Īssembling RNASeq data to produce high-quality transcriptome assemblies as a shortcut to a ‘functional genome’ is still not a trivial task, despite these data sets being typically smaller and consisting uniquely of gene rich data. Current popular tools to structurally annotate a genome include the automated pipelines MAKER-P specifically developed for plants and the generalist BRAKER1. This process has been covered in detail, and readers are referred to. Although this can rely on extensive ‘extrinsic evidence’ in the form of RNA sequence (RNASeq), this is often complemented by sophisticated statistical models of gene structures to find exon/intron structures in what is termed ab initio discovery. This process detects genes including their exon/intron structures within a given assembly. In the case of genome assemblies, a process called structural annotation is necessary. Extensive processing and analysis is necessary before the resource will yield scientific insights. Generating an assembly for a species is merely the first step in the elucidation of the genome. This remarkable surge is a testament to the genomics revolution that has provided us with the tools to quickly sequence whole transcriptomes on a relatively modest budget, which typically can yield sufficient data for a working quality transcriptomic inventory (‘the transcriptome’). This is further complemented by countless plant transcriptomes found in Supplemental Materials. As of August 2016, the transcriptome shotgun assembly database of the National Center for Biotechnology Information (NCBI) lists over 450 plant assemblies ( ), whereas the plant 1KP project alone () includes >1300 plant transcriptomes. This number is greatly enhanced by including plant transcriptome assemblies. Since the genome sequence of the model plant Arabidopsis thaliana was published in 2000, around 180 plant genome sequences have been published (, ). Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Plant genome annotation, plant ontologies, plant gene family databases, genome annotation pipelines Introduction
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |