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

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3400 ◽  
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.

scholarly journals Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

2017 ◽  
Author(s):  
Matthew Parks ◽  
Teofil Nakov ◽  
Elizabeth Ruck ◽  
Norman J. Wickett ◽  
Andrew J. Alverson
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Genome Duplication ◽  
Gene Tree ◽  
Genomic Diversity ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Gene Trees ◽  
Angiosperm Evolution ◽  
Polyploid Formation

ABSTRACTPremise of the studyDiatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.MethodsWe used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.Key resultsSeveral methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.ConclusionsWhole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.

scholarly journals Whole-Genome Duplication and Purifying Selection Contributes to the Functional Redundancy of Auxin Response Factor (ARF) Genes in Foxtail Millet (Setaria italica L.)

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
You Chen ◽  
Bin Liu ◽  
Yujun Zhao ◽  
Wenzhe Yu ◽  
Weina Si
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Expression Profiles ◽  
Foxtail Millet ◽  
Purifying Selection ◽  
Functional Redundancy ◽  
Setaria Italica ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
Auxin Response

Auxin response factors (ARFs) play crucial roles in auxin-mediated response, whereas molecular genetics of ARF genes was seldom investigated in Setaria italica, an important crop and C4 model plant. In the present study, genome-wide evolutionary analysis of ARFs was performed in S. italica. Twenty-four SiARF genes were identified and unevenly distributed on eight of the nine chromosomes in S. italica. Duplication mode exploration implied that 13 SiARF proteins were originated from whole-genome duplication and suffered purifying selection. Phylogeny reconstruction of SiARFs by maximum likelihood and neighbor-joining trees revealed SiARFs could be divided into four clades. SiARFs clustered within the same clade shared similar gene structure and protein domain composition, implying functional redundancy. Moreover, amino acid composition of the middle regions was conserved in SiARFs belonged to the same clade. SiARFs were categorized into either activators or repressors according to the enrichment of specific amino acids. Intrinsic disorder was featured in the middle regions of ARF activators. Finally, expression profiles of SiARFs under hormone and abiotic stress treatment not only revealed their potential function in stress response but also indicate their functional redundancy. Overall, our results provide insights into evolutionary aspects of SiARFs and benefit for further functional characterization.

scholarly journals Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Pierre Baduel ◽  
Leandro Quadrana ◽  
Ben Hunter ◽  
Kirsten Bomblies ◽  
Vincent Colot
Keyword(s):  
Transposable Element ◽  
Local Adaptation ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Purifying Selection ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Environmentally Responsive ◽  
Main Driver ◽  
Whole Genome Resequencing

AbstractPolyploidization is frequently associated with increased transposable element (TE) content. However, what drives TE dynamics following whole genome duplication (WGD) and the evolutionary implications remain unclear. Here, we leverage whole-genome resequencing data available for ~300 individuals of Arabidopsis arenosa, a well characterized natural diploid-autotetraploid plant species, to address these questions. Based on 43,176 TE insertions we detect in these genomes, we demonstrate that relaxed purifying selection rather than transposition bursts is the main driver of TE over-accumulation after WGD. Furthermore, the increased pool of TE insertions in tetraploids is especially enriched within or near environmentally responsive genes. Notably, we show that the major flowering-time repressor gene FLC is disrupted by a TE insertion specifically in the rapid-cycling tetraploid lineage that colonized mainland railways. Together, our findings indicate that tetrasomy leads to an enhanced accumulation of genic TE insertions, some of which likely contribute to local adaptation.

scholarly journals A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event

GigaScience ◽  
2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Zheng Fan ◽  
Tao Yuan ◽  
Piao Liu ◽  
Lu-Yu Wang ◽  
Jian-Feng Jin ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Hox Genes ◽  
Genome Duplication ◽  
Duplication Event ◽  
Whole Genome ◽  
High Quality ◽  
Genome Duplication Event ◽  
Whole Genome Duplication Event ◽  
Chromosome Level

Abstract Background The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event. Results We present a chromosome-level T. antipodiana genome constructed on the basis of PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. Hi-C scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the T. antipodiana genome architecture reveals an ancient whole-genome duplication event, based on 2 lines of evidence: (i) large-scale duplications from inter-chromosome synteny analysis and (ii) duplicated clusters of Hox genes. Conclusions The high-quality T. antipodiana genome represents a valuable resource for spider research and provides insights into this species’ adaptation to the environment.

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

2017 ◽  
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.

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

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.

scholarly journals Coevolution of retroviruses with SERINCs following whole-genome duplication divergence

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.

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

PLoS ONE ◽  
2017 ◽  
Vol 12 (7) ◽  
pp. e0180936 ◽  
Author(s):  
Emilien Voldoire ◽  
Frédéric Brunet ◽  
Magali Naville ◽  
Jean-Nicolas Volff ◽  
Delphine Galiana
Keyword(s):  
Gene Family ◽  
Teleost Fish ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Sox Gene

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

Plants ◽  
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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