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Factors influencing gene family size variation among related species in a plant family

View ORCID ProfilePeipei Wang, Bethany M. Moore, Nicholas L. Panchy, Fanrui Meng, View ORCID ProfileMelissa D. Lehti-Shiu, View ORCID ProfileShin-Han Shiu
doi: https://doi.org/10.1101/270009
Peipei Wang
1Department of Plant Biology, Michigan State University, East Lansing, MI 48824
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Bethany M. Moore
1Department of Plant Biology, Michigan State University, East Lansing, MI 48824
2Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI 48824
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Nicholas L. Panchy
3Genetics Program, Michigan State University, East Lansing, MI 48824
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Fanrui Meng
1Department of Plant Biology, Michigan State University, East Lansing, MI 48824
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Melissa D. Lehti-Shiu
1Department of Plant Biology, Michigan State University, East Lansing, MI 48824
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Shin-Han Shiu
1Department of Plant Biology, Michigan State University, East Lansing, MI 48824
2Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI 48824
3Genetics Program, Michigan State University, East Lansing, MI 48824
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  • For correspondence: shius@msu.edu
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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, we used the Solanaceae family as a model to investigate differences in gene family size and the likely factors contributing to these differences. We found that genes in highly variable families have high turnover rate 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 suggests 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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Posted February 23, 2018.
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Factors influencing gene family size variation among related species in a plant family
Peipei Wang, Bethany M. Moore, Nicholas L. Panchy, Fanrui Meng, Melissa D. Lehti-Shiu, Shin-Han Shiu
bioRxiv 270009; doi: https://doi.org/10.1101/270009
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Factors influencing gene family size variation among related species in a plant family
Peipei Wang, Bethany M. Moore, Nicholas L. Panchy, Fanrui Meng, Melissa D. Lehti-Shiu, Shin-Han Shiu
bioRxiv 270009; doi: https://doi.org/10.1101/270009

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