Genomic resources forGoniozus legneri,Aleochara bilineataandPaykullia maculata, representing three independent origins of the parasitoid lifestyle in insects

AbstractParasitoid insects are important model systems for a multitude of biological research topics and widely used as biological control agents against insect pests. While the parasitoid lifestyle has evolved numerous times in different insect groups, research has focused almost exclusively on Hymenoptera from the parasitica clade. The genomes of several members of this group have been sequenced, but no genomic resources are available from any of the other, independent evolutionary origins of the parasitoid lifestyle. Our aim here was to develop genomic resources for three parasitoid insects outside the parasitica. We present draft genome assemblies forGoniozus legneri, a parasitoid Hymenopteran more closely related to the non-parasitoid wasps and bees than to the parasitica wasps, the Coleopteran parasitoidAleochara bilineataand the Dipteran parasitoidPaykullia maculata.The genome assemblies are fragmented, but complete in terms of gene content. We also provide preliminary structural annotations. We anticipate that these genomic resources will be valuable for testing the generality of findings obtained from parasitica wasps in future comparative studies.Data availabilityThe Whole Genome Shotgun projects have been deposited at DDBJ/ENA/GenBank under the accessions NCVS00000000 (G. legneri), NBZA00000000 (A. bilineata) and NDXZ00000000 (P. maculata).The versions described in this paper are versions NCVS01000000, NBZA01000000 and NDXZ01000000, respectively. Mapped reads and genome annotations are available throughhttp://parasitoids.labs.vu.nl/parasitoids/. This website also includes genome browsers and viroblast instances for each genome.

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Draft Genome Assemblies and Annotations of Agrypnia Vestita Walker, and Hesperophylax Magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera)

Genome Biology and Evolution ◽

10.1093/gbe/evab013 ◽

2021 ◽

Author(s):

Lindsey K Olsen ◽

Jacqueline Heckenhauer ◽

John S Sproul ◽

Rebecca B Dikow ◽

Vanessa L Gonzalez ◽

...

Keyword(s):

Genome Size ◽

De Novo ◽

Draft Genome ◽

Freshwater Ecosystems ◽

Genomic Diversity ◽

Entire Genome ◽

Genomic Resources ◽

Genome Size Evolution ◽

Long Read ◽

Genome Assemblies

Abstract Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators. Knowledge on the genomic diversity of caddisflies can facilitate comparative and phylogenetic studies thereby allowing scientists to better understand the evolutionary history of caddisflies. While Trichoptera are the most diverse aquatic insect order, they remain poorly represented in terms of genomic resources. To date, all long-read based genomes have been sequenced from individuals in the retreat-making suborder, Annulipalpia, leaving ∼275 Ma of evolution without high-quality genomic resources. Here, we report the first long-read based de novo genome assemblies of two tube case-making Trichoptera from the suborder Integripalpia, Agrypnia vestita Walker and Hesperophylax magnus Banks. We find that these tube case-making caddisflies have genome sizes that are at least three-fold larger than those of currently sequenced annulipalpian genomes and that this pattern is at least partly driven by major expansion of repetitive elements. In H. magnus, long interspersed nuclear elements (LINEs) alone exceed the entire genome size of some annulipalpian counterparts suggesting that caddisflies have high potential as a model for understanding genome size evolution in diverse insect lineages.

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A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

BMC Genomics ◽

10.1186/s12864-019-6058-6 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 8

Author(s):

Jiorgos Kourelis ◽

Farnusch Kaschani ◽

Friederike M. Grosse-Holz ◽

Felix Homma ◽

Markus Kaiser ◽

...

Keyword(s):

Nicotiana Benthamiana ◽

Draft Genome ◽

Model Organism ◽

Functional Annotations ◽

Draft Genome Assembly ◽

Extracellular Proteome ◽

Protein Encoding ◽

Gene Models ◽

Genome Assemblies ◽

Encoding Genes

Abstract Background Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Results Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein-encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. Conclusions This proteome annotation provides the community working with Nicotiana benthamiana with an important new resource for functional proteomics.

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Homogenisation of a gridded snow water equivalent climatology for Alpine terrain: methodology and applications

The Cryosphere ◽

10.5194/tc-8-471-2014 ◽

2014 ◽

Vol 8 (2) ◽

pp. 471-485 ◽

Cited By ~ 16

Author(s):

S. Jörg-Hess ◽

F. Fundel ◽

T. Jonas ◽

M. Zappa

Keyword(s):

Land Surface ◽

Snow Water Equivalent ◽

Winter Season ◽

Data Availability ◽

Model Systems ◽

Added Value ◽

Data Sets ◽

Atmospheric Models ◽

Catchment Areas ◽

Snow Water

Abstract. Gridded snow water equivalent (SWE) data sets are valuable for estimating the snow water resources and verify different model systems, e.g. hydrological, land surface or atmospheric models. However, changing data availability represents a considerable challenge when trying to derive consistent time series for SWE products. In an attempt to improve the product consistency, we first evaluated the differences between two climatologies of SWE grids that were calculated on the basis of data from 110 and 203 stations, respectively. The "shorter" climatology (2001–2009) was produced using 203 stations (map203) and the "longer" one (1971–2009) 110 stations (map110). Relative to map203, map110 underestimated SWE, especially at higher elevations and at the end of the winter season. We tested the potential of quantile mapping to compensate for mapping errors in map110 relative to map203. During a 9 yr calibration period from 2001 to 2009, for which both map203 and map110 were available, the method could successfully refine the spatial and temporal SWE representation in map110 by making seasonal, regional and altitude-related distinctions. Expanding the calibration to the full 39 yr showed that the general underestimation of map110 with respect to map203 could be removed for the whole winter. The calibrated SWE maps fitted the reference (map203) well when averaged over regions and time periods, where the mean error is approximately zero. However, deviations between the calibrated maps and map203 were observed at single grid cells and years. When we looked at three different regions in more detail, we found that the calibration had the largest effect in the region with the highest proportion of catchment areas above 2000 m a.s.l. and that the general underestimation of map110 compared to map203 could be removed for the entire snow season. The added value of the calibrated SWE climatology is illustrated with practical examples: the verification of a hydrological model, the estimation of snow resource anomalies and the predictability of runoff through SWE.

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Cellular and Molecular Progression of Prostate Cancer: Models for Basic and Preclinical Research

Cancers ◽

10.3390/cancers12092651 ◽

2020 ◽

Vol 12 (9) ◽

pp. 2651 ◽

Cited By ~ 2

Author(s):

Sirin Saranyutanon ◽

Sachin Kumar Deshmukh ◽

Santanu Dasgupta ◽

Sachin Pai ◽

Seema Singh ◽

...

Keyword(s):

Prostate Cancer ◽

Racial Disparity ◽

Model Systems ◽

Basic Knowledge ◽

Biological Research ◽

Preclinical Research ◽

The Past ◽

Cancer Models ◽

Culture Models ◽

Prostate Cancer Research

We have witnessed noteworthy progress in our understanding of prostate cancer over the past decades. This basic knowledge has been translated into efficient diagnostic and treatment approaches leading to the improvement in patient survival. However, the molecular pathogenesis of prostate cancer appears to be complex, and histological findings often do not provide an accurate assessment of disease aggressiveness and future course. Moreover, we also witness tremendous racial disparity in prostate cancer incidence and clinical outcomes necessitating a deeper understanding of molecular and mechanistic bases of prostate cancer. Biological research heavily relies on model systems that can be easily manipulated and tested under a controlled experimental environment. Over the years, several cancer cell lines have been developed representing diverse molecular subtypes of prostate cancer. In addition, several animal models have been developed to demonstrate the etiological molecular basis of the prostate cancer. In recent years, patient-derived xenograft and 3-D culture models have also been created and utilized in preclinical research. This review is an attempt to succinctly discuss existing information on the cellular and molecular progression of prostate cancer. We also discuss available model systems and their tested and potential utility in basic and preclinical prostate cancer research.

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Draft Genome Assemblies of Xylose-Utilizing Candida tropicalis and Candida boidinii with Potential Application in Biochemical and Biofuel Production

Genome Announcements ◽

10.1128/genomea.01594-17 ◽

2018 ◽

Vol 6 (7) ◽

Cited By ~ 1

Author(s):

Abhishek Somani ◽

Daniel Smith ◽

Matthew Hegarty ◽

Narcis Fernandez-Fuentes ◽

Sreenivas R. Ravella ◽

...

Keyword(s):

Candida Tropicalis ◽

Potential Application ◽

Draft Genome ◽

Biofuel Production ◽

Candida Boidinii ◽

Industrial Biotechnology ◽

Genome Sequences ◽

Genome Assemblies

ABSTRACT Non- albicans Candida species are growing in prominence in industrial biotechnology due to their ability to utilize hemicellulose. Here, we present the draft genome sequences of an inhibitor-tolerant Candida tropicalis strain (Y6604) and Candida boidinii NCAIM Y01308 T .

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Draft genome of Santalum album L. provides genomic resources for accelerated trait improvement

Tree Genetics & Genomes ◽

10.1007/s11295-019-1334-9 ◽

2019 ◽

Vol 15 (3) ◽

Author(s):

Modhumita Ghosh Dasgupta ◽

Kandasamy Ulaganathan ◽

Suma Arun Dev ◽

Swathi Balakrishnan

Keyword(s):

Draft Genome ◽

Santalum Album ◽

Genomic Resources ◽

Trait Improvement ◽

Santalum Album L

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Public resources for chemical probes: the journey so far and the road ahead

Future Medicinal Chemistry ◽

10.4155/fmc-2019-0231 ◽

2019 ◽

Cited By ~ 3

Author(s):

Albert A Antolin ◽

Paul Workman ◽

Bissan Al-Lazikani

Keyword(s):

Small Molecule ◽

Specific Protein ◽

Data Availability ◽

Biological Research ◽

Chemical Probes ◽

The Road ◽

Expert Review ◽

Frequent Use ◽

Depth Analysis ◽

Public Resources

High-quality small molecule chemical probes are extremely valuable for biological research and target validation. However, frequent use of flawed small-molecule inhibitors produces misleading results and diminishes the robustness of biomedical research. Several public resources are available to facilitate assessment and selection of better chemical probes for specific protein targets. Here, we review chemical probe resources, discuss their current strengths and limitations, and make recommendations for further improvements. Expert review resources provide in-depth analysis but currently cover only a limited portion of the liganded proteome. Computational resources encompass more proteins and are regularly updated, but have limitations in data availability and curation. We show how biomedical scientists may use these resources to choose the best available chemical probes for their research.

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Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

PLoS Computational Biology ◽

10.1371/journal.pcbi.1003998 ◽

2014 ◽

Vol 10 (12) ◽

pp. e1003998 ◽

Cited By ~ 165

Author(s):

James F. Denton ◽

Jose Lugo-Martinez ◽

Abraham E. Tucker ◽

Daniel R. Schrider ◽

Wesley C. Warren ◽

...

Keyword(s):

Draft Genome ◽

Number Of Genes ◽

Genome Assemblies

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First High-Quality Draft Genome Sequence of Pasteurella multocida Sequence Type 128 Isolated from Infected Bone

Genome Announcements ◽

10.1128/genomea.00023-16 ◽

2016 ◽

Vol 4 (2) ◽

Cited By ~ 3

Author(s):

Niloofar Kavousi ◽

Wilhelm Wei Han Eng ◽

Yin Peng Lee ◽

Lian Huat Tan ◽

Ravindran Thuraisingham ◽

...

Keyword(s):

Genome Sequence ◽

Adult Female ◽

Pasteurella Multocida ◽

Draft Genome ◽

Sequence Type ◽

Domestic Dog ◽

Draft Genome Sequence ◽

High Quality ◽

Genomic Resources ◽

Valuable Addition

We report here the first high-quality draft genome sequence of Pasteurella multocida sequence type 128, which was isolated from the infected finger bone of an adult female who was bitten by a domestic dog. The draft genome will be a valuable addition to the scarce genomic resources available for P. multocida .

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