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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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Updated: Jan 26, 2026

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
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Marker genes as predictors of shared genomic function.

Joseph L Sevigny1,2, Derek Rothenheber3, Krystalle Sharlyn Diaz3,4

  • 1Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA. jlsevigny1@wildcats.unh.edu.

BMC Genomics
|April 6, 2019
PubMed
Summary
This summary is machine-generated.

Microbial community function cannot be fully predicted by marker gene identity. Even with high sequence similarity, genomes share less than 75% of protein-coding genes, limiting functional inference from marker genes.

Keywords:
16S rRNAAmpliconComparative genomicsFunctional capacityMarker geneMetabarcodingMetagenomics

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Area of Science:

  • Microbial genomics
  • Bioinformatics
  • Metagenomics

Background:

  • High-throughput marker gene studies reveal microbial diversity but not functional capacity.
  • Predicting microbial community function from phylogenetic data is an emerging area.
  • Previous studies lacked large-scale correlation analysis between marker gene identity and protein-coding gene conservation.

Purpose of the Study:

  • To investigate the relationship between marker gene identity and shared protein-coding gene content in prokaryotes.
  • To quantify the correlation between taxonomic identification from marker genes and functional gene conservation.
  • To assess the limitations of using marker genes for predicting microbial community function.

Main Methods:

  • Utilized 4872 representative prokaryotic genomes from NCBI.
  • Analyzed protein-coding gene content based on varying marker gene identities (V4 16S rRNA, complete 16S rRNA, multi-locus sequence analysis).
  • Examined intra-organism variation in 16S rRNA gene copies.

Main Results:

  • Genomes share less than 75% of protein-coding genes even at 99-100% marker gene identity.
  • This low conservation was consistent across different marker genes analyzed.
  • Significant intra-organism variation in 16S rRNA gene copies was observed in some genomes.

Conclusions:

  • Marker gene similarity is a poor predictor of shared protein-coding gene content.
  • Inferring microbial community function solely from marker gene phylogeny has significant limitations.
  • 16S rRNA and other marker genes are insufficient for fully predicting bacterial community functional potential.