST) presented in this study is sufficient for further analysis
Summary
Miscanthus is a promising biomass crop for temperate regions. 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. The genus Miscanthus has been considered attractive as a feedstock for cellulosic biofuel production because the plants are adapted to temperate latitudes yet utilize the Miscanthus belongs to the Andropogoneae tribe of grasses, including many economically important crops such as maize, sorghum, and sugarcane. Study of the large and complex Miscanthus genomes is challenging, the whole genome sequence of closely-related sorghum (2n = 2× = 20) [6] provides a valuable reference for molecular research in Miscanthus. Genomic study of Miscanthus is currently focused on the construction of genetic maps using AFLP [7], SSR [8], RNA-seq [9], and GBS (genotype by sequencing) [10]
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