ArticleGenome research2001
Lineage-specific gene expansions in bacterial and archaeal genomes.
Article in Genome research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
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- Genome mining reveals novel biosynthetic gene clusters in entomopathogenic bacteria.Scientific reports · 2023Article
- TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria.Database : the journal of biological databases and curation · 2023Article
- Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences.Genome biology and evolution · 2023Article
- Tubby-like proteins (TLPs) transcription factor in different regulatory mechanism in plants: a review.Plant molecular biology · 2022Review
- Transcriptomic Analysis of Early Flowering Signals in 'Royal' Flax.Plants (Basel, Switzerland) · 2022Article
- Genome-Wide Analysis and Characterization of the Proline-Rich Extensin-like Receptor Kinases (PERKs) Gene Family Reveals Their Role in Different Developmental Stages and Stress Conditions in Wheat (Plants (Basel, Switzerland) · 2022Article
- Genome-wide identification and expression analysis ofOpen life sciences · 2022Article
- Optimizing the Parametrization of Homologue Classification in the Pan-Genome Computation for a Bacterial Species: Case Study Streptococcus pyogenes.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Comparative Genomic Analysis of the Human PathogenFrontiers in cellular and infection microbiology · 2022Article
- Article
- Genome-Wide Identification and Characterization of PIN-FORMED (PIN) Gene Family Reveals Role in Developmental and Various Stress Conditions inInternational journal of molecular sciences · 2021Article
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- The SNAP hypothesis: Chromosomal rearrangements could emerge from positive Selection during Niche Adaptation.PLoS genetics · 2020Article
- First Steps in the Analysis of Prokaryotic Pan-Genomes.Bioinformatics and biology insights · 2020Review
- EvoMining reveals the origin and fate of natural product biosynthetic enzymes.Microbial genomics · 2019Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the diversification of the major prokaryotic lineages (lineage-specific expansions) were analyzed. Analysis of 21 completely sequenced prokaryotic genomes shows that lineage-specific expansions comprise a substantial fraction (approximately 5%-33%) of their coding capacities. A positive correlation exists between the fraction of the genes taken up by lineage-specific expansions and the total number of genes in a genome. Consistent with the notion that lineage-specific expansions are made up of relatively recently duplicated genes, >90% of the detected clusters consists of only two to four genes. The more common smaller clusters tend to include genes with higher pairwise similarity (as reflected by average score density) than larger clusters. Regardless of size, cluster members tend to be located more closely on bacterial chromosomes than expected by chance, which could reflect a history of tandem gene duplication. In addition to the small clusters, almost all genomes also contain rare large clusters of size > or =20. Several examples of the potential adaptive significance of these large clusters are explored. The presence or absence of clusters and their related genes was used as the basis for the construction of a similarity graph for completely sequenced prokaryotic genomes. The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss.
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