Plant and Animal Sequencing

De Novo Plant and Animal Sequencing

Whether a research project is focused on a novel species or one that has never been investigated before using genetic tools, de novo sequencing is a first step toward understanding the genetic underpinnings of a plant or animal’s functions and its interaction with the environment. Researchers can use a newly assembled genome to assign map positions and stack diverse breed information for subsequent resequencing to discover single nucleotide polymorphisms (SNPs) and other genetic variations.

Whole-Genome Resequencing

When a species’ reference genome is available, whole-genome animal and plant sequencing 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.

Plant and Animal Transcriptome Sequencing

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 discover new SNPs.

Animal and Plant Epigenetics

Adaptive responses to changes in the environment (such as food availability or drought conditions) 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

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 many samples, identifying common and rare variants such as SNPs and copy number variants (CNVs).

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

Genotyping by sequencing provides a low-cost genetic screening method to discover novel plant and animal SNPs and perform genotyping studies, often simultaneously in many specimens. By using animal and plant sequencing 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 genome studies.

Soil and Agricultural Metagenomics

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.

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Genome Editing

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) genome editing holds great potential for agriculture, food science, environmental science, and a broad range of other applications. NGS may be utilized at various stages of an editing workflow, from confirming gene knockouts to analyzing on- and off-target effects and assessing the the functional impact of gene edits.