Rui Xia

Abstract Various softwares or pipelines have been developed for biological information mining from high-throughput sequencing (HTS) data, and most of them relies on programming and command-line environment with which most biologists are unfamiliar. Bioinformatic tools with an user-friendly interface are preferred by wet-lab biologists. Here, we describe TBtools, a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface. It includes a large collection of functions, which facilitate many simple, routine but elaborate tasks working on HTS data, such as bulk sequence extraction, gene set functional enrichment, venn diagram and etc. TBtools can run under all operating systems with JRE1.6 and is freely available at github.com/CJ-Chen/TBtools. Since its development, it has been used by many researchers. It will be a useful toolkit for wet-lab biologists to work on all kinds of high-throughput data.

Plant genomes are the source of large numbers of small RNAs, generated via a variety of genetically separable pathways. Several of these pathways converge in the production of phased, secondary, small interfering RNAs (phasiRNAs), originally designated as trans-acting small interfering RNAs or tasiRNAs. PhasiRNA biogenesis requires the involvement of microRNAs as well as the cellular machinery for the production of siRNAs. PhasiRNAs in Arabidopsis thaliana have been well described for their ability to function in trans to suppress target transcript levels. Plant genomic data from an expanding set of species have demonstrated that Arabidopsis is relatively sparing in its use of phasiRNAs, while other genomes contain hundreds or even thousands of phasiRNA-generating loci. In the dicots, targets of those phasiRNAs include several large or conserved families of genes, such as those encoding disease resistance proteins or transcription factors. Suppression of nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes by small RNAs is particularly unusual because of a high level of redundancy. In this review, we discuss plant phasiRNAs and the possible mechanistic significance of phasiRNA-based regulation of the NB-LRRs.