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 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 Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amit Rai ◽  
Hideki Hirakawa ◽  
Ryo Nakabayashi ◽  
Shinji Kikuchi ◽  
Koki Hayashi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Experimental Validation ◽  
Genome Duplication ◽  
Indole Alkaloids ◽  
Whole Genome ◽  
Comparative Genome Analysis ◽  
Plant Genomes ◽  
Genome Triplication ◽  
Chromosome Level

AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

scholarly journals Integrating transcriptomes to investigate genes associated with adaptation to aquatic environments, and assess phylogenetic conflict and whole-genome duplications in Alismatales

2021 ◽  
Author(s):  
Lingyun Chen ◽  
Bei Lu ◽  
Diego F. Morales-Briones ◽  
Michael L. Moody ◽  
Fan Liu ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Incomplete Lineage Sorting ◽  
Recent Common Ancestor ◽  
Aquatic Environments ◽  
Whole Genome ◽  
Freshwater Species ◽  
Freshwater Algae ◽  
Terrestrial Plants ◽  
Most Recent Common Ancestor

Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times beyond. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptation to aquatic environments by including 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptation, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as ((Tofieldiaceae, Araceae), core Alismatids). There is phylogenetic conflict among the backbone of the three main clades that could be due to incomplete lineage sorting and introgression. We identified 18 putative WGD events. One of them had occurred at the most recent common ancestor of core Alismatids, and four occurred at seagrass lineages. Other events are distributed in terrestrial, emergent, and submersed life-forms and seagrasses across Alismatales. We also found that lineage and life-form were each important for different evolutionary patterns for the genes related to freshwater/marine adaptation. For example, some light or ethylene-related genes were lost in the seagrass Zosteraceae, but present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments, phylogeny, and whole-genome duplication of Alismatales.

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 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 A high‐quality walnut genome assembly reveals extensive gene expression divergences after whole‐genome duplication

2020 ◽  
Vol 18 (9) ◽  
pp. 1848-1850 ◽  
Author(s):  
Junpei Zhang ◽  
Wenting Zhang ◽  
Feiyang Ji ◽  
Jie Qiu ◽  
Xiaobo Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
High Quality

scholarly journals Whole Genome Assembly and Annotation of Northern Wild Rice, Zizania palustris L., Supports a Whole Genome Duplication in the Zizania Genus

2021 ◽  
Author(s):  
Matthew Haas ◽  
Thomas Kono ◽  
Marissa Macchietto ◽  
Reneth Millas ◽  
Lillian McGilp ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Wild Rice ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Zizania Palustris

scholarly journals A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Ao Li ◽  
Ai Liu ◽  
Xin Du ◽  
Jin-Yuan Chen ◽  
Mou Yin ◽  
...  
Keyword(s):  
Medicago Sativa ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genomic Sequence ◽  
Close Relative ◽  
Whole Genome ◽  
Forage Crops ◽  
Genome Duplication Event ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractAlfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Based on Illumina, Nanopore and Hi-C data, we assembled a chromosome-scale assembly of Medicago sativa spp. caerulea (voucher PI464715), the direct diploid progenitor of autotetraploid alfalfa. The assembled genome comprises 793.2 Mb of genomic sequence and 47,202 annotated protein-coding genes. The contig N50 length is 3.86 Mb. This genome is almost twofold larger and contains more annotated protein-coding genes than that of its close relative, Medicago truncatula (420 Mb and 44,623 genes). The more expanded gene families compared with those in M. truncatula and the expansion of repetitive elements rather than whole-genome duplication (i.e., the two species share the ancestral Papilionoideae whole-genome duplication event) may have contributed to the large genome size of M. sativa spp. caerulea. Comparative and evolutionary analyses revealed that M. sativa spp. caerulea diverged from M. truncatula ~5.2 million years ago, and the chromosomal fissions and fusions detected between the two genomes occurred during the divergence of the two species. In addition, we identified 489 resistance (R) genes and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.

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 Whole Genome Assembly and Annotation of Northern Wild Rice, Zizania palustris L., Supports a Whole Genome Duplication in the Zizania Genus

2021 ◽  
Author(s):  
Matthew Haas ◽  
Thomas Kono ◽  
Marissa Macchietto ◽  
Reneth Millas ◽  
Lillian McGilp ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Assembly ◽  
Wild Rice ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
The United States ◽  
Whole Genome ◽  
Important Species ◽  
Zizania Palustris ◽  
Speciation Event

ABSTRACTNorthern Wild Rice (NWR; Zizania palustris L.) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural, and agricultural significance, specifically in the Great Lakes region of the United States. Using long- and short-range sequencing, Hi-C scaffolding, and RNA-seq data from eight tissues, we generated an annotated whole genome de novo assembly of NWR. The assembly is 1.29 Gb, highly repetitive (∼76.0%), and contains 46,421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole genome duplication prior to the Zizania-Oryza speciation event have both led to an increase in genome size of NWR in comparison with O. sativa and Z. latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed conservation of large syntenic blocks with Oryza sativa L., which were used to identify putative seed shattering genes. Estimates of divergence times revealed the Zizania genus diverged from Oryza ∼26-30 million years ago (MYA), while NWR and Zizania latifolia diverged from one another ∼6-8 MYA. Comparative genomics confirmed evidence of a whole genome duplication in the Zizania genus and provided support that the event was prior to the NWR-Z. latifolia speciation event. This high-quality genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.

Sign in / Sign up

Export Citation Format

Share Document