MicroRNAs (miRNA) are small (21–24 nt) non-coding RNAs involved in many biological processes in both plants and animals. The biogenesis of plant miRNAs starts with the transcription of MIRNA (MIR) genes by RNA polymerase II; then, the
Cloning systems like Gateway and Golden Gate/Braid are known because of their efficiency and accuracy. While the main drawback of Gateway is the expensive cost of the enzymes used in its two-step (LR and BP) reaction, Golden Gate requires
Genetic transformation is a powerful method for the investigation of gene function and improvement of crop plants. The transgenes copy number in the transgenic line is involved in gene expression level and phenotypes. Additionally, identification of
High-throughput chromosome conformation capture (Hi-C) technology has become an economical and robust tool for generating a chromosome-scale assembly. However, high-quality chromosome scaffoldings are limited by the number of short and chimeric
Long sequencing reads have greatly improved assemblies of genomes with all sizes. The current Oxford Nanopore technology can regularly produce reads longer than 20 kb with less than 10% sequencing errors. To use long reads that contain relatively
Hi-C is a chromosome conformation capture method originally developed to detect genome-wide chromatin interactions. Nowadays, it is widely applied in scaffolding de novo assembled contigs into chromosome-scale genome sequences. Multiple open-source
In bulk RNA-seq analysis, normalization and batch effect removal are two procedures necessary to scale the read counts and reduce technical errors. Many differential expression analysis tools require a raw count matrix as input and embed the
Quality control and preprocessing of sequences are essential before analyzing high-throughput sequence data. After raw read data is generated from high-through sequencing platforms, quality control and preprocessing of sequencing reads should
Identifying differentially expressed (DE) genes across specific conditions is vital in understanding phenotypic variation. The fast-growing RNA sequencing (RNA-seq) provides much information that efficiently quantifies gene expression. Methods and
Assembly of high-quality genomes is critical for the characterization of structural variations (SV), for the development of a high-resolution map of polymorphisms, and to serve as the foundation for gene annotation. In recent years, the advent