Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods

AbstractDue to their key phylogenetic position, cartilaginous fishes, which includes the largest fish speciesRhincodon typus(whale shark), are an important vertebrate lineage for understanding the origin and evolution of vertebrates. However, until recently, this lineage has been understudied in vertebrate genomics. Using newly-generated long read sequences, we produced the best gapless cartilaginous fish genome assembly to date. The assembly has fewer missing ancestral genes thanCallorhinchus milii, which has been widely-used for evolutionary studies up to now. We used the new assembly to study the evolution of gene families in the whale shark and other vertebrates, focusing on historical patterns of gene family origins and loss across early vertebrate evolution, innate immune receptor repertoire evolution, and dynamics of gene family evolution size in relation to gigantism. From inferring the pattern of origin of gene families across the most recent common ancestors of major vertebrate clades, we found that there were many shared gene families between the whale shark and bony vertebrates that were present in the most recent common ancestor of jawed vertebrates, with a large increase in novel genes at the origin of jawed vertebrates independent of whole genome duplication events. The innate immune system in the whale shark, which consisted of diverse pathogen recognition receptors (PRRs) including NOD-like receptors, RIG-like receptors, and Toll-like receptors. We discovered a unique complement of Toll-like receptors and triplication of NOD1 in the whale shark genome. Further, we found diverse patterns of gene family evolution between PRRs within vertebrates demonstrating that the origin of adaptive immunity in jawed vertebrates is more complicated than simply replacing the need for a vast repertoire of germline encoded PRRs. We then studied rates of amino acid substitution and gene family size evolution across origins of vertebrate gigantism. While we found that cartilaginous fishes and giant vertebrates tended to have slower substitution rates than the background rate in vertebrates, the whale shark genome substitution rate was not significantly slower thanCallorhinchus. Furthermore, rates of gene family size evolution varied among giants and the background, suggesting that differences in rate of substitution and gene family size evolution relative to gigantism are decoupled. We found that the gene families that have shifted in duplication rate in whale shark are enriched for genes related to driving cancer in humans, consistent with studies in other giant vertebrates than support the hypothesis that evolution of increased body size requires adaptations that result in reduction of per cell cancer rate.

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The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families

Gene ◽

10.1016/j.gene.2008.02.014 ◽

2008 ◽

Vol 414 (1-2) ◽

pp. 85-94 ◽

Cited By ~ 13

Author(s):

Timothy Hughes ◽

David A. Liberles

Keyword(s):

Gene Family ◽

Family Size ◽

Power Law ◽

Gene Families ◽

Power Law Distribution

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Ecological correlates of gene family size: the draft genome of the redheaded pine sawfly Neodiprion lecontei

10.1101/2021.03.14.435331 ◽

2021 ◽

Author(s):

Kim Vertacnik ◽

Danielle Herrig ◽

R Keating Godfrey ◽

Tom Hill ◽

Scott Geib ◽

...

Keyword(s):

Gene Family ◽

Family Size ◽

Draft Genome ◽

Gene Families ◽

Gene Family Evolution ◽

Gene Gain ◽

Ecological Specialization ◽

Dietary Specialization ◽

Pine Sawfly ◽

Neodiprion Lecontei

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions and characterized their genomic distributions and evolutionary history. Our results suggest that expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), and antimicrobial peptide (AMP) subfamilies may have contributed to pine adaptation. By contrast, there was no evidence of recent gene family contraction via pseudogenization. Next, we compared the number of genes in these same families across insect taxa that vary in diet, dietary specialization, and social behavior. In Hymenoptera, herbivory was associated with large GR and small olfactory receptor (OR) families, eusociality was associated with large OR and small AMP families, and--unlike investigations among more closely related taxa--ecological specialization was not related to gene family size. Overall, our results suggest that gene families that mediate ecological interactions may expand and contract predictably in response to particular selection pressures, however, the ecological drivers and temporal pace of gene gain and loss likely varies considerably across gene families.

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Comparative Genomics of the Major Chemosensory Gene Families in Arthropods

Encyclopedia of Life Sciences ◽

10.1002/9780470015902.a0022848 ◽

2011 ◽

Cited By ~ 14

Author(s):

Alejandro Sánchez-Gracia ◽

Filipe G Vieira ◽

Francisca C Almeida ◽

Julio Rozas

Keyword(s):

Comparative Genomics ◽

Gene Families ◽

Chemosensory Gene

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Global Evolutionary Analysis of 11 Gene Families Part of Reactive Oxygen Species (ROS) Gene Network in Four Eucalyptus Species

Antioxidants ◽

10.3390/antiox9030257 ◽

2020 ◽

Vol 9 (3) ◽

pp. 257

Author(s):

Qiang Li ◽

Hélène San Clemente ◽

Yongrui He ◽

Yongyao Fu ◽

Christophe Dunand

Keyword(s):

Reactive Oxygen Species ◽

Comparative Analysis ◽

Gene Network ◽

Expression Patterns ◽

Reactive Oxygen ◽

Evolutionary Process ◽

Gene Families ◽

Eucalyptus Species ◽

Gene Gain ◽

Oxygen Species

Eucalyptus is a worldwide hard-wood species which increasingly focused on. To adapt to various biotic and abiotic stresses, Eucalyptus have evolved complex mechanisms, increasing the cellular concentration of reactive oxygen species (ROS) by numerous ROS controlling enzymes. To better analyse the ROS gene network and discuss the differences between four Eucalyptus species, ROS gene network including 11 proteins families (1CysPrx, 2CysPrx, APx, APx-R, CIII Prx, Diox, GPx, Kat, PrxII, PrxQ and Rboh) were annotated and compared in an expert and exhaustive manner from the genomic data available from E. camaldulensis, E. globulus, E. grandis, and E. gunnii. In addition, a specific sequencing strategy was performed in order to determine if the missed sequences in at least one organism are the results of gain/loss events or only sequencing gaps. We observed that the automatic annotation applied to multigenic families is the source of miss-annotation. Base on the family size, the 11 families can be categorized into duplicated gene families (CIII Prx, Kat, 1CysPrx, and GPx), which contain a lot of gene duplication events and non-duplicated families (APx, APx-R, Rboh, DiOx, 2CysPrx, PrxII, and PrxQ). The gene family sizes are much larger in Eucalyptus than most of other angiosperms due to recent gene duplications, which could give higher adaptability to environmental changes and stresses. The cross-species comparative analysis shows gene gain and loss events during the evolutionary process. The 11 families possess different expression patterns, while in the Eucalyptus genus, the ROS families present similar expression patterns. Overall, the comparative analysis might be a good criterion to evaluate the adaptation of different species with different characters, but only if data mining is as exhaustive as possible. It is also a good indicator to explore the evolutionary process.

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