Complete Chloroplast Genomes of Erianthus arundinaceus and Miscanthus sinensis: Comparative Genomics and Evolution of the Saccharum Complex

Abstract

The genera Erianthus and Miscanthus, both members of the Saccharum complex, are of interest as potential resources for sugarcane improvement and as bioenergy crops. Recent studies have mainly focused on the conservation and use of wild accessions of these genera as breeding materials. However, the sequence data are limited, which hampers the studies of phylogenetic relationships, population structure, and evolution of these grasses. Here, we determined the complete chloroplast genome sequences of Erianthus arundinaceus and Miscanthus sinensis by using 454 GS FLX pyrosequencing and Sanger sequencing. Alignment of the E. arundinaceus and M. sinensis chloroplast genome sequences with the known sequence of Saccharum officinarum demonstrated a high degree of conservation in gene content and order. Using the data sets of 76 chloroplast protein-coding genes, we performed phylogenetic analysis in 40 taxa including E. arundinaceus and M. sinensis. Our results show that S. officinarum is more closely related to M. sinensis than to E. arundinaceus. We estimated that E. arundinaceus diverged from the subtribe Sorghinae before the divergence of Sorghum bicolor and the common ancestor of S. officinarum and M. sinensis. This is the first report of the phylogenetic and evolutionary relationships inferred from maternally inherited variation in the Saccharum complex. Our study provides an important framework for understanding the phylogenetic relatedness of the economically important genera Erianthus, Miscanthus, and Saccharum.

Assembly of 23 Plastid Genomes Provides the Chloroplast View onMiscanthusOrigins

“…The next clade is bounded by Miscanthus olygostachyus at its root. Interestingly, this species is sister to Miscanthus sinensis var Purpurascens and two previously published sequences of M. sinensis and Miscanthus floridulus (Lloyd Evans and Joshi 2016;Nah et al 2016;Tsuruta et al 2017). This would indicate that the M. sinensis forms have either been misidentified or they represent hybrids of M. oligostachyus with M. sinensis.…”

Plastome phylogenomics of sugarcane and relatives confirms the segregation of the genus Tripidium (Poaceae: Andropogoneae)

“…Sun & al., ; Duvall & al., ; Zhang & al., ; Medina & al., ; Saarela & al., ; Yan & al., ). Several plastome phylogenomic analyses in Andropogoneae have also successfully recovered evolutionary relationships among taxa, helping to define their taxonomic circumscriptions (Evans & Joshi, ; Welker & al., ; Arthan & al., ; Tsuruta & al., ). The phylogenomic investigation of Arthan & al.…”

“…The analysis of Tsuruta & al. (), based on 76 plastid genes, showed that Saccharum officinarum is more closely related to Miscanthus sinensis Andersson than to Erianthus arundinaceus (Retz.) Jeswiet.…”

Saccharum×Miscanthusintergeneric hybrids (miscanes) exhibit greater chilling tolerance of C4photosynthesis and postchilling recovery than sugarcane (Saccharumspp. hybrids)

“…Molecular genetics studies indicate that Miscanthus and Saccharum are closely related (Amalraj & Balasundaram, 2006;Sacks, Juvik, Lin, Stewart, & Yamada, 2013;Sobral, Braga, LaHood, & Keim, 1994). The two genera were estimated to have separated from a common ancestor about 3.64 mya (Tsuruta, Ebina, Kobayashi, & Takahashi, 2017). Moreover, intergeneric hybrids of Saccharum and Miscanthus have been bred previously, and these intergeneric hybrids are often termed miscanes.…”