The reference genome of Miscanthus floridulus illuminates the evolution of Saccharinae

Abstract

Miscanthus, a member of the Saccharinae subtribe that includes sorghum and sugarcane, has been widely studied as a feedstock for cellulosic biofuel production. Here, we report the sequencing and assembly of the Miscanthus floridulus genome by the integration of PacBio sequencing and Hi-C mapping, resulting in a chromosome-scale, high-quality reference genome of the genus Miscanthus. Comparisons among Saccharinae genomes suggest that Sorghum split first from the common ancestor of Saccharum and Miscanthus, which subsequently diverged from each other, with two successive whole-genome duplication events occurring independently in the Saccharum genus and one whole-genome duplication occurring in the Miscanthus genus. Fusion of two chromosomes occurred during rediploidization in M. floridulus and no significant subgenome dominance was observed. A survey of cellulose synthases (CesA) in M. floridulus revealed quite high expression of most CesA genes in growing stems, which is in agreement with the high cellulose content of this species. Resequencing and comparisons of 75 Miscanthus accessions suggest that M. lutarioriparius is genetically close to M. sacchariflorus and that M. floridulus is more distantly related to other species and is more genetically diverse. This study provides a valuable genomic resource for molecular breeding and improvement of Miscanthus and Saccharinae crops.

Genome-Wide Investigation of the NAC Transcription Factor Family in Miscanthus sinensis and Expression Analysis Under Various Abiotic Stresses

“…However, owing to the complexity of Miscanthus genome, the lack of reliable genome information and unavailable genetic databases limited related research within genus. Recently, chromosome-scale assembly of Miscanthus lutarioriparius genome ( Miao et al, 2020 ), Miscanthus floridulus genome ( Zhang et al, 2021 ), and M. sinensis genome ( Mitros et al, 2020 ) was published, which would provide valuable genetic resource for Miscanthus breeding improvement and molecular regulation network of stress resistance. The NAC gene family is a crucial plant-specific transcription factor family that is well known by its involvement in plant growth and developmental activities along with resistance to biotic and abiotic stresses ( Wang et al, 2014 ; Dalman et al, 2017 ).…”

Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses

“…A heterozygosity rate of 0.48% was estimated from the frequency peaks of 17-mers from the Illumina reads following [35], with a main peak depth of 52 [Additional file 1: Fig. S2c (sequence depth), Additional file 2: Table S4a (Illumina read statistics)].…”

Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq

“…This is a heterogeneous gramineous plant that hybridizes interspecifically and hence has a complex genetic background. Recent molecular studies have revealed that the Miscanthus genome is unusually large (2.07–2.6 GB) [ 5 – 9 ]. In Miscanthus , inter- and intraspecific hybridization is common which is why this genus is characterized by rich genetic diversity and heterosis [ 6 , 9 ].…”

“…Recent molecular studies have revealed that the Miscanthus genome is unusually large (2.07–2.6 GB) [ 5 – 9 ]. In Miscanthus , inter- and intraspecific hybridization is common which is why this genus is characterized by rich genetic diversity and heterosis [ 6 , 9 ]. The genetic diversity has been exploited to develop Miscanthus hybrids, which can deliver higher biomass yields and exhibit better adaptability to diverse climatic conditions than their parent species.…”

“…First-generation molecular markers cover restriction fragment length polymorphisms (RFLPs) [ 7 , 8 ], random amplified polymorphic DNA (RAPD) [ 9 , 10 ], and amplified fragment length polymorphisms (AFLPs) [ 11 ], while second-generation molecular markers include simple sequence repeats (SSRs) [ 12 ] and inter-simple sequence repeats (ISSRs) [ 13 ]. However, these markers have several limitations: they are low throughput, inaccurate, time-consuming, labor-intensive, and costly [ 3 ].…”