Whether a research project is focused on a novel species or just one that has never been investigated before using genetic tools, de novo sequencing with next-generation sequencing (NGS) is a first step toward understanding the genetic underpinnings of a plant or animal’s functions and its interaction with the environment. With long-paired and mate-pair sequence data, some researchers use the assembled genome to assign map positions and stack diverse breed information for subsequent resequencing to discover SNPs and other genetic variations.
When a species’ reference genome is available, whole-genome resequencing is an efficient approach for discovering genes, SNPs, and structural variants, while simultaneously determining genotypes. Information from these studies will fill in the gaps that exist in the genetic maps of many plant and animal species, improving plant breeding and selection, and enabling definitive comparative genomic analyses within and across species.
RNA sequencing is revolutionizing the exploration of gene expression in plants and animals, providing novel insights into changing expression levels that occur in development, and during disease and stress conditions. It can be used to elucidate gene and protein function and interactions, identify tissue-specific list of RNA transcripts produced by an animal or plant genome (mRNAs, non-coding RNAs, and small RNAs), and for SNP discovery.
Adaptive responses to changes in the environment (food availability, drought conditions, etc.) can trigger phenotypic changes in plants and animals that affect their viability and reproductive fitness. By using sequencing to identify changes in DNA methylation, chromatin structure, and small RNA expression, researchers can better understand how epigenetic factors contribute to controlling these and other traits in a species of interest.
Targeted resequencing digs deeper into the exome or specific genomic regions of interest identified from large-scale association or linkage studies. This efficient and economical method sequences predetermined areas of genetic variation over a large number of samples, identifying common and rare variants (SNPs, CNVs, etc.). These variants may represent beneficial mutations that can help inform breeding decisions and may reveal causative mutations responsible for plant or animal disease, or parasite susceptibility.
Genotyping by sequencing, or next-generation genotyping (NGG), provides a low-cost genetic screening method to discover novel plant and animal SNPs and perform genotyping studies, often simultaneously in many specimens. With a low-cost tool for routine screening, researchers can accelerate the return on investment in breeding practice.
Applications of this method include genetic mapping, screening backcross lines, purity testing, constructing haplotype maps, and performing association and genomic evaluation for plant agrigenomic studies.
Sequencing has transformed environmental metagenomics, enabling the study of large microbial communities directly in their natural environment without prior culturing. These studies can yield important information about diverse microbial populations associated with animal and plant development, from rumen flora that enhance animal digestion to root-associated bacteria involved in nitrogen fixation.
NGS has been instrumental in advancing microbiology research. With NGS, you can measure changes anywhere in the genome without prior knowledge, which is critical for unculturable organisms. Single-base resolution allows tracking of microbial adaptation over short periods of time, both in the laboratory and in the environment.