scholarly journals The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

2017 ◽  
Author(s):  
Evelyn E. Schwager ◽  
Prashant P. Sharma ◽  
Thomas Clarke ◽  
Daniel J. Leite ◽  
Torsten Wierschin ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Hox Genes ◽  
Genome Duplication ◽  
Whole Genome ◽  
Parasteatoda Tepidariorum ◽  
Evolutionary Diversification ◽  
Horseshoe Crabs ◽  
The Common ◽  
House Spider

AbstractThe duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neofunctionalization and/or subfunctionalization since their duplication, and therefore may have contributed to the diversification of spiders and other pulmonate arachnids.

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 Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication

2020 ◽  
Author(s):  
Wenyan Nong ◽  
Zhe Qu ◽  
Yiqian Li ◽  
Tom Barton-Owen ◽  
Annette Y.P. Wong ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Horseshoe Crab ◽  
Genome Duplication ◽  
Gene Families ◽  
Whole Genome ◽  
Breeding Programs ◽  
Horseshoe Crabs ◽  
The Common ◽  
Evolutionary Consequences ◽  
High Quality Genome

AbstractWhole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7Gb, N50 = 90.2Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7Gb, N50 = 109.7Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD, and that these WGD events are shared with spiders. Comparison of the genomes of C. rotundicauda and T. tridentatus populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for a better understanding of the consequences of invertebrate WGD events on evolutionary fates of genes and microRNAs at individual and population levels, and highlights the genetic diversity with practical values for breeding programs and conservation of horseshoe crabs.

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 De Novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication

2018 ◽  
Author(s):  
Zelin Chen ◽  
Yoshihiro Omori ◽  
Sergey Koren ◽  
Takuya Shirokiya ◽  
Takuo Kuroda ◽  
...  
Keyword(s):  
Carassius Auratus ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
De Novo ◽  
Close Relative ◽  
Whole Genome ◽  
Draft Sequence ◽  
Zebrafish Model ◽  
Goldfish Carassius Auratus ◽  
The Common

SummaryFor over a thousand years throughout Asia, the common goldfish (Carassius auratus) was raised for both food and as an ornamental pet. Selective breeding over more than 500 years has created a wide array of body and pigmentation variation particularly valued by ornamental fish enthusiasts. As a very close relative of the common carp (Cyprinus carpio), goldfish shares the recent genome duplication that occurred approximately 14-16 million years ago (mya) in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies is an exciting opportunity to link genotype to phenotype as well as understanding the dynamics of genome evolution and speciation. Here we generated a high-quality draft sequence of a “Wakin” goldfish using 71X PacBio long-reads. We identified 70,324 coding genes and more than 11,000 non-coding transcripts. We found that the two sub-genomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, “ohnologous” genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged significantly across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression across all tissues, while loss of conserved, non-coding elements determined expression variance between different tissues. This draft assembly also provides an important resource for comparative genomics with the very commonly used zebrafish model (Danio rerio), and for understanding the underlying genetic causes of goldfish variants.

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 Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs

Heredity ◽  
2015 ◽  
Vol 116 (2) ◽  
pp. 190-199 ◽  
Author(s):  
N J Kenny ◽  
K W Chan ◽  
W Nong ◽  
Z Qu ◽  
I Maeso ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Horseshoe Crabs

scholarly journals Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Wenyan Nong ◽  
Zhe Qu ◽  
Yiqian Li ◽  
Tom Barton-Owen ◽  
Annette Y. P. Wong ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Horseshoe Crab ◽  
Genome Duplication ◽  
Population Level ◽  
Gene Families ◽  
Whole Genome ◽  
Horseshoe Crabs ◽  
The Individual ◽  
Evolutionary Consequences ◽  
High Quality Genome

AbstractWhole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7 Gb, N50 = 90.2 Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7 Gb, N50 = 109.7 Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD. Comparison of C. rotundicauda and T. tridentatus genomes from populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for improving our understanding of invertebrate WGD events on the evolutionary fates of genes and microRNAs, at both the individual and population level. We also provide improved genomic resources for horseshoe crabs, of applied value for breeding programs and conservation of this fascinating and unusual invertebrate lineage.

scholarly journals Fossilized cell structures identify an ancient origin for the teleost whole-genome duplication

2021 ◽  
Vol 118 (30) ◽  
pp. e2101780118
Author(s):  
Donald Davesne ◽  
Matt Friedman ◽  
Armin D. Schmitt ◽  
Vincent Fernandez ◽  
Giorgio Carnevale ◽  
...  
Keyword(s):  
Genome Size ◽  
Whole Genome Duplication ◽  
Large Scale ◽  
Genome Duplication ◽  
Bone Cell ◽  
Whole Genome ◽  
Crown Group ◽  
Stem Group ◽  
Genome Size Evolution ◽  
Stem Lineage

Teleost fishes comprise one-half of all vertebrate species and possess a duplicated genome. This whole-genome duplication (WGD) occurred on the teleost stem lineage in an ancient common ancestor of all living teleosts and is hypothesized as a trigger of their exceptional evolutionary radiation. Genomic and phylogenetic data indicate that WGD occurred in the Mesozoic after the divergence of teleosts from their closest living relatives but before the origin of the extant teleost groups. However, these approaches cannot pinpoint WGD among the many extinct groups that populate this 50- to 100-million-y lineage, preventing tests of the evolutionary effects of WGD. We infer patterns of genome size evolution in fossil stem-group teleosts using high-resolution synchrotron X-ray tomography to measure the bone cell volumes, which correlate with genome size in living species. Our findings indicate that WGD occurred very early on the teleost stem lineage and that all extinct stem-group teleosts known so far possessed duplicated genomes. WGD therefore predates both the origin of proposed key innovations of the teleost skeleton and the onset of substantial morphological diversification in the clade. Moreover, the early occurrence of WGD allowed considerable time for postduplication reorganization prior to the origin of the teleost crown group. This suggests at most an indirect link between WGD and evolutionary success, with broad implications for the relationship between genomic architecture and large-scale evolutionary patterns in the vertebrate Tree of Life.

scholarly journals A high-resolution comparative atlas across 74 fish genomes illuminates teleost evolution after whole-genome duplication

2022 ◽  
Author(s):  
Elise Parey ◽  
Alexandra Louis ◽  
Jerome Monfort ◽  
Yann Guiguen ◽  
Hugues Roest Crollius ◽  
...  
Keyword(s):  
High Resolution ◽  
Teleost Fish ◽  
Whole Genome Duplication ◽  
Large Scale ◽  
Genome Duplication ◽  
Large Fraction ◽  
Whole Genome ◽  
History Of ◽  
Genomic Regions ◽  
Reference Genomes

Teleost fish are one of the most species-rich and diverse clades amongst vertebrates, which makes them an outstanding model group for evolutionary, ecological and functional genomics. Yet, despite a growing number of sequence reference genomes, large-scale comparative analysis remains challenging in teleosts due to the specifics of their genomic organization. As legacy of a whole genome duplication dated 320 million years ago, a large fraction of teleost genomes remain in duplicate paralogous copies. This ancestral polyploidy confounds the detailed identification of orthologous genomic regions across teleost species. Here, we combine tailored gene phylogeny methodology together with the state-of-the art ancestral karyotype reconstruction to establish the first high resolution comparative atlas of paleopolyploid regions across 74 teleost fish genomes. We show that this atlas represents a unique, robust and reliable resource for fish genomics. We then use the comparative atlas to study the tetraploidization and rediploidization mechanisms that affected the ancestor of teleosts. Although the polyploid history of teleost genomes appears complex, we uncover that meiotic recombination persisted between duplicated chromosomes for over 60 million years after polyploidization, suggesting that the teleost ancestor was an autotetraploid.

scholarly journals The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages and chelicerate genome architecture

2021 ◽  
Author(s):  
Guilherme Gainett ◽  
Vanessa L. González ◽  
Jesús A. Ballesteros ◽  
Emily V. W. Setton ◽  
Caitlin M. Baker ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Hox Genes ◽  
Genome Duplication ◽  
Draft Genome ◽  
Growth Factor Receptor ◽  
Single Copy ◽  
Developmental Genetics ◽  
Genome Architecture ◽  
Whole Genome ◽  
Duplication Events

AbstractChelicerates exhibit dynamic evolution of genome architecture, with multiple whole genome duplication events affecting groups like spiders, scorpions, and horseshoe crabs. Yet, genomes remain unavailable for several chelicerate orders, such as Opiliones (harvestmen), which has hindered comparative genomics and developmental genetics across arachnids. We assembled a draft genome of the daddy-long-legs Phalangium opilio, which revealed no signal of whole genome duplication. To test the hypothesis that single-copy Hox genes of the harvestman exhibit broader functions than subfunctionalized spider paralogs, we performed RNA interference against Deformed in P. opilio. Knockdown of Deformed incurred homeotic transformation of the two anterior pairs of walking legs into pedipalpal identity; by comparison, knockdown of the spatially restricted paralog Deformed-A in the spider affects only the first walking leg. To investigate the genetic basis for leg elongation and tarsomere patterning, we identified and interrogated the function of an Epidermal growth factor receptor (Egfr) homolog. Knockdown of Egfr incurred shortened appendages and the loss of distal leg structures. The overlapping phenotypic spectra of Egfr knockdown experiments in the harvestman and multiple insect models are striking because tarsomeres have evolved independently in these groups. Our results suggest a conserved role for Egfr in patterning distal leg structures across arthropods, as well as cooption of EGFR signaling in tarsomere patterning in both insects and arachnids. The establishment of genomic resources for P. opilio, together with functional investigations of appendage fate specification and distal patterning mechanisms, are key steps in understanding how daddy-long-legs make their long legs.

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