Expansion by whole genome duplication and evolution of the sox gene family in teleost fish

Abstract All vertebrates including human have evolved from an ancestor that underwent two rounds of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional third round of genome duplication (3R-WGD). The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, development and susceptibility to genetic diseases. However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD. We previously identified vertebrate ohnologs using a novel synteny comparison across multiple genomes. Here, we refine and apply this approach on 27 vertebrate genomes to identify ohnologs from both 2R- and 3R-WGD, while taking into account the phylogenetically biased sampling of available species. We assemble vertebrate ohnolog pairs and families in an expanded OHNOLOGS v2 database. We find that teleost fish have retained more 2R-WGD ohnologs than mammals and sauropsids, and that these 2R-ohnologs have retained significantly more ohnologs from the subsequent 3R-WGD than genes without 2R-ohnologs. Interestingly, species with fewer extant genes, such as sauropsids, have retained similar or higher proportions of ohnologs. OHNOLOGS v2 should allow deeper evolutionary genomic analysis of the impact of WGD on vertebrates and can be freely accessed at http://ohnologs.curie.fr.

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Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae

PeerJ ◽

10.7717/peerj.3400 ◽

2017 ◽

Vol 5 ◽

pp. e3400 ◽

Cited By ~ 7

Author(s):

Yunpeng Cao ◽

Yahui Han ◽

Dandan Meng ◽

Dahui Li ◽

Qing Jin ◽

...

Keyword(s):

Gene Family ◽

Whole Genome Duplication ◽

Large Scale ◽

Prunus Persica ◽

Genome Duplication ◽

Purifying Selection ◽

Whole Genome ◽

Environmental Selection ◽

Rosaceae Species ◽

High Level

The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.

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Whole-Genome Duplication and the Functional Diversification of Teleost Fish Hemoglobins

Molecular Biology and Evolution ◽

10.1093/molbev/mss212 ◽

2012 ◽

Vol 30 (1) ◽

pp. 140-153 ◽

Cited By ~ 55

Author(s):

Juan C. Opazo ◽

G. Tyler Butts ◽

Mariana F. Nery ◽

Jay F. Storz ◽

Federico G. Hoffmann

Keyword(s):

Teleost Fish ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Whole Genome ◽

Functional Diversification

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De-novoassembly of zucchini genome reveals a whole genome duplication associated with the origin of theCucurbitagenus

10.1101/147702 ◽

2017 ◽

Cited By ~ 1

Author(s):

Javier Montero-Pau ◽

José Blanca ◽

Aureliano Bombarely ◽

Peio Ziarsolo ◽

Cristina Esteras ◽

...

Keyword(s):

Gene Family ◽

Genome Size ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Core Gene ◽

The Other ◽

Whole Genome ◽

High Quality ◽

Small Genome ◽

Cucurbitaceae Family

AbstractTheCucurbitagenus (squashes, pumpkins, gourds) includes important domesticated species such asC. pepo,C. maximaandC. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb, 34,240 gene models, includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules, that represent 81.4% of the assembly, and it is integrated with a genetic map of 7,718 SNPs. Despite its small genome size three independent evidences support that theC. pepogenome is the result of a Whole Genome Duplication: the topology of the gene family phylogenies, the karyotype organization, and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analyzed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all theCucurbitaspecies analyzed, includingC. maximaandC. moschata, but not in the more distant cucurbits belonging to theCucumisandCitrullusgenera, and it is likely to have happened 30 ± 4 Mya in the ancestral species that gave rise to the genus.

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Comparative Genomics of Six Juglans Species Reveals Patterns of Disease-associated Gene Family Contractions

10.1101/561738 ◽

2019 ◽

Author(s):

Alex Trouern-Trend ◽

Taylor Falk ◽

Sumaira Zaman ◽

Madison Caballero ◽

David B. Neale ◽

...

Keyword(s):

Gene Family ◽

Whole Genome Duplication ◽

Common Ancestor ◽

Genome Duplication ◽

Gene Prediction ◽

Gene Families ◽

Whole Genome ◽

High Quality ◽

Gene Models ◽

Genome Annotations

ABSTRACTJuglans (walnuts), the most speciose genus in the walnut family (Juglandaceae) represents most of the family’s commercially valuable fruit and wood-producing trees and includes several species used as rootstock in agriculture for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional in-house developed tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multiexonic and monoexonic putative genes to yield between 27,000 and 44,000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 89.6%. We utilized these high quality annotations to assess gene family evolution within Juglans and among Juglans and selected Eurosid species, which revealed significant contractions in several gene families in J. hindsii including disease resistance-related Wall-associated Kinase (WAK) and Catharanthus roseus Receptor-like Kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.SIGNIFICANCEHigh-quality full genome annotations for six species of walnut (Juglans) and a wingnut (Pterocarya) outgroup were constructed using semi-unsupervised gene prediction followed by gene model filtering and functional characterization. These annotations represent the most comprehensive set for any hardwood genus to date. Comparative analyses based on the gene models uncovered rapid evolution in multiple gene families related to disease-response and a whole genome duplication in a Juglandaceae common ancestor.

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Coevolution of retroviruses with SERINCs following whole-genome duplication divergence

10.1101/2020.02.24.962506 ◽

2020 ◽

Author(s):

Pavitra Ramdas ◽

Vipin Bhardwaj ◽

Aman Singh ◽

Nagarjun Vijay ◽

Ajit Chande

Keyword(s):

Gene Family ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Foamy Virus ◽

Arms Race ◽

Whole Genome ◽

Virus Envelope ◽

Foamy Viruses ◽

Hiv 1

AbstractThe SERINC gene family comprises of five paralogs in humans of which SERINC3 and SERINC5 inhibit HIV-1 infectivity and are counteracted by Nef. The origin of this anti-retroviral activity, its prevalence among the remaining paralogs, and its ability to target retroviruses remain largely unknown. Here we show that despite their early divergence, the anti-retroviral activity is functionally conserved among four human SERINC paralogs with SERINC2 being an exception. The lack of activity in human SERINC2 is associated with its post-whole genome duplication (WGD) divergence, as evidenced by the ability of pre-WGD orthologs from yeast, fly, and a post-WGD-proximate SERINC2 from coelacanth to inhibit nef-defective HIV-1. Intriguingly, potent retroviral factors from HIV-1 and MLV are not able to relieve the SERINC2-mediated particle infectivity inhibition, indicating that such activity was directed towards other retroviruses that are found in coelacanth (like foamy viruses). However, foamy-derived vectors are intrinsically resistant to the action of SERINC2, and we show that a foamy virus envelope confers this resistance. Despite the presence of weak arms-race signatures, the functional reciprocal adaptation among SERINC2 and SERINC5 and, in response, the emergence of antagonizing ability in foamy virus appears to have resulted from a long-term conflict with the host.

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Complex Genes Are Preferentially Retained After Whole-Genome Duplication in Teleost Fish

Journal of Molecular Evolution ◽

10.1007/s00239-017-9794-8 ◽

2017 ◽

Vol 84 (5-6) ◽

pp. 253-258 ◽

Cited By ~ 6

Author(s):

Baocheng Guo

Keyword(s):

Teleost Fish ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Whole Genome

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Reconstructing the evolutionary history of the oxytocin and vasotocin receptor gene family: Insights on whole genome duplication scenarios

Developmental Biology ◽

10.1016/j.ydbio.2021.07.012 ◽

2021 ◽

Author(s):

Constantina. Theofanopoulou

Keyword(s):

Gene Family ◽

Whole Genome Duplication ◽

Evolutionary History ◽

Genome Duplication ◽

Receptor Gene ◽

Whole Genome ◽

History Of ◽

Receptor Gene Family

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Genome-Wide Analysis of the COBRA-Like Gene Family Supports Gene Expansion through Whole-Genome Duplication in Soybean (Glycine max)

Plants ◽

10.3390/plants10010167 ◽

2021 ◽

Vol 10 (1) ◽

pp. 167

Author(s):

Sara Sangi ◽

Paula M. Araújo ◽

Fernanda S. Coelho ◽

Rajesh K. Gazara ◽

Fabrício Almeida-Silva ◽

...

Keyword(s):

Cell Wall ◽

Gene Family ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Expression Patterns ◽

Whole Genome ◽

Comprehensive Overview ◽

Genome Wide ◽

Duplication Events ◽

Cell Wall Expansion

The COBRA-like (COBL) gene family has been associated with the regulation of cell wall expansion and cellulose deposition. COBL mutants result in reduced levels and disorganized deposition of cellulose causing defects in the cell wall and inhibiting plant development. In this study, we report the identification of 24 COBL genes (GmCOBL) in the soybean genome. Phylogenetic analysis revealed that the COBL proteins are divided into two groups, which differ by about 170 amino acids in the N-terminal region. The GmCOBL genes were heterogeneously distributed in 14 of the 20 soybean chromosomes. This study showed that segmental duplication has contributed significantly to the expansion of the COBL family in soybean during all Glycine-specific whole-genome duplication events. The expression profile revealed that the expression of the paralogous genes is highly variable between organs and tissues of the plant. Only 20% of the paralogous gene pairs showed similar expression patterns. The high expression levels of some GmCOBLs suggest they are likely essential for regulating cell expansion during the whole soybean life cycle. Our comprehensive overview of the COBL gene family in soybean provides useful information for further understanding the evolution and diversification of COBL genes in soybean.

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