A genome is the complete set of genetic material belonging to an organism or virus. In cellular organisms, it consists of DNA, including all genes and the sequences between and within them. Viral genomes may instead consist of RNA. A genome therefore includes much more than instructions for making proteins: it also contains regulatory sequences, structural regions, and sequences whose functions remain unknown. Its study forms the basis of genomics, which examines genetic material at the scale of whole genomes rather than individual genes alone. (genome.gov)
Composition and organization
DNA stores information in the order of its nucleotides, conventionally represented by A, T, C, and G. In double-stranded DNA, A pairs with T and C with G, so genome lengths are commonly expressed in base pairs. These sequences are organized into chromosomes, whose number, shape, and size differ among organisms. Genome organization includes both the physical arrangement of DNA and the distribution of genes and other sequence elements along it. (genome.gov)
In a eukaryotic organism, most DNA lies in the cell nucleus, generally in multiple linear chromosomes. Nuclear DNA associates with proteins to form chromatin. Additional genomes occur in mitochondria and, in plants and algae, chloroplasts. Consequently, “genome” may mean all an organism’s genetic material or, when explicitly qualified, its nuclear, mitochondrial, or chloroplast genome. These distinct genetic compartments differ substantially in size and gene content. (ncbi.nlm.nih.gov)
Many bacteria have a principal circular chromosome, although some have linear chromosomes or several chromosomes. Their genetic complement can also include plasmids, independently replicating DNA molecules that may carry additional traits. Viral genomes exhibit still broader variation: they can contain DNA or RNA, and their nucleic acid may be single-stranded or double-stranded. Thus, neither a particular chromosome structure nor DNA itself is a universal requirement for something to be called a genome. (ncbi.nlm.nih.gov)
Genes and noncoding sequences
Some genes encode a protein, whereas others produce functional RNA molecules. Protein production involves transcription of DNA into RNA followed by translation of the RNA message. A genome sequence identifies the underlying genetic information, but understanding its use also requires examining when, where, and how strongly genes are expressed. Different cellular activities can arise from different patterns of gene expression without requiring different genome sequences. (genome.gov)
Noncoding DNA comprises sequences that do not encode the amino-acid sequence of proteins. It includes regulatory elements, genes for functional RNAs, intervening sequences within genes, and repetitive regions. Some noncoding sequences have established biological functions, while others have no known function. Transposable elements and their remnants constitute a substantial component of many eukaryotic genomes. “Noncoding” therefore does not mean “nonfunctional,” but it also does not establish that every such sequence has a function. (genome.gov)
Genome size and inheritance
Genome size usually describes the amount of DNA in one haploid chromosome complement, rather than the total DNA present in a cell. One human nuclear complement contains approximately three billion base pairs distributed among 23 chromosomes. Most human nucleated cells are diploid, containing two chromosome sets, one inherited from each parent. The human genome contains roughly 20,000 protein-coding genes, and protein-coding sequence accounts for only a small percentage of its total length. (genome.gov)
Genome size varies greatly among species and is not a straightforward measure of organismal complexity. Differences in repetitive DNA, gene duplication, and other noncoding regions contribute to this variation. Individuals within a species also differ genetically: variation includes nucleotide substitutions, insertions, deletions, and larger structural changes. A mutation introduces a sequence change; mutations arising after fertilization can produce mosaicism, in which different cells within one individual carry different genetic variants. Consequently, an organism’s genome need not be identical in every cell. (ncbi.nlm.nih.gov)
Sequencing and reference genomes
DNA sequencing determines the order of bases. Whole-genome sequencing typically produces many sequence fragments, or reads, which computational methods assemble or compare with an existing sequence. Repetitive DNA presents particular difficulties because similar reads may originate from several genomic locations. A sequence assembly must therefore be distinguished from a completely resolved genome: assemblies can contain gaps, errors, or regions whose placement remains uncertain. (genome.gov)
A reference genome provides a coordinate system and comparison sequence for identifying genes and genetic variants. It is an analytical resource, not a definition of a normal or ideal individual. A single reference cannot represent all variation within a species. A pangenome incorporates sequences from multiple individuals, allowing alternative sequences and structural arrangements to be represented. A draft human pangenome published in 2023 included 94 haplotype assemblies from 47 individuals. (genome.gov)
Human genome research and comparative study
The Human Genome Project, conducted from 1990 to 2003, produced the foundational human reference sequence, although difficult regions remained unresolved. In 2022, the Telomere-to-Telomere Consortium published T2T-CHM13, with gapless assemblies of the autosomes and X chromosome; it did not include a Y chromosome. These achievements illustrate how sequencing completeness depends on both available technology and the particular genetic material being represented. (genome.gov)
Comparative genomics examines similarities and differences between genomes to investigate gene function, shared ancestry, and evolution. Sequences conserved across species can help identify biologically important regions, while differences reveal changes in genome organization and genetic content. Genome comparisons also support agricultural research and the study of endangered species. Sequence similarity supplies evidence for these investigations, but interpreting biological function requires integrating sequence comparisons with experimental and other biological information. (genome.gov)