Reconciling Gene and Genome Duplication Events: Using Multiple Nuclear Gene Families to Infer the Phylogeny of the Aquatic Plant Family Pontederiaceae

ABSTRACT Gene duplication is key to molecular evolution in all three domains of life and may be the first step in the emergence of new gene function. It is a well-recognized feature in large DNA viruses but has not been studied extensively in the largest known virus to date, the recently discovered Acanthamoeba polyphaga Mimivirus. Here, I present a systematic analysis of gene and genome duplication events in the mimivirus genome. I found that one-third of the mimivirus genes are related to at least one other gene in the mimivirus genome, either through a large segmental genome duplication event that occurred in the more remote past or through more recent gene duplication events, which often occur in tandem. This shows that gene and genome duplication played a major role in shaping the mimivirus genome. Using multiple alignments, together with remote-homology detection methods based on Hidden Markov Model comparison, I assign putative functions to some of the paralogous gene families. I suggest that a large part of the duplicated mimivirus gene families are likely to interfere with important host cell processes, such as transcription control, protein degradation, and cell regulatory processes. My findings support the view that large DNA viruses are complex evolving organisms, possibly deeply rooted within the tree of life, and oppose the paradigm that viral evolution is dominated by lateral gene acquisition, at least in regard to large DNA viruses.

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Constraining the timing of whole genome duplication in plant evolutionary history

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.0912 ◽

2017 ◽

Vol 284 (1858) ◽

pp. 20170912 ◽

Cited By ~ 18

Author(s):

James W. Clark ◽

Philip C. J. Donoghue

Keyword(s):

Whole Genome Duplication ◽

Genome Duplication ◽

Gene Families ◽

Plant Evolution ◽

Resistance Testing ◽

Whole Genome ◽

Evolutionary Innovation ◽

Major Genome ◽

Duplication Events ◽

Clock Analysis

Whole genome duplication (WGD) has occurred in many lineages within the tree of life and is invariably invoked as causal to evolutionary innovation, increased diversity, and extinction resistance. Testing such hypotheses is problematic, not least since the timing of WGD events has proven hard to constrain. Here we show that WGD events can be dated through molecular clock analysis of concatenated gene families, calibrated using fossil evidence for the ages of species divergences that bracket WGD events. We apply this approach to dating the two major genome duplication events shared by all seed plants ( ζ ) and flowering plants ( ɛ ), estimating the seed plant WGD event at 399–381 Ma, and the angiosperm WGD event at 319–297 Ma. These events thus took place early in the stem of both lineages, precluding hypotheses of WGD conferring extinction resistance, driving dramatic increases in innovation and diversity, but corroborating and qualifying the more permissive hypothesis of a ‘lag-time’ in realizing the effects of WGD in plant evolution.

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Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽

10.1093/genetics/156.3.1249 ◽

2000 ◽

Vol 156 (3) ◽

pp. 1249-1257

Author(s):

Ilya Ruvinsky ◽

Lee M Silver ◽

Jeremy J Gibson-Brown

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Gene Families ◽

Vertebrate Evolution ◽

Whole Genome ◽

Vertebrate Genome ◽

T Box ◽

Genetic Complexity ◽

History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

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Genome Duplication in Soybean (Glycine subgenus soja)

Genetics ◽

10.1093/genetics/144.1.329 ◽

1996 ◽

Vol 144 (1) ◽

pp. 329-338 ◽

Cited By ~ 6

Author(s):

R C Shoemaker ◽

K Polzin ◽

J Labate ◽

J Specht ◽

E C Brummer ◽

...

Keyword(s):

Seed Protein ◽

Genome Duplication ◽

Fragment Length Polymorphism ◽

Gene Families ◽

Soybean Genome ◽

Seed Composition ◽

Linkage Groups ◽

Mapping Data ◽

Or Gene ◽

Average Size

Abstract Restriction fragment length polymorphism mapping data from nine populations (Glycine max × G. soja and G. max × G. max) of the Glycine subgenus soja genome led to the identification of many duplicated segments of the genome. Linkage groups contained up to 33 markers that were duplicated on other linkage groups. The size of homoeologous regions ranged from 1.5 to 106.4 cM, with an average size of 45.3 cM. We observed segments in the soybean genome that were present in as many as six copies with an average of 2.55 duplications per segment. The presence of nested duplications suggests that at least one of the original genomes may have undergone an additional round of tetraploidization. Tetraploidization, along with large internal duplications, accounts for the highly duplicated nature of the genome of the subgenus. Quantitative trait loci for seed protein and oil showed correspondence across homoeologous regions, suggesting that the genes or gene families contributing to seed composition have retained similar functions throughout the evolution of the chromosomes.

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Genome-wide identification of ascorbate-glutathione cycle gene families in soybean (Glycine max) reveals gene duplication events and specificity of gene members linked to development and stress conditions

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2021.07.103 ◽

2021 ◽

Author(s):

José Hélio Costa ◽

André Luiz Maia Roque ◽

Shahid Aziz ◽

Clesivan Pereira dos Santos ◽

Thais Andrade Germano ◽

...

Keyword(s):

Glycine Max ◽

Gene Duplication ◽

Gene Families ◽

Stress Conditions ◽

Genome Wide ◽

Duplication Events ◽

Glutathione Cycle

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Giant African snail genomes provide insights into molluscan whole-genome duplication and aquatic-terrestrial transition

10.1101/2020.02.02.930693 ◽

2020 ◽

Cited By ~ 2

Author(s):

Conghui Liu ◽

Yuwei Ren ◽

Zaiyuan Li ◽

Qi Hu ◽

Lijuan Yin ◽

...

Keyword(s):

Whole Genome Duplication ◽

Genome Duplication ◽

Terrestrial Ecosystems ◽

Gene Families ◽

Gene Clusters ◽

Immune Defense ◽

Whole Genome ◽

Genomic Plasticity ◽

Ecological Adaptability ◽

Chromosome Level

AbstractWhole-genome duplication (WGD) has been observed across a wide variety of eukaryotic groups, contributing to evolutionary diversity and environmental adaptability. Mollusks are the second largest group of animals, and are among the organisms that have successfully adapted to the nonmarine realm through aquatic-terrestrial (A-T) transition, and no comprehensive research on WGD has been reported in this group. To explore WGD and the A-T transition in Mollusca, we assembled a chromosome-level reference genome for the giant African snail Achatina immaculata, a global invasive species, and compared the genomes of two giant African snails (A. immaculata and Achatina fulica) to the other available mollusk genomes. The chromosome-level macrosynteny, colinearity blocks, Ks peak and Hox gene clusters collectively suggested the occurrence of a WGD event shared by A. immaculata and A. fulica. The estimated timing of this WGD event (∼70 MYA) was close to the speciation age of the Sigmurethra-Orthurethra (within Stylommatophora) lineage and the Cretaceous-Tertiary (K-T) mass extinction, indicating that the WGD reported herein may have been a common event shared by all Sigmurethra-Orthurethra species and could have conferred ecological adaptability and genomic plasticity allowing the survival of the K-T extinction. Based on macrosynteny, we deduced an ancestral karyotype containing 8 conserved clusters for the Gastropoda-Bivalvia lineage. To reveal the mechanism of WGD in shaping adaptability to terrestrial ecosystems, we investigated gene families related to the respiration, aestivation and immune defense of giant African snails. Several mucus-related gene families expanded early in the Stylommatophora lineage, functioning in water retention, immune defense and wound healing. The hemocyanins, PCK and FBP families were doubled and retained after WGD, enhancing the capacity for gas exchange and glucose homeostasis in aestivation. After the WGD, zinc metalloproteinase genes were highly tandemly duplicated to protect tissue against ROS damage. This evidence collectively suggests that although the WGD may not have been the direct driver of the A-T transition, it provided an important legacy for the terrestrial adaptation of the giant African snail.

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Fructosyltransferase and invertase genes evolved by gene duplication and rearrangements: rice, perennial ryegrass, and wheat gene families

Genome ◽

10.1139/g06-066 ◽

2006 ◽

Vol 49 (9) ◽

pp. 1081-1091 ◽

Cited By ~ 14

Author(s):

Michael G. Francki ◽

Esther Walker ◽

John W. Forster ◽

German Spangenberg ◽

Rudi Appels

Keyword(s):

Perennial Ryegrass ◽

Abiotic Stress Tolerance ◽

Gene Families ◽

Amino Acid Similarity ◽

Gene Variation ◽

Wheat Gene ◽

Multiple Copies ◽

Duplication Events ◽

Invertase Gene ◽

Gene Orthologs

The invertase enzyme family is responsible for carbohydrate metabolism in rice, perennial ryegrass, and wheat. Fructan molecules accumulate in cell vacuoles of perennial ryegrass and wheat and are associated with abiotic stress tolerance. High levels of amino acid similarity between the fructosyltransferases responsible for fructan accumulation indicates that they may have evolved from invertase-like ancestral genes. In this study, we have applied comparative genomics to determine the mechanisms that lead to the evolution of fructosytransferase and invertase genes in rice, perennial ryegrass, and wheat. Duplications and rearrangements have been inferred to generate variant forms of the rice invertases since divergence from a common grass progenitor. The occurrence of multiple copies of fructosyltransferase genes indicated that duplication events continued during evolution of the wheat and perennial ryegrass lineages. Further gene rearrangements were evident in perennial ryegrass genes, albeit at a reduced level compared with the rice invertases. Gene orthologs were largely static after duplication during evolution of the wheat lineage. This study details evolutionary events that contribute to fructosyltransferase and invertase gene variation in grasses.

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Ancient Genome Duplications Did Not Structure the Human Hox-Bearing Chromosomes

Genome Research ◽

10.1101/gr.160001 ◽

2001 ◽

Vol 11 (5) ◽

pp. 771-780 ◽

Cited By ~ 2

Author(s):

Austin L. Hughes ◽

Jack da Silva ◽

Robert Friedman

Keyword(s):

Phylogenetic Analysis ◽

Gene Duplication ◽

Genome Duplication ◽

Gene Families ◽

Gene Duplications ◽

Human Chromosomes ◽

Time Period ◽

Genome Duplications

The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition, it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the fourHox-bearing chromosomes (the chromosomes bearing theHox clusters; i.e., human chromosomes 2, 7, 12, and 17), and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the humanHox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene duplications before the origin of vertebrates, and of 15 gene duplication times estimated for gene families evolving in a clock-like manner, only six were dated to the same time period early in vertebrate history during which the Hox clusters duplicated. Furthermore, of gene families duplicated around the same time as the Hoxclusters, the majority showed topologies inconsistent with their having duplicated simultaneously with the Hox clusters. The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes.

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Bioinformatic methods applied to the analysis of the genes retained after the whole genome duplication events in the sterlet genome (Acipenser ruthenus)

2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB) ◽

10.1109/csgb51356.2020.9214587 ◽

2020 ◽

Author(s):

Mikhail Fofanov ◽

Tatyana Sheglova ◽

Vladimir Trifonov ◽

Manfred Schartl

Keyword(s):

Whole Genome Duplication ◽

Genome Duplication ◽

Whole Genome ◽

Acipenser Ruthenus ◽

Duplication Events

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The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)

Genes ◽

10.3390/genes10080622 ◽

2019 ◽

Vol 10 (8) ◽

pp. 622 ◽

Cited By ~ 2

Author(s):

Yi Sun ◽

Chao Liu ◽

Moli Huang ◽

Jian Huang ◽

Changhong Liu ◽

...

Keyword(s):

Circadian Clock ◽

Teleost Fish ◽

Clock Gene ◽

Genome Duplication ◽

Clock Genes ◽

Gene Families ◽

Regulatory Mechanisms ◽

Spotted Gar ◽

Circadian Clock Genes ◽

Lepisosteus Oculatus

Circadian rhythms are biological rhythms with a period of approximately 24 h. While canonical circadian clock genes and their regulatory mechanisms appear highly conserved, the evolution of clock gene families is still unclear due to several rounds of whole genome duplication in vertebrates. The spotted gar (Lepisosteus oculatus), as a non-teleost ray-finned fish, represents a fish lineage that diverged before the teleost genome duplication (TGD), providing an outgroup for exploring the evolutionary mechanisms of circadian clocks after whole-genome duplication. In this study, we interrogated the spotted gar draft genome sequences and found that spotted gar contains 26 circadian clock genes from 11 families. Phylogenetic analysis showed that 9 of these 11 spotted gar circadian clock gene families have the same number of genes as humans, while the members of the nfil3 and cry families are different between spotted gar and humans. Using phylogenetic and syntenic analyses, we found that nfil3-1 is conserved in vertebrates, while nfil3-2 and nfil3-3 are maintained in spotted gar, teleost fish, amphibians, and reptiles, but not in mammals. Following the two-round vertebrate genome duplication (VGD), spotted gar retained cry1a, cry1b, and cry2, and cry3 is retained in spotted gar, teleost fish, turtles, and birds, but not in mammals. We hypothesize that duplication of core clock genes, such as (nfil3 and cry), likely facilitated diversification of circadian regulatory mechanisms in teleost fish. We also found that the transcription factor binding element (Ahr::Arnt) is retained only in one of the per1 or per2 duplicated paralogs derived from the TGD in the teleost fish, implicating possible subfuctionalization cases. Together, these findings help decipher the repertoires of the spotted gar’s circadian system and shed light on how the vertebrate circadian clock systems have evolved.

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