The method involves classifying functional components along a genome's sequence and thus providing meaning is known as genome annotation. It's required because DNA sequencing generates sequences with unknown functions.
Annotate Transposable Genes
The first step in the genome annotation process is to identify and mask repeats.
Low-complexity sequences (such as homopolymeric nucleotide runs) and transposable components are the two kinds of repeat sequences. Transposable Elements (TEs) play an important role in the structure of nearly all eukaryotic genomes (animals, plants, fungi).
Their abundance, which can reach up to 90% in some genomes like wheat, is usually linked to genome size and organization. Because of their capacity to move and build up within genomes, TEs are important players in genome composition, plasticity, genetic diversity, and evolution. They can influence gene expression, composition, and function when inserted near genes, and they can also influence gene expression, composition, and function through epigenetic mechanisms.
According to mechanistic and enzymatic criteria, TEs are divided into two classes that include subclasses, orders, and superfamilies. These two classes are distinguished by their transposition processes, which are based on copy-and-paste (Class I) or cut-and-paste (Class II) through RNA or DNA intermediates, respectively.
Nowadays, TE annotation is regarded as a critical task in genome works, and it should be completed before any other genome annotation activity, such as gene prediction. As a result, there has been increasing attention in improving new methods for detecting, annotating, and analyzing these TEs computationally, particularly when they are nested and degenerated. To identify and annotate TEs, a variety of software has been developed.
Annotate Genes with High-Quality Experimental Evidence
Structural Annotation
Most biologists consider a raw genomic sequence to be of little value. Genome annotation entails attaching biologically necessary details to genome sequences by evaluating their structure and composition, as well as considering what we know from closely related species that can be used as a basis While genome annotation entails identifying a slew of biologically critical components in a genome sequence, the majority of the focus is on the proper classification of protein-coding genes.
Gene prediction, the procedure of properly identifying the location and structure of protein-coding genes in a genome, is well established, with many effective algorithms grown over the years. Overall, three methods for predicting genes in a genome are used: intrinsic (or ab-initio), extrinsic, and combiners. The intrinsic method uses resemblance to other sequence kinds (e.g. transcripts and/or polypeptides) as information, whereas the extrinsic method uses likeness to other sequence forms (e.g. transcripts and/or polypeptides) as information. Each of these has its own set of benefits and drawbacks.
Functional Annotation
The functional annotation application's sole objective is to contribute biologically necessary details to anticipated polypeptides and the attributes that they gain from. Due to the ability to sequence, assemble, and annotate full genomes in short periods of time, this system is particularly relevant today in the sense of the NGS era. There are two main outcomes of the functional annotation process. The task of functional elements to genes is the first step. Downstream assessment of these elements enables researchers to develop a better understanding of particular genome properties, such as metabolic pathways, as well as similarities between closely related species. The added quality check for the predicted gene set is the second outcome of the functional annotation. The existence of particular situations, suspicious orthology assignment, and/or the unavailability of other functional elements, such as functional completeness, can be used to recognize problematic and/or suspicious genes. Contaminated genes, those detected as TEs, non-functional and/or genes annotated by mistake are all examples of problematic genes.
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References
- Jung H, Ventura T, Chung JS, et al. Twelve quick steps for genome assembly and annotation in the classroom. PLoS Computational Biology. 2020, 16(11).
- Li SF, Wang J, Dong R, et al. Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus. Horticulture research. 2020, 7(1).
- Del Angel VD, Hjerde E, Sterck L, et al. Ten steps to get started in Genome Assembly and Annotation. F1000Research. 2018, 7.
