Recent polyploidization events in three Saccharum founding species

Abstract

The complexity of polyploid Saccharum genomes hindered progress of genome research and crop improvement in sugarcane. To understand their genome structure, transcriptomes of 59 F individuals derived from S. officinarumLA Purple and S. robustum Molokai 5829 (2n = 80, x = 10 for both) were sequenced, yielding 11 157 and 8998 SNPs and 83 and 105 linkage groups, respectively. Most markers in each linkage group aligned to single sorghum chromosome. However, 71 interchromosomal rearrangements were detected between sorghum and S. officinarum or S. robustum, and 24 (33.8%) of them were shared between S. officinarum and S. robustum, indicating their occurrence before the speciation event that separated these two species. More than 2000 gene pairs from S. spontaneum, S. officinarum and S. robustum were analysed to estimate their divergence time. Saccharum officinarum and S. robustum diverged about 385 thousand years ago, and the whole-genome duplication events occurred after the speciation event because of shared interchromosomal rearrangements. The ancestor of these two species diverged from S. spontaneum about 769 thousand years ago, and the reduction in basic chromosome number from 10 to 8 in S. spontaneum occurred after the speciation event but before the two rounds of whole-genome duplication. Our results proved that S. officinarum is a legitimate species in its own right and not a selection from S. robustum during the domestication process in the past 10 000 years. Our findings rejected a long-standing hypothesis and clarified the timing of speciation and whole-genome duplication events in Saccharum.

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

“…On the other hand, the gene density in Ssp is less skewed towards subtelomeric regions (Zhang et al, 2018), which might explain why we did not observe such a clear pattern of PK gene distribution along Ssp chromosomes. An analogous observation was made in a recent analysis that compared the genomic structure of Sbi and those of two Saccharum species (Zhang et al, 2019a). Although the three species exhibited considerable collinearity among homologous chromosomes, genes that were widely dispersed in S. officinarum and S. robustum linkage groups were much more tightly clustered in subtelomeric regions on Sbi chromosomes.…”

The Role of Sugarcane Catalase Gene ScCAT2 in the Defense Response to Pathogen Challenge and Adversity Stress

“…At the amino acid level, the homology of ScCAT2 to previously reported sugarcane CATs, such as ScCAT1 (KF664183), SoCAT-1a (KF864224), SoCAT-1b (KF864225), SoCAT-1c (KF864231), SsCAT-1a (KF864226), SsCAT-1b (KF864227), and EaCAT-1b (KF864228), were 71.81%, 71.81%, 71.81%, 71.20%, 71.60%, 71.20%, and 71.60%, respectively. The genetic background of sugarcane is complex, as Saccharum hybrids are highly polyploid and derived from interspecific hybridization between S. officinarum and S. spontaneum , and each gene has 8–10 copies [ 26 ]. Furthermore, the catalase family also consists of different members that are homologous in sequence.…”

“…As is known, Saccharum spp., are members of a complex genus characterized by high polyploidy, frequent aneuploidy and heterozygosity, large genomes, low fertility rates, and long growth periods [ 26 , 50 , 51 ]. These factors make it a prime candidate for improvement through genetic engineering instead of traditional breeding, but at the same time, may impact the expression and heredity stabilization of target genes in transgenic sugarcane, and result in sugarcane transgenic technology with low transformation efficiency and long experimental periods [ 52 , 53 , 54 ].…”

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

“…Despite the lack of a Miscanthus genomic sequence, the availability of complete genome sequences of rice, maize, sorghum, and more recently sugarcane makes it possible to conduct comparative genomic analyses to gain a greater understanding of the Miscanthus transcriptome. 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 [30], maize [31], sorghum [32], and sugarcane [33], respectively (Table 4). For all the species, mapping ratios were highest with PacBio FLNC ROIs (35.23-93.57%), followed by clustered transcripts (10.06-79.72%), and then…”

“…As an international standardized gene functional classi cation system, GO offers a dynamic updated controlled vocabulary and a strictly de ned concept to describe properties of genes and their products in any organism [33,34]. A total of 154,759 transcripts that were assigned to GO terms were classi ed into 50 functional groups under three major functional categories (biological process, cellular component, and molecular function) ( Fig.…”