Dataset Information

Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants.

ABSTRACT:

Background

Gene duplication is considered a major driving force for evolution of genetic novelty, thereby facilitating functional divergence and organismal diversity, including the process of speciation. Animals, fungi and plants are major eukaryotic kingdoms and the divergences between them are some of the most significant evolutionary events. Although gene duplications in each lineage have been studied extensively in various contexts, the extent of gene duplication prior to the split of plants and animals/fungi is not clear.

Results

Here, we have studied gene duplications in early eukaryotes by phylogenetic relative dating. We have reconstructed gene families (with one or more orthogroups) with members from both animals/fungi and plants by using two different clustering strategies. Extensive phylogenetic analyses of the gene families show that, among nearly 2,600 orthogroups identified, at least 300 of them still retain duplication that occurred before the divergence of the three kingdoms. We further found evidence that such duplications were also detected in some highly divergent protists, suggesting that these duplication events occurred in the ancestors of most major extant eukaryotic groups.

Conclusions

Our phylogenetic analyses show that numerous gene duplications happened at the early stage of eukaryotic evolution, probably before the separation of known major eukaryotic lineages. We discuss the implication of our results in the contexts of different models of eukaryotic phylogeny. One possible explanation for the large number of gene duplication events is one or more large-scale duplications, possibly whole genome or segmental duplication(s), which provides a genomic basis for the successful radiation of early eukaryotes.

SUBMITTER: Zhou X

PROVIDER: S-EPMC2884541 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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Publications

Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants.

Zhou Xiaofan X Lin Zhenguo Z Ma Hong H

Genome biology 20100406 4

<h4>Background</h4>Gene duplication is considered a major driving force for evolution of genetic novelty, thereby facilitating functional divergence and organismal diversity, including the process of speciation. Animals, fungi and plants are major eukaryotic kingdoms and the divergences between them are some of the most significant evolutionary events. Although gene duplications in each lineage have been studied extensively in various contexts, the extent of gene duplication prior to the split o ...[more]

PMID: 20370904

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Project description:BackgroundThe use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods for reconstruction, where conflict is presumed to be explained by incomplete lineage sorting (ILS); or through concatenation, where noise is presumed to be the dominant source of conflict. The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding of the underlying conflict within these datasets.ResultsHere we examined two published transcriptomic datasets, the angiosperm group Caryophyllales and the aculeate Hymenoptera, for the presence of conflict, concordance, and gene duplications in individual homologs across the phylogeny. We found significant conflict throughout the phylogeny in both datasets and in particular along the backbone. While some nodes in each phylogeny showed patterns of conflict similar to what might be expected with ILS alone, the backbone nodes also exhibited low levels of phylogenetic signal. In addition, certain nodes, especially in the Caryophyllales, had highly elevated levels of strongly supported conflict that cannot be explained by ILS alone.ConclusionThis study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets. Further insight into the conflict and processes underlying these complex datasets is necessary to improve and develop adequate models for sequence analysis and downstream applications. To aid this effort, we developed the open source software phyparts ( https://bitbucket.org/blackrim/phyparts ), which calculates unique, conflicting, and concordant bipartitions, maps gene duplications, and outputs summary statistics such as internode certainy (ICA) scores and node-specific counts of gene duplications.

Project description:The transient receptor potential vanilloid (TRPV) ion channel family is involved in multiple sensory and physiological functions including thermosensing and temperature-dependent neuroendocrine regulation. The objective of the present study was to investigate the number, origin and evolution of TRPV genes in metazoans, with special focus on the impact of the vertebrate whole-genome duplications (WGD). Gene searches followed by phylogenetic and synteny analyses revealed multiple previously undescribed TRPV genes. The common ancestor of Cnidaria and Bilateria had three TRPV genes that became four in the deuterostome ancestor. Two of these were lost in the vertebrate ancestor. The remaining two genes gave rise to two TRPV subfamilies in vertebrates, consisting of subtypes 1, 2, 3, 4, 9 and 5, 6, 7, 8, respectively. This gene expansion resulted from the two basal vertebrate WGD events (1R and 2R) and three local duplications before the radiation of gnathostomes. TRPV1, 4 and 5 have been retained in all gnathostomes investigated, presumably reflecting important functions. TRPV7 and 8 have been lost independently in various lineages but are still retained in cyclostomes, actinistians (coelacanth), amphibians, prototherians and basal actinopterygians (Polypteridae). TRPV3 and 9 are present in extant elasmobranchs, while TRPV9 was lost in the osteichthyan ancestor and TRPV3 in the actinopterygian ancestor. The coelacanth has retained the ancestral osteichthyan repertoire of TRPV1, 3, 4, 5, 7 and 8. TRPV2 arose in the tetrapod ancestor. Duplications of TRPV5 occurred independently in various lineages, such as cyclostomes, chondrichthyans, anuran amphibians, sauropsids, mammals (where the duplicate is called TRPV6), and actinopterygians (Polypteridae and Esocidae). After the teleost-specific WGD (3R) only TRPV1 retained its duplicate, whereas TRPV4 and 5 remained as single genes. Both 3R-paralogs of TRPV1 were kept in some teleost species, while one paralog was lost in others. The salmonid-specific WGD (4R) duplicated TRPV1, 4, and 5 leading to six TRPV genes. The largest number was found in Xenopus tropicalis with no less than 15 TRPV genes. This study provides a comprehensive evolutionary scenario for the vertebrate TRPV family, revealing additional TRPV types and proposing a phylogeny-based classification of TRPV across metazoans.

Dataset Information

Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants.

Background

Results

Conclusions

Publications

Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants.

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