Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.
Sugarcane is a major crop used for food and bioenergy production. Modern cultivars are hybrids derived from crosses between Saccharum officinarum and Saccharum spontaneum. Hybrid cultivars combine favorable characteristics from ancestral species and contain a genome that is highly polyploid and aneuploid, containing 100-130 chromosomes. These complex genomes represent a huge challenge for molecular studies and for the development of biotechnological tools that can facilitate sugarcane improvement. Here, we describe full-length enriched cDNA libraries for Saccharum officinarum, Saccharum spontaneum, and one hybrid genotype (SP803280) and analyze the set of open reading frames (ORFs) in their genomes (i.e., their ORFeomes). We found 38,195 (19%) sugarcane-specific transcripts that did not match transcripts from other databases. Less than 1.6% of all transcripts were ancestor-specific (i.e., not expressed in SP803280). We also found 78,008 putative new sugarcane transcripts that were absent in the largest sugarcane expressed sequence tag database (SUCEST). Functional annotation showed a high frequency of protein kinases and stress-related proteins. We also detected natural antisense transcript expression, which mapped to 94% of all plant KEGG pathways; however, each genotype showed different pathways enriched in antisense transcripts. Our data appeared to cover 53.2% (17,563 genes) and 46.8% (937 transcription factors) of all sugarcane full-length genes and transcription factors, respectively. This work represents a significant advancement in defining the sugarcane ORFeome and will be useful for protein characterization, single nucleotide polymorphism and splicing variant identification, evolutionary and comparative studies, and sugarcane genome assembly and annotation.
The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Herein, we review knowledge useful for their improvement and synergies gained by their parallel study.
Many plant species of great economic value (e.g., potato, wheat, cotton, and sugarcane) are polyploids. Despite the essential roles of autopolyploid plants in human activities, our genetic understanding of these species is still poor. Recent progress in instrumentation and biochemical manipulation has led to the accumulation of an incredible amount of genomic data. In this study, we demonstrate for the first time a successful genetic analysis in a highly polyploid genome (sugarcane) by the quantitative analysis of single-nucleotide polymorphism (SNP) allelic dosage and the application of a new data analysis framework. This study provides a better understanding of autopolyploid genomic structure and is a sound basis for genetic studies. The proposed methods can be employed to analyse the genome of any autopolyploid and will permit the future development of high-quality genetic maps to assist in the assembly of reference genome sequences for polyploid species.
Commercial sugarcane (Saccharum hybrid) is a highly polyploid and aneuploid grass that stores large amounts of sucrose in its stem. We have measured circadian rhythms of sense and antisense transcription in a commercial cultivar (RB855453) using a custom oligoarray with 14,521 probes that hybridize to sense transcripts (SS) and 7,380 probes that hybridize to antisense transcripts (AS).We estimated that 32% of SS probes and 22% AS probes were rhythmic. This is a higher proportion of rhythmic probes than the usually found in similar experiments in other plant species. Orthologs and inparalogs of Arabidopsis thaliana, sugarcane, rice, maize and sorghum were grouped in ortholog clusters. When ortholog clusters were used to compare probes among different datasets, sugarcane also showed a higher proportion of rhythmic elements than the other species. Thus, it is possible that a higher proportion of transcripts are regulated by the sugarcane circadian clock. Thirty-six percent of the identified AS/SS pairs had significant correlated time courses and 64% had uncorrelated expression patterns. The clustering of transcripts with similar function, the anticipation of daily environmental changes and the temporal compartmentation of metabolic processes were some properties identified in the circadian sugarcane transcriptome. During the day, there was a dominance of transcripts associated with photosynthesis and carbohydrate metabolism, including sucrose and starch synthesis. During the night, there was dominance of transcripts associated with genetic processing, such as histone regulation and RNA polymerase, ribosome and protein synthesis. Finally, the circadian clock also regulated hormone signalling pathways: a large proportion of auxin and ABA signalling components were regulated by the circadian clock in an unusual biphasic distribution.
In recent years, efforts to improve sugarcane have focused on the development of biotechnology for this crop. It has become clear that sugarcane lacks tools for the biotechnological route of improvement and that the initial efforts in sequencing ESTs had limited impact for breeding. Until recently, the models used by breeders in statistical genetics approaches have been developed for diploid organisms, which are not ideal for a polyploid genome such as that of sugarcane. Breeding programs are dealing with decreasing yield gains. The contribution of multiple alleles to complex traits such as yield is a basic question underlining the breeding efforts that could only be addressed by the development of specific tools for this grass. However, functional genomics has progressed and gene expression profiling is leading to the definition of gene networks. The sequencing of the sugarcane genome, which is underway, will greatly contribute to numerous aspects of research on grasses. We expect that both the transgenic and the marker-assisted route for sugarcane improvement will contribute to increased sugar, stress tolerance, and higher yield and that the industry for years to come will be able to rely on sugarcane as the most productive energy crop.
The protein kinase YakA is responsible for the growth arrest and induction of developmental processes that occur upon starvation of Dictyostelium cells. yakA- cells are aggregation deficient, have a faster cell cycle and are hypersensitive to oxidative and nitrosoative stress. With the aim of isolating members of the YakA pathway, suppressors of the death induced by nitrosoative stress in the yakA- cells were identified. One of the suppressor mutations occurred in keaA, a gene identical to DG1106 and similar to Keap1 from mice and the Kelch protein from Drosophila, among others that contain Kelch domains.
An increasing number of plant scientists, including breeders, agronomists, physiologists and molecular biologists, are working towards the development of new and improved energy crops. Research is increasingly focused on how to design crops specifically for bioenergy production and increased biomass generation for biofuel purposes. The most important biofuel to date is bioethanol produced from sugars (sucrose and starch). Second generation bioethanol is also being targeted for studies to allow the use of the cell wall (lignocellulose) as a source of carbon. If a crop is to be used for bioenergy production, the crop should be high yielding, fast growing, low lignin content and requiring relatively small energy inputs for its growth and harvest. Obtaining high yields in nonprime agricultural land is a key for energy crop development to allow sustainability and avoid competition with food production. Sugarcane is the most efficient bioenergy crop of tropical and subtropical regions, and biotechnological tools for the improvement of this crop are advancing rapidly. We focus this review on the studies of sugarcane genes associated with sucrose content, biomass and cell wall metabolism and the preliminary physiological characterization of cultivars that contrast for sugar and biomass yield.
Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges. Sugarcane cultivars differ in their capacity to accumulate sucrose and breeding programs routinely perform crosses to identify genotypes able to produce more sucrose. Sucrose content in the mature internodes reach around 20% of the culms dry weight. Genotypes in the populations reflect their genetic program and may display contrasting growth, development, and physiology, all of which affect carbohydrate metabolism. Few studies have profiled gene expression related to sugarcanes sugar content. The identification of signal transduction components and transcription factors that might regulate sugar accumulation is highly desirable if we are to improve this characteristic of sugarcane plants.
Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.
Sugarcane (Saccharum spp.) is the most promising crop for renewable energy. Among the diverse stresses that affect plant productivity, drought stress frequently causes losses in sugarcane fields. Although several studies have addressed plant responses to drought using controlled environments, plant responses under field conditions are largely unknown. Recently, microRNA (miRNA)-mediated post-transcriptional regulation has been described as an important and decisive component in vegetal development and stress resistance modulation. The role of miRNAs in sugarcane responses to drought under field conditions is currently not known. Two sugarcane cultivars differing in drought tolerance were grown in the field with and without irrigation (rainfed) for 7 months. By using small RNA deep sequencing, we were able to identify 18 miRNA families comprising 30 mature miRNA sequences. Among these families, we found 13 mature miRNAs that were differentially expressed in drought-stressed plants. Seven miRNAs were differentially expressed in both cultivars. The target genes for many of the differentially expressed mature miRNAs were predicted, and some of them were validated by quantitative reverse transcription PCR. Among the targets, we found transcription factors, transporters, proteins associated with senescence, and proteins involved with flower development. All of these data increase our understanding of the role of miRNAs in the complex regulation of drought stress in field-grown sugarcane, providing valuable tools to develop new sugarcane cultivars tolerant to drought stress.
Drought is a major abiotic stress that affects crop productivity worldwide. Sugarcane can withstand periods of water scarcity during the final stage of culm maturation, during which sucrose accumulation occurs. Meanwhile, prolonged periods of drought can cause severe plant losses.
Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90%. From the probes presented on the array, 75% of the sense probes and 11.9% of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.
Related JoVE Video
Journal of Visualized Experiments
What is Visualize?
JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.
How does it work?
We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.
Video X seems to be unrelated to Abstract Y...
In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.