scholarly journals Frequent ploidy changes in Salicaceae indicates widespread sharing of the salicoid whole genome duplication by the relatives of Populus L. and Salix L.

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhong-Shuai Zhang ◽  
Qing-Yin Zeng ◽  
Yan-Jing Liu
Keyword(s):  
Genome Size ◽  
Whole Genome Duplication ◽  
Woody Plant ◽  
Genome Duplication ◽  
Nuclear Dna ◽  
Plant Traits ◽  
Populus Euphratica ◽  
Nuclear Dna Content ◽  
Whole Genome ◽  
Ploidy Changes

Abstract Backgrounds Populus and Salix belong to Salicaceae and are used as models to investigate woody plant physiology. The variation of karyotype and nuclear DNA content can partly reflect the evolutionary history of the whole genome, and can provide critical information for understanding, predicting, and potentially ameliorating the woody plant traits. Therefore, it is essential to study the chromosome number (CN) and genome size in detail to provide information for revealing the evolutionary process of Salicaceae. Results In this study, we report the somatic CNs of seventeen species from eight genera in Salicaceae. Of these, CNs for twelve species and for five genera are reported for the first time. Among the three subfamilies of Salicaceae, the available data indicate CN in Samydoideae is n = 21, 22, 42. The only two genera, Dianyuea and Scyphostegia, in Scyphostegioideae respectively have n = 9 and 18. In Salicoideae, Populus, Salix and five genera closely related to them (Bennettiodendron, Idesia, Carrierea, Poliothyrsis, Itoa) are based on relatively high CNs from n = 19, 20, 21, 22 to n = 95 in Salix. However, the other genera of Salicoideae are mainly based on relatively low CNs of n = 9, 10, 11. The genome sizes of 35 taxa belonging to 14 genera of Salicaceae were estimated. Of these, the genome sizes of 12 genera and all taxa except Populus euphratica are first reported. Except for Dianyuea, Idesia and Bennettiodendron, all examined species have relatively small genome sizes of less than 1 pg, although polyploidization exists. Conclusions The variation of CN and genome size across Salicaceae indicates frequent ploidy changes and a widespread sharing of the salicoid whole genome duplication (WGD) by the relatives of Populus and Salix. The shrinkage of genome size after WGD indicates massive loss of genomic components. The phylogenetic asymmetry in clade of Populus, Salix, and their close relatives suggests that there is a lag-time for the subsequent radiations after the salicoid WGD event. Our results provide useful data for studying the evolutionary events of Salicaceae.

scholarly journals A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
David A. Ayala-Usma ◽  
Martha Cárdenas ◽  
Romain Guyot ◽  
Maryam Chaib De Mares ◽  
Adriana Bernal ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Phytophthora Infestans ◽  
Genome Size ◽  
Whole Genome Duplication ◽  
Plant Pathogens ◽  
Genome Duplication ◽  
Sister Group ◽  
Whole Genome ◽  
Long Read ◽  
Etiological Agents

Abstract Background Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology. Results Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270 Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens. Conclusions This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c.

scholarly journals Spontaneous whole-genome duplication restores fertility in interspecific hybrids

2019 ◽  
Author(s):  
Guillaume Charron ◽  
Souhir Marsit ◽  
Mathieu Hénault ◽  
Hélène Martin ◽  
Christian R. Landry
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Mitotic Cell ◽  
Whole Genome ◽  
Hybrid Speciation ◽  
Evolutionary Potential ◽  
Interspecies Hybrids ◽  
Ploidy Changes ◽  
Established Species ◽  
Fertility Recovery

AbstractInterspecies hybrids often show advantages over parents but suffer from reduced fertility, which can sometimes be overcome through sexual reproduction that sorts out incompatibilities. Sex is however inefficient due to the low viability or fertility of hybrid offspring and thus limits their evolutionary potential. Mitotic cell division could be an alternative to fertility recovery in facultative sexual species. To test this, we evolved under relaxed selection more than 600 diploid yeast hybrids between species that span 100,000 to 15 M years of divergence. We find that hybrids can recover fertility spontaneously and rapidly through whole-genome duplication. These events occurred in both hybrids between young and well-established species. Our results show that the instability of hybrid ploidy is a spontaneous path to fertility recovery.One Sentence SummaryPloidy changes potentiate hybrid speciation by leading to fertility recovery.

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 Two ancient genome duplication events shape diversity in Hibiscus L. (Malvaceae)

2020 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Genome Size ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Genome Doubling ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole genome duplication events, we tested a series of scenarios describing different polyploidization events.Results: Using target sequence capture, we generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. Species of Hibiscus shared one genome duplication with H. syriacus and one whole genome duplication occurred along the branch leading to H. syriacus.Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Le Zhang ◽  
Jingtian Zhao ◽  
Hao Bi ◽  
Xiangyu Yang ◽  
Zhiyang Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Populus Euphratica ◽  
Epigenetic Modifications ◽  
Chromatin Organization ◽  
Whole Genome ◽  
Duplicated Genes

AbstractThe nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.

scholarly journals Retrotransposon proliferation coincident with the evolution of dioecy in Asparagus

2016 ◽  
Author(s):  
Alex Harkess ◽  
Francesco Mercati ◽  
Loredana Abbate ◽  
Michael McKain ◽  
J. Chris Pires ◽  
...  
Keyword(s):  
Genome Size ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Sex Chromosome ◽  
Duplication Event ◽  
Whole Genome ◽  
Dioecious Species ◽  
Genome Duplication Event ◽  
Chromosome Fusion ◽  
Whole Genome Duplication Event

AbstractCurrent phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n=2x=20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion or retrotransposon proliferation in dioecious species. We first estimate genome sizes or use published values for four hermaphrodites and four dioecious species distributed across the phylogeny and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements in particular have undergone a marked proliferation in dioecious species. In the absence of a detectable whole genome duplication event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species.

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 very recent whole genome duplication in Potamopyrgus antipodarum predates multiple origins of asexuality & associated polyploidy

2017 ◽  
Author(s):  
John Logsdon ◽  
Maurine Neiman ◽  
Jeffrey Boore ◽  
Joel Sharbrough ◽  
Laura Bankers ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Potamopyrgus Antipodarum ◽  
Recent Common Ancestor ◽  
Close Relative ◽  
Whole Genome ◽  
Evolutionary Trajectory ◽  
Initial Genome

Potamopyrgus antipodarum, a New Zealand freshwater snail, is a powerful system to study the maintenance of sexual reproduction. Obligate asexual P. antipodarum (herein, Pa) lineages include both triploids and tetraploids that are products of multiple separate transitions from diploid sexual ancestors. Distinct diploid sexual and polyploid asexual lineages coexist and compete; these separate lineages can be considered replicated natural experiments. We have shown that harmful mutations are accumulating at a higher rate in asexual than in sexual Pa, demonstrating the utility of this system as a model for investigating the evolution of sex at the genomic level. In order to better understand the causes and consequences of transitions to asexuality, we have sequenced multiple genomes and transcriptomes of Pa and a close relative, P. estuarinus (herein, Pe) a diploid sexual species. The diploid genome size of Pe is ~0.6X of the genome size of diploid Pa, inspiring us to investigate whether the most recent common ancestor of Pa had experienced a whole-genome duplication (WGD) event prior to the diversification of its many sexual and asexual lineages. In addition to its clear relevance to understanding the evolutionary history of this species, by being so recent, this apparent WGD will also be especially powerful in understanding events immediately following WGD. Our initial genome assembly of a model sexual Pa lineage was consistent with this possibility, indicating high fractions (~35%) of scaffolds containing extended, nearly identical, duplicated regions. This result also partly explains our general difficulty with assembling the genome, despite generating >100X genome coverage using multiple methodologies. Even considering the limitations of our current genome assembly, we used the assembly to test a series of predictions under the hypothesis of recent whole-genome duplication, all of which are consistent with WGD. These tests have shown: 1) a marked excess of duplicated copies of genes in Pa which are maintained in single copy in other animals, 2) implausibly high "heterozygosity" estimates in our model Pa sexual genome, presumably resulting from non-allelic comparisons, 3) higher sequence identity between thousands of Pa-specific paralogous genes, when compared to their Pe orthologs. These and additional lines of evidence will be presented and evaluated. Together, our results suggest that this initial genome-wide duplication event might have played a key role in the subsequent evolutionary trajectory of this species, potentially facilitating its repeated diversification into multiple asexual lineages. We are now generating additional long-range genome scaffolds for Pa using multiple methods, as well as improving the coverage and quality of the Pe genome. We will use these new data to conduct definitive phylogenomic tests of this especially remarkable whole genome duplication.

scholarly journals Estimation of nuclear genome size of the genus Mycetophylax Emery, 1913: Evidence of no whole-genome duplication in Neoattini

2012 ◽  
Vol 335 (10-11) ◽  
pp. 619-624 ◽  
Author(s):  
Danon Clemes Cardoso ◽  
Carlos Roberto Carvalho ◽  
Maykon Passos Cristiano ◽  
Fernanda Aparecida Ferrari Soares ◽  
Mara Garcia Tavares
Keyword(s):  
Genome Size ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Nuclear Genome ◽  
Whole Genome

scholarly journals Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities

mSystems ◽  
2022 ◽  
Author(s):  
Julian C. B. Ponsford ◽  
Charley J. Hubbard ◽  
Joshua G. Harrison ◽  
Lois Maignien ◽  
C. Alex Buerkle ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Whole Genome Duplication ◽  
Evolutionary History ◽  
Genome Duplication ◽  
Plant Traits ◽  
Whole Genome ◽  
Genetic Determinants ◽  
Host Genotype ◽  
Duplication Events ◽  
History Of

Plants influence the composition of their associated microbial communities, yet the underlying host-associated genetic determinants are typically unknown. Genome duplication events are common in the evolutionary history of plants and affect many plant traits.

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