ArticleGenome biology and evolution2018
Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 101 citations in OpenAlex.
- Article
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- PAHG: the database of human multi-gene families.BMC genomic data · 2025Article
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- Genome-wide identification and expression pattern analysis of the chloride channel gene family in potato (Frontiers in plant science · 2025Article
- Identification of Kunitz-Type Inhibitor Gene Family ofInternational journal of molecular sciences · 2024Article
- Identification and characterization of the Quinoa AP2/ERF gene family and their expression patterns in response to salt stress.Scientific reports · 2024Article
- Article
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- Adaptation in Unstable Environments and Global Gene Losses: Small but Stable Gene Networks by the May-Wigner Theory.Molecular biology and evolution · 2024Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene duplication and loss contribute to gene content differences as well as phenotypic divergence across species. However, the extent to which gene content varies among closely related plant species and the factors responsible for such variation remain unclear. Here, using the Solanaceae family as a model and Pfam domain families as a proxy for gene families, we investigated variation in gene family sizes across species and the likely factors contributing to the variation. We found that genes in highly variable families have high turnover rates and tend to be involved in processes that have diverged between Solanaceae species, whereas genes in low-variability families tend to have housekeeping roles. In addition, genes in high- and low-variability gene families tend to be duplicated by tandem and whole genome duplication, respectively. This finding together with the observation that genes duplicated by different mechanisms experience different selection pressures suggest that duplication mechanism impacts gene family turnover. We explored using pseudogene number as a proxy for gene loss but discovered that a substantial number of pseudogenes are actually products of pseudogene duplication, contrary to the expectation that most plant pseudogenes are remnants of once-functional duplicates. Our findings reveal complex relationships between variation in gene family size, gene functions, duplication mechanism, and evolutionary rate. The patterns of lineage-specific gene family expansion within the Solanaceae provide the foundation for a better understanding of the genetic basis underlying phenotypic diversity in this economically important family.
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