Theory and application of genome assembly in red deer genome project

Abstract

The entire inheritance of living organisms is contained in its genomic DNA, the sequence of which can be determined by various DNA sequencing methods. Researchers have long used clone-based methods for this purpose, but today the first, second (next-generation sequencing, NGS) and third-generation sequencing procedures are preferred. With the most widespread next-generation sequencing methods, a mammal's entire DNA can be read within hours. The single read sequences (reads) are only a few hundred basepairs, but summing up their lengths, they could cover the whole genome several times. The reads are assembled to longer sequences by using bioinformatics programs. The goal is to regain the sequence of the original DNA. First, contiguous sequences can be created from matching and overlapping reads, they are called contigs and contigs become settled for scaffolds. The sequences in the scaffolds are incomplete, there remain gaps, which are undetermined segments in the sequence. The most important farm animals have at least scaffold-level online genome assemblies. The most complete genome assemblies are ordered according to the pseudochromosomes. In the construction of pseudochromosomes, scaffolds are mapped to the genetic map of the organism in question, which was determined by genetic markers of known DNA sequences. In double-reference-guided assembling, de novo scaffolds are mapped/probed to the known genome of a closely related species and to the genetic map of the living entity targeted. The scaffolds are assorted and ordered following the colinearities and syntenies. This method is useful for completely new genomes. The annotation process describes the locations, structures, functions of the genes and other genomic structures along the reference genome resulted. The annotated reference genomes can be used in many ways, e.g. in animal breeding and husbandry, in the game management, in population genetics studies or in forensic cases/wildlife programs.