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 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 Diversified regulation of circadian clock gene expression following whole genome duplication

PLoS Genetics ◽  
2020 ◽  
Vol 16 (10) ◽  
pp. e1009097
Author(s):  
Alexander C. West ◽  
Marianne Iversen ◽  
Even H. Jørgensen ◽  
Simen R. Sandve ◽  
David G. Hazlerigg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Whole Genome Duplication ◽  
Clock Gene ◽  
Genome Duplication ◽  
Whole Genome ◽  
Circadian Clock Gene ◽  
Clock Gene Expression

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 Effects of whole genome duplication on cell size and gene expression in mouse embryonic stem cells

2016 ◽  
Vol 62 (6) ◽  
pp. 571-576 ◽  
Author(s):  
Hiroyuki IMAI ◽  
Wataru FUJII ◽  
Ken Takeshi KUSAKABE ◽  
Yasuo KISO ◽  
Kiyoshi KANO
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Cell Size ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Whole Genome

scholarly journals Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome

2017 ◽  
Vol 328 (7) ◽  
pp. 709-721 ◽  
Author(s):  
Jeremy Pasquier ◽  
Ingo Braasch ◽  
Peter Batzel ◽  
Cedric Cabau ◽  
Jérome Montfort ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Spotted Gar

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 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.

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 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.

Sign in / Sign up

Export Citation Format

Share Document