Perspectives on the genomics research of important crops in the tribe Andropogoneae: Focusing on the Saccharum complex

Abstract

Climate changes are shifting the perception of C4 photosynthetic crops due to their superior adaptability to harsh conditions. The tribe Andropogoneae includes some economically important grasses, such as Zea mays, Sorghum bicolor, Miscanthus spp., and Saccharum spp., representing C4 photosynthetic grasses. Although the Andropogoneae grasses diverged fairly recently, their genomic structures are remarkably different from each other. As previously reported, the family Poaceae shares the pan-cereal duplication event occurring ca. 65 MYA. Since this event, Sorghum bicolor has never experienced any additional duplication event. However, some lineage-specific duplication events were reported in Z. mays and Saccharum spp., and, more recently, it was revealed that a shared allotetraploidization event occurred before the divergence between Miscanthus and Saccharum (but after the divergence from S. bicolor), which provided important clues to those two species having large genome sizes with complicated ploidy numbers. The complex genomic structures of sugarcane and Miscanthus (defined as the Saccharum complex along with some other taxa) have had a limiting effect on the use of their molecular information in breeding programs. For the last decade, genomics-associated technologies have become an important tool for molecular crop breeding (genomics-assisted breeding, GAB), but it has not been directly applied to sugarcane and Miscanthus due to their complicated genome structures. As genomics research advances, molecular breeding of those crops can take advantage of technical improvements at a reasonable cost through comparative genomic approaches. Active genomic research of non-model species using closely related model species will facilitate the improvement of those crops in the future.

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

“…As a non-model species in the Andropogoneae tribe, a draft chromosome-scale genome sequence for M. sinensis has recently been released, which is insufficient compared to other Andropogoneae crops with high quality, well annotated genomes such as rice, maize, sorghum, and sugarcane [ 29 , 30 ]. The transcriptome is the comprehensive, functional readout of the genome.…”

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

“…1a). The ltered Illumina read sequences of each sample were then aligned against the PacBio isoforms of the corresponding sample using Bowtie 2 [27] with the default highly sensitive settings. More than 90% of Illumina reads were completely mapped to the PacBio isoforms of each sample, which revealed a good agreement between the short-read datasets and the long-read datasets at the nucleotide level ( Table 2).…”

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

“…As a non-model species in the Andropogoneae tribe, a draft chromosome-scale genome sequence for M. sinensis has recently been released, which is insu cient compared to other Andropogoneae crops with high quality, well annotated genomes such as rice, maize, sorghum, and sugarcane [29,30]. The transcriptome is the comprehensive, functional readout of the genome.…”

“…The transcriptome is the comprehensive, functional readout of the genome. The availability of complete genome sequences of rice, maize, sorghum, sugarcane and the recently released miscanthus genome makes it possible to conduct comparative genomic analyses to gain a better understanding of the Miscanthus transcriptome [29][30][31][32][33][34][35]. In our study, the six sequenced datasets including two sets of PacBio FLNC ROIs and four sets of Illumina clean reads as well as all the nal clustered transcripts were mapped to the genomes of rice [31], maize [32], sorghum [33], sugarcane [34] and Miscanthus [29] respectively (Table 4).…”