Initial genome sequencing of the sugarcane CP 96-1252 complex hybrid

Miller, Jason R.; Dilley, Kari A.; Harkins, Derek M.; Torralba, Manolito; Moncera, Kelvin; Beeri, Karen; Goglin, Karrie; Stockwell, Timothy B.; Shabman, Reed S.

doi:10.12688/f1000research.11629.1

Cited by 8 publications

(5 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The sugarcane genome is complex, interspeci c, polyploid, and displays extensive aneuploidy [39], but research in sugarcane genomics has advanced [40][41][42][43][44][45][46][47][48][49][50][51]. One monoploid mosaic reference genome for the sugarcane hybrid R570 was released [52] along with a high-quality chromosome level genome for S. spontaneum, one of the parentals of sugarcane hybrids [53].…”

Section: Introductionmentioning

confidence: 99%

Bioinformatic Analyses to Uncover Genes Involved in Trehalose Metabolism in the Polyploid Sugarcane

Oliveira

Navarro

Pereira

et al. 2022

Preprint

View full text Add to dashboard Cite

Trehalose-6-phosphate (T6P) is an intermediate of trehalose biosynthesis that plays an essential role in plant metabolism and development. Here, we comprehensively analyzed sequences from enzymes of trehalose metabolism in sugarcane, one of the main crops used for bioenergy production. We identified protein domains, phylogeny, and in silico expression levels for all classes of enzymes. However, post-translational modifications and residues involved in catalysis and substrate binding were analyzed only in trehalose-6-phosphate synthase (TPS) sequences. We retrieved 71 putative full-length TPS, 93 trehalose-6-phosphate phosphatase (TPP), and 3 trehalase (TRE) of sugarcane, showing all their conserved domains, respectively. Putative TPS (Classes I and II) and TPP sugarcane sequences were categorized into well-known groups reported in the literature. We measured the expression levels of the sequences from one sugarcane leaf transcriptomic dataset. Furthermore, TPS Class I has specific N-glycosylation sites inserted in conserved motifs and carries catalytic and binding residues in its TPS domain. Some of these residues are mutated in TPS Class II members, which implies loss of enzyme activity. Our approach retrieved many homo(eo)logous sequences for genes involved in trehalose metabolism, paving the way to discover the role of T6P signaling in sugarcane.

show abstract

Section: Introductionmentioning

confidence: 99%

Bioinformatic Analyses to Uncover Genes Involved in Trehalose Metabolism in the Polyploid Sugarcane

Oliveira

Navarro

Pereira

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Despite the significant challenges imposed by the complex structure of the sugarcane genome, many efforts for sequencing and annotating genes accomplished essential advances. The initial step came from the expression sequence tags (ESTs) collection (SUCEST) that provided around 238,000 high-quality sequences from multiple sugarcane organs and tissues (Vettore et al, 2003), followed by several partial sequencing studies (Tan et al, 2013;de Setta et al, 2014;Grativol et al, 2014;Okura et al, 2016;Miller et al, 2017). Gene-enrichment approach using methyl filtration sequencing allowed the coverage of 97.2% of the sugarcane ESTs and 98.4% of sorghum coding sequences (CDS), providing valuable information on single nucleotide polymorphisms (SNPs) from genes associated with sucrose and starch metabolism, identifying the contribution of the two sugarcane ancestor species (Grativol et al, 2014).…”

Section: Notable Strategies For the Partial Sequencing Of Sugarcane C...mentioning

confidence: 99%

Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential

et al. 2021

View full text Add to dashboard Cite

Sugarcane (Saccharum spp.), a C4 grass, has a peculiar feature: it accumulates, gradient-wise, large amounts of carbon (C) as sucrose in its culms through a complex pathway. Apart from being a sustainable crop concerning C efficiency and bioenergetic yield per hectare, sugarcane is used as feedstock for producing ethanol, sugar, high-value compounds, and products (e.g., polymers and succinate), and bioelectricity, earning the title of the world’s leading biomass crop. Commercial cultivars, hybrids bearing high levels of polyploidy, and aneuploidy, are selected from a large number of crosses among suitable parental genotypes followed by the cloning of superior individuals among the progeny. Traditionally, these classical breeding strategies have been favoring the selection of cultivars with high sucrose content and resistance to environmental stresses. A current paradigm change in sugarcane breeding programs aims to alter the balance of C partitioning as a means to provide more plasticity in the sustainable use of this biomass for metabolic engineering and green chemistry. The recently available sugarcane genetic assemblies powered by data science provide exciting perspectives to increase biomass, as the current sugarcane yield is roughly 20% of its predicted potential. Nowadays, several molecular phenotyping tools can be applied to meet the predicted sugarcane C potential, mainly targeting two competing pathways: sucrose production/storage and biomass accumulation. Here we discuss how molecular phenotyping can be a powerful tool to assist breeding programs and which strategies could be adopted depending on the desired final products. We also tackle the advances in genetic markers and mapping as well as how functional genomics and genetic transformation might be able to improve yield and saccharification rates. Finally, we review how “omics” advances are promising to speed up plant breeding and reach the unexplored potential of sugarcane in terms of sucrose and biomass production.

show abstract

“…This database is a large platform that supports the development of System Biology projects of sugarcane providing information regarding the genome, gene expression and regulatory network. Apart from the SUCEST-FUN project, many other studies have made noteworthy contributions on the molecular basis of sugarcane 14 . Recently, a draft genome from sugarcane covering around 40% of the monoploid genome and more than 25,000 genes was published using a combination of BACs (Bacterial Artificial chromosomes), Illumina and PacBio sequencing 15 .…”

Section: Introductionmentioning

confidence: 99%

Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler

et al. 2019

View full text Add to dashboard Cite

The Polyploid Gene Assembler (PGA), developed and tested in this study, represents a new strategy to perform gene-space assembly from complex genomes using low coverage DNA sequencing. The pipeline integrates reference-assisted loci and de novo assembly strategies to construct high-quality sequences focused on gene content. Pipeline validation was conducted with wheat ( Triticum aestivum ), a hexaploid species, using barley ( Hordeum vulgare ) as reference, that resulted in the identification of more than 90% of genes and several new genes. Moreover, PGA was used to assemble gene content in Saccharum spontaneum species, a parental lineage for hybrid sugarcane cultivars. Saccharum spontaneum gene sequence obtained was used to reference-guided transcriptome analysis of six different tissues. A total of 39,234 genes were identified, 60.4% clustered into known grass gene families. Thirty-seven gene families were expanded when compared with other grasses, three of them highlighted by the number of gene copies potentially involved in initial development and stress response. In addition, 3,108 promoters (many showing tissue specificity) were identified in this work. In summary, PGA can reconstruct high-quality gene sequences from polyploid genomes, as shown for wheat and S. spontaneum species, and it is more efficient than conventional genome assemblers using low coverage DNA sequencing.

show abstract

Initial genome sequencing of the sugarcane CP 96-1252 complex hybrid

Cited by 8 publications

References 12 publications

Bioinformatic Analyses to Uncover Genes Involved in Trehalose Metabolism in the Polyploid Sugarcane

Bioinformatic Analyses to Uncover Genes Involved in Trehalose Metabolism in the Polyploid Sugarcane

Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential

Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler

Contact Info

Product

Resources

About