Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae

Genome Biology and Evolution
Peipei WangShin-Han Shiu

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 ...Continue Reading

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Citations

Feb 19, 2019·Communications Biology·Aleksia VaattovaaraMichael Wrzaczek
Jan 30, 2020·BMC Biology·Irene Adrian-KalchhauserSylke Winkler
Nov 27, 2020·Scientific Reports·Zhen LiaoChristina Dixelius
Feb 4, 2021·BMC Genomics·Peipei WangShin-Han Shiu
Jan 12, 2020·Communications Biology·Aleksia VaattovaaraMichael Wrzaczek

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