Sugarcane crop constitutes one of the most vital sources of sugar and bioenergy globally; however, higher level of polyploidy makes its genome editing an intricate task. Recently, genome editing has become easier with CRISPR/Cas9 system that uses Cas9 to target sequence-specific regions and introduce double-strand breaks into the target region. This technique has been successfully employed to develop new varieties of sugarcane having desired phenotypic and physiological traits. Several genes can be fused with the CRISPR/Cas9 system leading to successful metabolic engineering and biological improvement for ensuring sustainable enhancement in sugarcane production. This simple RNA-guided genome editing technique has become a revolutionary tool and innovative application in biology that might be effectively employed for inducing specified genomic modifications in plant tissues. This review attempts to synthesize fundamentals of genome editing techniques with an ultimate aim to find out opportunities and challenges of sugarcane genome editing. It also tends to summarize the advances and achievements of gene editing via CRISPR-based genome editing technique for numerous field crops. Lastly, the enormous potential of CRISPR/Cas9 for gene editing in sugarcane, major challenges and future perspectives have been objectively elaborated.

Here, a new superfamily of IS630-Tc1-mariner (ITm) DNA transposons, termed Sailor, is identified, that is characterized by a DD82E catalytic domain and is distinct from all previously known superfamilies of the ITm group. Phylogenetic analyses revealed that Sailor forms a monophyletic clade with a more intimate link to the clades of Tc1/mariner and DD34E/Gambol. Sailor was detected in both prokaryotes and eukaryotes and invaded a total of 256 species across six kingdoms. Sailor is present in nine species of bacteria, two species of plantae, four species of protozoa, 23 species of Chromista, 12 species of Fungi and 206 species of animals. Moreover, Sailor is extensively distributed in invertebrates (a total of 206 species from six phyla) but is absent in vertebrates. Sailor transposons are 1.38–6.98 kb in total length and encoded transposases of ~676 aa flanked by TIRs with lengths between 18, 1362 and 4 bp (TATA) target-site duplications. Furthermore, our analysis provided strong evidence of Sailor transmissions from prokaryotes to eukaryotes and internal transmissions in both. These data update the classification of the ITm group and will contribute to the understanding of the evolution of ITm transposons and that of their hosts.

Bees (Apoidea), the largest and most crucial radiation of pollinators, play a vital role in the ecosystem balance. Transposons are widely distributed in nature and are important drivers of species diversity. However, transposons are rarely reported in important pollinators such as bees. Here, we surveyed 37 bee genomesin Apoidea, annotated the pogo and Tc1/mariner transposons in the genome of each species, and performed a phylogenetic analysis and determined their overall distribution. The pogo and Tc1/mariner families showed high diversity and low abundance in the 37 species, and their proportion was significantly higher in solitary bees than in social bees. DD34D/mariner was found to be distributed in almost all species and was found in Apis mellifera, Apis mellifera carnica, Apis mellifera caucasia, and Apis mellifera mellifera, and Euglossa dilemma may still be active. Using horizontal transfer analysis, we found that DD29-30D/Tigger may have experienced horizontal transfer (HT) events. The current study displayed the evolution profiles (including diversity, activity, and abundance) of the pogo and Tc1/mariner transposons across 37 species of Apoidea. Our data revealed their contributions to the genomic variations across these species and facilitated in understanding of the genome evolution of this lineage.

Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis, and an array/repeat analysis. In our analysis, we identified and mined a total of 93 Cas14-homology proteins that ranged in size from 344 aa to 843 aa. The majority of the Cas14-homology proteins discovered in this analysis were found within the Firmicutes group, which contained 37 species, representing 42% of all the Cas14-homology proteins identified. In archaea, the DPANN group had the highest number of species containing Cas14-homology proteins, a total of three species. The phylogenetic analysis results demonstrate the division of Cas14-homology proteins into three clades: Cas14-A, Cas14-B, and Cas14-U. Extensive similarity was observed at the C-terminal end (CTD) through a domain comparison of the three clades, suggesting a potentially shared mechanism of action due to the presence of cutting domains in that region. Additionally, a sequence similarity analysis of all the identified Cas14 sequences indicated a low level of similarity (18%) between the protein variants. The analysis of repeats/arrays in the extended nucleotide sequences of the identified Cas14-homology proteins highlighted that 44 out of the total mined proteins possessed CRISPR-associated repeats, with 20 of them being specific to Cas14. Our study contributes to the increased understanding of Cas14 proteins across prokaryotic genomes. These homologous proteins have the potential for future applications in the mining and engineering of Cas14 proteins.

Corn stover is one of the most agricultural residue abundances over the world; however, it is extremely prevented from microbial and enzymatic degradation into monomers because of the complex chemical and physical structure. In order to degrade corn stover, a large variety of enzymes with different specificities are required. However, each enzyme has its own reaction condition such as optimal pH and temperature to express its maximum activity. We hypothesize that the best sequence of an enzyme reaction could influence the degradation of corn stover. Therefore, the objective of this study was to investigate the effect of enzyme sequence action on the degradation of corn stover. A complete randomized design was used for this study. Four enzymes were used, cellulase (Cel) (pH 4.8 at 50 °C), hemicellulase (Hem) (pH 5 at 50 °C), pectinase (Pec) (pH 4 at 50 °C) and laccase (Lac) (pH 3 at 30 °C). This was subsequently submitted to enzyme sequence digestion following four steps (6 h incubation for each step) during which a single enzyme in each step was evaluated. The substrate (raw corn stover) was placed in sodium acetate buffer with an enzyme. The supernatant was then collected in each step for further chemical analysis. The results showed that there was a significant difference at p < 0.05 between treatments, suggesting that sequential action of fiber-degrading enzymes affected the chemical composition of corn stover. The best enzyme sequence (in terms of the total reducing sugar in different steps) was Hem-Cel-Pec-Lac (2.2 mg/mL) at p < 0.05; however, the worst enzyme sequence was Lac-Pec-Hem-Cel (0.8 mg/mL) at p < 0.05. Almost all the first steps in the process showed an increasing level of reducing sugar except the step which started with Lac where a lower reducing sugar level was observed. Similarly, xylose showed a higher level in all the processes in the first steps regardless of the enzyme type. It was observed that glucose production was totally dependent on the position of Cel in the enzyme sequence. Therefore, enzyme sequence action may be a useful method for corn stover to improve its degradation as feed stock.