Genome Survey Sequence and the Development of Simple Sequence Repeat (SSR) Markers in Erianthus arundinaceus

Abstract

Erianthus arundinaceus possesses high biomass, vigor, ratoonability and resistance to biotic and abiotic stresses and is considered to be an ideal species for improving sugarcane. In this study, a genome survey sequence was performed in E. arundinaceus, and SSR markers were developed based on a genome survey sequence. A total of 167.36 Gb raw data were obtained and were assembled into 3161 Mb genome sequences, including 15,238,738 scaffolds. The genome size was estimated to be approximately 3.23 Gp based on kmer analysis. In total, 36,616 SSR motifs were identified and characterized, including 60.69% dinucleotide, 34.27% trinucleotide, 3.34% tetranucleotide, 0.98% pentanucleotide and 0.71% hexanucleotide repeats. AG/CT repeat motifs were the most abundant, and GC/CG repeat motifs were somewhat rare, accounting for 54.16% and 2.69% of dinucleotide repeat motifs, respectively. A total of 365 SSR loci were obtained by 20 SSR primer pairs amplified in 20 clones of E. arundinaceus and its related species, and 188 SSR loci were specific to E. arundinaceus. Genetic similarity coefficient analysis by UPMGA methods clustered 20 clones of E. arundinaceus and its related species into two groups. Five clones of E. arundinaceus clustered separately with the remaining clones. These results may establish a foundation for further research investigating the E. arundinaceus genome and identifying genuine hybrids between sugarcane and E. arundinaceus.