Large Genome Size Research Articles

Establishment of a Simple and Efficient Reverse Genetics System for Canine Adenoviruses Using Bacterial Artificial Chromosomes.

Canine adenoviruses (CAdVs) are divided into pathotypes CAdV1 and CAdV2, which cause infectious hepatitis and laryngotracheitis in canid animals, respectively. They can be the backbones of viral vectors that could be applied in recombinant vaccines or for gene transfer in dogs and in serologically naïve humans. Although conventional plasmid-based reverse genetics systems can be used to construct CAdV vectors, their large genome size creates technical difficulties in gene cloning and manipulation. In this study, we established an improved reverse genetics system for CAdVs using bacterial artificial chromosomes (BACs), in which genetic modifications can be efficiently and simply made through BAC recombineering. To validate the utility of this system, we used it to generate CAdV2 with the early region 1 gene deleted. This mutant was robustly generated and attenuated in cell culture. The results suggest that our established BAC-based reverse genetics system for CAdVs would be a useful and powerful tool for basic and advanced practical studies with these viruses.

Progress and Prospects of Association Mapping in Sugarcane (Saccharum Species Hybrid), a Complex Polyploid Crop

Sugarcane is one of the most important economic crops and contributes more than 80% of the sugar globally. Developing superior sugarcane varieties is a long-term process due to polyploidy, high chromosome numbers, large complex genome size and also many other practical constraints like long breeding cycle, etc. The recent advancements in molecular markers, next-gen sequencing tools and development of robust statistical models have the potential to lead to affordable genomics-assisted breeding in sugarcane. In order to identify genes linked to trait(s) of interest, association mapping has good prospects as a feasible approach in sugarcane. Association mapping (AM) is a recent technique that identifies quantitative trait loci (QTLs) by investigating marker–trait associations that arise due to the linkage disequilibrium between the genotypic polymorphic loci and the phenotypic variation in a diverse panel of genotypes. In last decade, the understanding of association mapping has increased significantly, due to which focussed efforts are now been made in developing association mapping population, genome-wide association studies and detection of QTLs for several important traits in sugarcane. In contrast to linkage mapping, detecting QTLs through AM approach in sugarcane has certain advantages as historical phenotypic data could be used and there is no need to artificially develop a structured segregating population. The last few years have witnessed a more concerted effort in AM studies in sugarcane where a range of marker tools like SSRs, DArT, GBS, targeted sequence enrichment, etc. were exploited to find out QTLs linked to traits of economic importance. In this review, the recent developments in the area of association mapping in sugarcane and the various methodologies and statistical tools that are being adopted have been discussed.

Adaptation to Extreme Antarctic Environments Revealed by the Genome of a Sea Ice Green Alga

The unicellular green alga Chlamydomonas sp. ICE-L thrives in polar sea ice, where it tolerates extreme low temperatures, high salinity, and broad seasonal fluctuations in light conditions. Despite the high interest in biotechnological uses of this species, little is known about the adaptations that allow it to thrive in this harsh and complex environment. Here, we assembled a high-quality genome sequence of ∼542 Mb and found that retrotransposon proliferation contributed to the relatively large genome size of ICE-L when compared to other chlorophytes. Genomic features that may support the extremophilic lifestyle of this sea ice alga include massively expanded gene families involved in unsaturated fatty acid biosynthesis, DNA repair, photoprotection, ionic homeostasis, osmotic homeostasis, and reactive oxygen species detoxification. The acquisition of multiple ice binding proteins through putative horizontal gene transfer likely contributed to the origin of the psychrophilic lifestyle in ICE-L. Additional innovations include the significant upregulation under abiotic stress of several expanded ICE-L gene families, likely reflecting adaptive changes among diverse metabolic processes. Our analyses of the genome, transcriptome, and functional assays advance general understanding of the Antarctic green algae and offer potential explanations for how green plants adapt to extreme environments.

A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura:Limnodynastidae).

Amphibian genomes are usually challenging to assemble due to their large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and amphibian genome evolution.

Environmental pressures on stomatal size may drive plant genome size evolution: evidence from a natural experiment with Cape geophytes.

The idea that genome (size) evolution in eukaryotes could be driven by environmental factors is still vigorously debated. In extant plants, genome size correlates positively with stomatal size, leading to the idea that conditions enabling the existence of large stomata in fossil plants also supported growth of their genome size. We test this inductive assumption in drought-adapted, prostrate-leaved Cape (South Africa) geophytes where, compared with their upright-leaved geophytic ancestors, stomata develop in a favourably humid microclimate formed underneath their leaves. Stomatal parameters (leaf cuticle imprints) and genome size (flow cytometry) were measured in 16 closely related geophytic species pairs from seven plant families. In each pair, representing a different genus, we contrasted a prostrate-leaved species with its upright-leaved phylogenetic relative, the latter whose stomata are exposed to the ambient arid climate. Except for one, all prostrate-leaves species had larger stomata, and in 13 of 16 pairs they also had larger genomes than their upright-leaved relatives. Stomatal density and theoretical maximum conductance were less in prostrate-leaved species with small guard cells (<1 pL) but showed no systematic difference in species pairs with larger guard cells (>1 pL). Giant stomata were observed in the prostrate-leaved Satyrium bicorne (89-137 µm long), despite its relatively small genome (2C = 9 Gbp). Our results imply that climate, through selection on stomatal size, might be able to drive genome size evolution in plants. The data support the idea that plants from 'greenhouse' geological periods with large stomata might have generally had larger genome sizes when compared with extant plants, though this might not have been solely due to higher atmospheric CO2 in these periods but could also have been due to humid conditions prevailing at fossil deposit sites.

Investigation of Growth, Lipid Productivity, and Fatty Acid Profiles in Marine Bloom-Forming Dinoflagellates as Potential Feedstock for Biodiesel

Microalgae-based biodiesel is increasingly recognized as an alternative to crop-based biodiesel. In this study, 10 local strains of dinoflagellates collected from Hong Kong waters, including a monoculture and field sample of Scrippsiella sp. isolated from an algal bloom, were evaluated against the performance of green alga Tetraselmis suecica. The specific growth rate, biomass production, lipid productivity, and fatty acid profile were investigated. The total lipid content of isolated strains ranged from 16.2% to 32.2% of the total dry biomass, whereas palmitic acid (C16:0) and docosahexaenoic acid (DHA, C22:6n3) were dominant in the fatty acid profile. Scrippsiella sp. has a high lipid productivity (47.3 mg/L/day) and fatty acid methyl esters (FAME) content (55.2–73 mg/g dry weight (dw)), which were comparable to that in green alga T. suecica. Further, monoculture and field sampled blooming Scrippsiella sp. showed no significant difference in most parameters, suggesting the possibility of harvesting a natural algal bloom population as a mitigation strategy to harmful algal bloom and to use as biodiesel feedstock. Overall, dinoflagellate species showed a slower growth rate (0.04–0.57 day−1) than most compared species (0.07–1.34 day−1), likely due to a large genome size and low chlorophyll to carbon ratio. Notably, most investigated dinoflagellates were not ideal for mass biodiesel production due to the low growth rate and lipid productivity. However, a high level of polyunsaturated fatty acids (PUFA) in dinoflagellates are prospective for further studies in other biotechnological applications. Though effectively harvesting algal blooming biomass can be complex, it can be further explored as a strategy for algal bloom mitigation and potentially creating values at the advantage of natural bloom when applying harvested biomass for biodiesel and bioactive compounds extraction.

Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions

BackgroundDinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking.ResultsHere, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates.ConclusionsOur results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution.

CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table.

Calculating the frequency of occurrence of each substring of length k in DNA sequences is a common task in many bioinformatics applications, including genome assembly, error correction, and sequence alignment. Although the problem is simple, efficient counting of datasets with high sequencing depth or large genome size is a challenge. We propose a robust and efficient method, CHTKC, to solve the k-mer counting problem with a lock-free hash table that uses linked lists to resolve collisions. We also design new mechanisms to optimize memory usage and handle situations where memory is not enough to accommodate all k-mers. CHTKC has been thoroughly tested on seven datasets under multiple memory usage scenarios and compared with Jellyfish2 and KMC3. Our work shows that using a hash-table-based method to effectively solve the k-mer counting problem remains a feasible solution.

The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes.

A number of species in Bipolaris are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of Bipolaris based solely on morphology. In this study, we sequenced the complete mitochondrial genome of Bipolaris sorokiniana, and presented the detailed annotation of the genome. The B. sorokiniana mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core protein-coding genes, 38 tRNA genes. In addition, two ribosomal protein genes (rps3 gene and rps5 gene) and the fungal mitochondrial RNase P gene (rnpB) are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core protein-coding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of Capnodiales, Botryosphaeriales and Pleosporales are consistently supported in all analyses. The Venturiaceae forms an independent lineage, with a distant phylogenetic relationship to Pleosporales. At the family level, the Mycosphaerellaceae, Botryosphaeriaceae. Phaeosphaeriaceae, and Pleosporaceae are recognized in the majority of trees.

The molecular biology of intracellular events during Coronavirus infection cycle.

CoV-2 which is the causative agent of COVID-19 belongs to genus betacoronaviruses. The sequence analysis of S protein of CoV-2 has shown that it has acquired a ‘polybasic cleavage site’ consisting of 12 aminoacids that has been predicted to enable its cleavage by other cellular proteases possibly increasing its transmissibility. The aminoacids present in receptor binding domain of S protein of SARS CoV which are critical for its binding to cellular receptor are different in CoV-2. The presence of heptanucleotide slippery sequence in ORF1 resulting in ribosomal frameshifting, and presence of transcription regulatory sequences between ORFs resulting in discontinuous transcription, are peculiar features of Coronavirus infection cycle. The exonuclease activity of nsp14 provides possible proofreading ability to RNA polymerase makes coronaviruses different from other RNA viruses allowing coronaviruses to maintain their relatively large genome size. This mini-review summarizes the peculiar features of Coronaviruses genome and the critical events during the infection cycle with focus on CoV-2.

The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution

The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution

Doubled haploid production in onion (Allium cepa L.): from gynogenesis to chromosome doubling

Bulb onion (Allium cepa L.) is an allogamous diploid (2n = 16) important for its culinary uses, nutritional value, and medicinal benefits. Despite its economic importance, onion yields and bulb quality are declining, emphasizing the need for new and improved strategies for maintaining and enhancing overall crop quality. Development of inbred lines in onion through traditional breeding is often difficult due to its biennial life cycle, inbreeding depression, and comparatively high heterozygosities. Moreover, genetic research in onion has been hampered by large nuclear genome size. In this regard, gynogenic doubled haploids promise several advantages over inbred lines in support of onion breeding programs and genetic studies. These include complete homozygosity in doubled haploid lines, reduced DNA methylation, elimination of deleterious alleles, and amenability to genetic analysis. This review focuses on the application of in vitro gynogenesis for producing doubled haploids in onion. Factors influencing haploid induction, methods for inducing chromosome doubling and ploidy assessment, evaluation of haploid progenies and doubled haploid lines, and features of doubled haploids potentially useful in crop improvement and genetic studies, are discussed. We identify four major limitations to the success and efficiency of in vitro gynogenesis in onion and discuss strategies for mitigating the negative impacts they pose. This review may be useful to research programs producing doubled haploids in onion or other Allium species using in vitro gynogenesis. In onion, doubled haploids (DHs) were generated by gynogenesis using in vitro culturing of unfertilized ovules, ovaries or whole flowers. Genotype, geographical origin, photoperiodicity and genetic structure all affect gynogenic efficiency in onion. Despite higher doubling efficiencies, there are several disadvantages with induced chromosome doubling inlcuding low survival rates of explants, cytotoxicity, vitrification and polyploidization.

The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians

Amphibians evolved in the Devonian period about 400 Mya and represent a transition step in tetrapod evolution. Among amphibians, high-throughput sequencing data are very limited for Caudata, due to their largest genome sizes among terrestrial vertebrates. In this paper we present the transcriptome from the fire bellied newt Cynops orientalis. Data here presented display a high level of completeness, comparable to the fully sequenced genomes available from other amphibians. Moreover, this work focused on genes involved in gametogenesis and sexual development. Surprisingly, the gsdf gene was identified for the first time in a tetrapod species, so far known only from bony fish and basal sarcopterygians. Our analysis failed to isolate fgf24 and foxl3, supporting the possible loss of both genes in the common ancestor of Rhipidistians. In Cynops, the expression analysis of genes described to be sex-related in vertebrates singled out an expected functional role for some genes, while others displayed an unforeseen behavior, confirming the high variability of the sex-related pathway in vertebrates.

Helping decision making for reliable and cost-effective 2b-RAD sequencing and genotyping analyses in non-model species.

High-throughput sequencing has revolutionized population and conservation genetics. RAD sequencing methods, such as 2b-RAD, can be used on species lacking a reference genome. However, transferring protocols across taxa can potentially lead to poor results. We tested two different IIB enzymes (AlfI and CspCI) on two species with different genome sizes (the loggerhead turtle Caretta caretta and the sharpsnout seabream Diplodus puntazzo) to build a set of guidelines to improve 2b-RAD protocols on non-model organisms while optimising costs. Good results were obtained even with degraded samples, showing the value of 2b-RAD in studies with poor DNA quality. However, library quality was found to be a critical parameter on the number of reads and loci obtained for genotyping. Resampling analyses with different number of reads per individual showed a trade-off between number of loci and number of reads per sample. The resulting accumulation curves can be used as a tool to calculate the number of sequences per individual needed to reach a mean depth ≥20 reads to acquire good genotyping results. Finally, we demonstrated that selective-base ligation does not affect genomic differentiation between individuals, indicating that this technique can be used in species with large genome sizes to adjust the number of loci to the study scope, to reduce sequencing costs and to maintain suitable sequencing depth for a reliable genotyping without compromising the results. Here, we provide a set of guidelines to improve 2b-RAD protocols on non-model organisms with different genome sizes, helping decision-making for a reliable and cost-effective genotyping.

Insights into the Identification of the Specific Spoilage Organisms in Chicken Meat.

Poultry meat deterioration is caused by environmental conditions, as well as proliferation of different bacterial groups, and their interactions. It has been proposed that meat spoilage involves two bacterial groups: one group that initiates the deterioration process, known as specific spoilage organisms (SSOs), and the other known as spoilage associated organisms (SAOs) which represents all bacteria groups recovered from meat samples before, during, and after the spoilage process. Numerous studies have characterized the diversity of chicken meat SAOs; nonetheless, the identification of the SSOs remains a long-standing question. Based on recent genomic studies, it is suggested that the SSOs should possess an extensive genome size to survive and proliferate in raw meat, a cold, complex, and hostile environment. To evaluate this hypothesis, we performed comparative genomic analyses in members of the meat microbiota to identify microorganisms with extensive genome size and ability to cause chicken meat spoilage. Our studies show that members of the Pseudomonadaceae family have evolved numerous biological features such as large genomic size, slow-growing potential, low 16S rRNA copy number, psychrotrophic, and oligotrophic metabolism to initiate the spoilage of poultry meat. Moreover, inoculation experiments corroborated that these biological traits are associated with the potential to cause chicken meat deterioration. Together, these results provide new insights into the identification of SSO. Further studies are in progress to elucidate the impact of the SSO on meat quality and microbiota diversity.

Effect of Phenotype Selection on Genome Size Variation in Two Species of Diptera.

Genome size varies widely across organisms yet has not been found to be related to organismal complexity in eukaryotes. While there is no evidence for a relationship with complexity, there is evidence to suggest that other phenotypic characteristics, such as nucleus size and cell-cycle time, are associated with genome size, body size, and development rate. However, what is unknown is how the selection for divergent phenotypic traits may indirectly affect genome size. Drosophila melanogaster were selected for small and large body size for up to 220 generations, while Cochliomyia macellaria were selected for 32 generations for fast and slow development. Size in D. melanogaster significantly changed in terms of both cell-count and genome size in isolines, but only the cell-count changed in lines which were maintained at larger effective population sizes. Larger genome sizes only occurred in a subset of D. melanogaster isolines originated from flies selected for their large body size. Selection for development time did not change average genome size yet decreased the within-population variation in genome size with increasing generations of selection. This decrease in variation and convergence on a similar mean genome size was not in correspondence with phenotypic variation and suggests stabilizing selection on genome size in laboratory conditions.

Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

Somatic and Meiotic Instabilities Cause Hypo-aneuploidy in Synthesized Wheat–Aegilops triuncialis Amphiploids

In newly formed allopolyploids, meiotic instability in early generations contributes to reduced fertility, but less is known about their mitotic accuracy and somatic instability. Here, the authors report somatic numerical chromosome variation (somatic aneuploidy) among different individuals of newly synthesized wheat–Aegilops triuncialis amphiploids (AABBDDUtUtCtCt genome) over three successive generations. In total, 21 seeds in the F2 to F4 generations descended from three different F1 hybrids (2n = 5x = 35, ABDUtCt genome) were analyzed by chromosome counting and fluorescent in situ hybridization. Somatic aneuploidy was detected in 17 (81%) investigated individuals. Somatic chromosome numbers of the cells (among and within the evaluated individuals) ranged from 62 to 70. Furthermore, flow cytometry revealed variation in genome size within and between individual amphiploids that may be due to variable chromosome numbers. There was no evidence that somatic aneuploidy leads to stable cytotypes, at least in the early generations. The authors conclude that both newly formed status and large genome sizes may contribute to somatic and meiotic instability in synthetic wheat–Aegilops triuncialis amphiploids.

The genome sequence of celery (Apium graveolens L.), an important leaf vegetable crop rich in apigenin in the Apiaceae family

Celery (Apium graveolens L.) is a vegetable crop in the Apiaceae family that is widely cultivated and consumed because it contains necessary nutrients and multiple biologically active ingredients, such as apigenin and terpenoids. Here, we report the genome sequence of celery based on the use of HiSeq 2000 sequencing technology to obtain 600.8 Gb of data, achieving ~189-fold genome coverage, from 68 sequencing libraries with different insert sizes ranging from 180 bp to 10 kb in length. The assembled genome has a total sequence length of 2.21 Gb and consists of 34,277 predicted genes. Repetitive DNA sequences represent 68.88% of the genome sequences, and LTR retrotransposons are the main components of the repetitive sequences. Evolutionary analysis showed that a recent whole-genome duplication event may have occurred in celery, which could have contributed to its large genome size. The genome sequence of celery allowed us to identify agronomically important genes involved in disease resistance, flavonoid biosynthesis, terpenoid metabolism, and other important cellular processes. The comparative analysis of apigenin biosynthesis genes among species might explain the high apigenin content of celery. The whole-genome sequences of celery have been deposited at CeleryDB (http://apiaceae.njau.edu.cn/celerydb). The availability of the celery genome data advances our knowledge of the genetic evolution of celery and will contribute to further biological research and breeding in celery as well as other Apiaceae plants.

Prospects of ‘Omic’ Approaches towards Accelerating Sugarcane Improvement: Recent Advancements and Challenges

Sugarcane is an economically important crop and is cultivated throughout the world for its sugar and ethanol. Present sugarcane varieties are derived from inter-specific hybridization between Saccharum officinarum and Saccharum spontaneum, resulting in highly polyploid and aneuploid plants with chromosomes ranging from 80 to 120. This complex nature has hindered advances in marker assisted breeding of this crop. Though an array of methodologies have been adopted by different research groups from all over the world who have well established protocols for developing genetically modified (GM) sugarcane. Several genes of economic interest have been transformed in sugarcane, despite variable success in transgene integration and expression. Recently, genome editing approaches (the zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and CRISPR/Cas9 system) have opened new and unique opportunities for researchers to enhance crop production. However, as far as sugarcane is considered, there are still several challenges/constraints (large genome size, polyploidy, low transformation efficiency, transgene silencing and lack of high throughput screening techniques) ahead that deter sugarcane improvement through genetic engineering and need to be resolved to achieve a complete exploitation of the crop through these biotechnological tools. This review is an attempt to unravel the various sugarcane genomic approaches and their applications towards accelerating sugarcane improvement.