93 Works

Data from: A DNA barcode library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae)

Zhaofu Yang, Jean-François Landry & Paul D. N. Hebert
Although members of the crambid subfamily Pyraustinae are frequently important crop pests, their identification is often difficult because many species lack conspicuous diagnostic morphological characters. DNA barcoding employs sequence diversity in a short standardized gene region to facilitate specimen identifications and species discovery. This study provides a DNA barcode reference library for North American pyraustines based upon the analysis of 1589 sequences recovered from 137 nominal species, 87% of the fauna. Data from 125 species...

Autopolyploidy-driven range expansion of a temperate-originated plant to pan-tropic under global change

Jiliang Cheng, Jun Li, Zheng Zhang, Huan Lu, Guoqi Chen, Beibei Yao, Yingxue Dong, Ling Ma, Xiaoxiao Yuan, Jingxuan Xu, Ying Zhang, Weimin Dai, Xianghong Yang, Lifang Xue, Yu Zhang, Chaobin Zhang, Rodney Mauricio, Gary Peng, Shuijin Hu, Bernal Valverde, Xiaoling Song, Yi Li, Marc Stift & Sheng Qiang
Angiosperms are believed to have emerged initially in the tropics and expanded their distribution range polewards through diverse mechanisms, for example polyploidization-driven cold-tolerance evolution. Reversed expansion from temperate to pantropic climate through a polyploidization-driven shift in heat-tolerance remains largely unknown. Here, we found autopolyploidy in relation to the global expansion of Solidago canadensis from its temperate-climate native range in North American to hot-summer climate in an introduced range. Our cytogeographical study of 2062 accessions from...

Core genome phylogenetic tree of two Campylobacter novaezeelandiae and four unclassified thermophilic Campylobacter isolates from Canadian agricultural surface water

Mirena Ivanova, Bonnie Oh, Izhar Khan, Kendra Nightingale, Marie Bugarel, Amanda Brown & Guy Loneragan
This dataset includes 1) concatenated alignment of 135 core gene sequences and 2) phylogenomic tree of the 38 currently described Campylobacter spp., including Campylobacter novaezeelandiae and four additional novel Campylobacter species isolated from agricultural water in Canada. The original alignment of 120 kb was produced by Roary v.3.13.0. Gblocks v.0.91b was used to remove ambiguous alignments and phylogenetically uninformative positions. The final alignment (110 kb) was used as input to RAxML-NG v.0.9.0 to infer a...

Experimental variation in the spatial deposition of trace metals in feathers revealed using synchrotron x-ray fluorescence

Fardausi Akhter, Graham Fairhurst, Peter Blanchard, Karen Machin, Rob Blyth, Julie Thompson, Jamille McLeod, Renfei Feng & Catherine Soos
Feathers can be used to investigate exposure to pollution in birds because they are a secondary route for the excretion of trace elements. Evidence based on analytical imaging and spectroscopy suggests that the spatial distribution of the essential trace element zinc within feathers is related to melanin pigmentation. However, our understanding of how trace elements are deposited into growing feathers is poor and has been hampered by a lack of analytical tools to examine the...

Additional file 2 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

Shiye Sang, Wen Chen, Di Zhang, Xuan Zhang, Wenjing Yang & Changning Liu
Additional file 2. Conserved lncRNAs ratios for each species.

SolCAP 8K array genotyping of population 15143

Helen Tai, Sai Reddy Achakkagari, Maria Kyriakidou, Kyle Gardner, David De Koeyer, Hielke De Jong & Martina Stromvik
The dataset is a tab-deliminted text file with genotyping information for a diploid potato progeny population derived from a cross of diploid potato clones 12120-03 X 07506-01. The SolCap 8303 Infinium Chip was used for SNP genotyping. It was originally generated for study on genetic mapping of Verticillium wilt resistance. The data was used again for analysis of segregation distortion in the most recent manuscript.

Data from: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium

Hai D. T. Nguyen, Annette Dodge, Kasia Dadej, Tara L. Rintoul, Ekaterina Ponomareva, Frank N. Martin, Arthur W. A. M. De Cock, C. Andre Levesque, Scott A. Redhead & Christoffel F. J. Spies
The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1–D2 domains of nuc 28S rDNA. Although...

Genetic structure and genome-wide association study of a genomic panel of two-row, spring barley (Hordeum vulgare L.) with differential reaction to Fusarium head blight (Fusarium graminearum Schwabe) and deoxynivalenol production

James R. Tucker, Anita L. Brûlé-Babel, Colin W. Hiebert, Roger Larios, William G. Legge, Ana Badea & W. G. Dilantha Fernando
Fusarium head blight (FHB), primarily incited by Fusarium graminearum Schwabe, is the most devastating disease of barley (Hordeum vulgare L.) in Canada. Contaminated grains are unsuitable for use as livestock feed or by the malting industry, primarily due to contamination by mycotoxins such as deoxynivalenol (DON). Reducing DON content has been a long-term goal of barley breeders; however, the complex genetics of resistance and laborious testing required have made it difficult to develop resistant cultivars....

New molecular markers for distinguishing the main phylogenetic lineages within Alternaria section Alternaria

Jeremy R. Dettman & Quinn Eggertson
Several members of Alternaria section Alternaria are economically important plant-pathogenic fungi that cause disease on a wide range of host types and plant tissues. The production of Alternaria-derived mycotoxins can lead to significant post-harvest losses due to contamination of agricultural products. Multiple Alternaria species are listed as regulated organisms, which are monitored by international plant protection programmes. These taxa often share high levels of both morphological and phylogenetic similarity, and the establishment of molecular markers...

Additional file 1 of The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Hiba Mohammed Taha, Reza Aalizadeh, Nikiforos Alygizakis, Jean-Philippe Antignac, Hans Peter H. Arp, Richard Bade, Nancy Baker, Lidia Belova, Lubertus Bijlsma, Evan E. Bolton, Werner Brack, Alberto Celma, Wen-Ling Chen, Tiejun Cheng, Parviel Chirsir, Ľuboš Čirka, Lisa A. D’Agostino, Yannick Djoumbou Feunang, Valeria Dulio, Stellan Fischer, Pablo Gago-Ferrero, Aikaterini Galani, Birgit Geueke, Natalia Głowacka, Juliane Glüge … & Emma L. Schymanski
Additional file 1: Summary of the NORMAN-SLE datasets (CSV format) as of 4 May 2022 [81].

Additional file 7 of Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

Mengqi Wang, Nathalie Bissonnette, Mario Laterrière, Pier-Luc Dudemaine, David Gagné, Jean-Philippe Roy, Xin Zhao, Marc-André Sirard & Eveline M. Ibeagha-Awemu
Additional file 7: Table S2. Read mapping statistics of whole-genome bisulfite sequencing data and RNA sequencing data of six cows.

Additional file 17 of Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

Mengqi Wang, Nathalie Bissonnette, Mario Laterrière, Pier-Luc Dudemaine, David Gagné, Jean-Philippe Roy, Xin Zhao, Marc-André Sirard & Eveline M. Ibeagha-Awemu
Additional file 17: Table S12. The cluster of functional annotations enriched by differential methylated and expressed genes (MetGDE genes).

Additional file 10 of The pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB

Ryan Gourlie, Megan McDonald, Mohamed Hafez, Rodrigo Ortega-Polo, Kristin E. Low, D. Wade Abbott, Stephen E. Strelkov, Fouad Daayf & Reem Aboukhaddour
Additional file 10. List of GenBank accession numbers associated with the genomes generated by this study and of the genomes downloaded and used for comparison.

Additional file 10 of Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

Mengqi Wang, Nathalie Bissonnette, Mario Laterrière, Pier-Luc Dudemaine, David Gagné, Jean-Philippe Roy, Xin Zhao, Marc-André Sirard & Eveline M. Ibeagha-Awemu
Additional file 10: Table S5. The list of DMRs and annotation.

Additional file 11 of Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

Mengqi Wang, Nathalie Bissonnette, Mario Laterrière, Pier-Luc Dudemaine, David Gagné, Jean-Philippe Roy, Xin Zhao, Marc-André Sirard & Eveline M. Ibeagha-Awemu
Additional file 11: Table S6. The list of genes harboring DMCs or overlapping with DMRs.

Additional file 13 of Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

Mengqi Wang, Nathalie Bissonnette, Mario Laterrière, Pier-Luc Dudemaine, David Gagné, Jean-Philippe Roy, Xin Zhao, Marc-André Sirard & Eveline M. Ibeagha-Awemu
Additional file 13: Table S8. The list of differentially methylated haplotype blocks (dMHBs) and functional enrichment for hyper dMHBs.

Annotated VCF of 192 Verticillium dahliae isolates

Benjamin Mimee, Joel Lafond-Lapalme & Mario Tenuta
Verticillium dahliae is an important soil-borne pathogen causing Verticillium wilt. It is also the primary causal agent of the Potato Early Dying, a disease complex involving the root-lesion nematode. Here, we report the whole-genome sequencing of 192 isolates of V. dahliae originating from the major potato production areas across Canada. Our results yielded a resource of 259,497 SNPs that will be useful for genetic analyses and revealed the presence of two major lineages, both present...

Data from: A scenario for the evolution of selective egg colouration: the roles of enemy-free space, camouflage, thermoregulation, and pigment limitation

Inmaculada Torres-Campos, Paul K. Abram, Eric Guerra-Grenier, Guy Boivin & Jacques Brodeur
Behavioural plasticity can drive the evolution of new traits in animals. In oviparous species, plasticity in oviposition behaviour could promote the evolution of new egg traits by exposing them to different selective pressures in novel oviposition sites. Individual females of the predatory stink bug Podisus maculiventris are able to selectively colour their eggs depending on leaf side, laying lightly pigmented eggs on leaf undersides and more pigmented eggs, which are more resistant to ultraviolet (UV)...

Data from: Hybridization rate and hybrid fitness for Camelina microcarpa Andrz. ex DC (♀) and Camelina sativa (L.) Crantz(Brassicaceae) (♂)

Sara L. Martin, Beatriz E. Lujan-Toro, Connie A. Sauder, Tracey James, Sara Ohadi & Linda M. Hall
Hybridization between crops and their wild relatives has the potential to introduce novel variation into wild populations. Camelina (Camelina sativa) is a promising oilseed and cultivars with modified seed characteristics and herbicide resistance are in development, prompting a need to evaluate the potential for novel trait introgression into weedy relatives. Little-podded false flax (littlepod; Camelina microcarpa) is a naturalized weed in Canada and the USA. Here we evaluated the hybridization rate between the three cytotypes...

Additional file 2 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

Shiye Sang, Wen Chen, Di Zhang, Xuan Zhang, Wenjing Yang & Changning Liu
Additional file 2. Conserved lncRNAs ratios for each species.

Additional file 4 of Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants

Shiye Sang, Wen Chen, Di Zhang, Xuan Zhang, Wenjing Yang & Changning Liu
Additional file 4 Significant enrichment functions (n = 39) of conserved lncRNA set (n = 196).

Raw data on acceptance and emergence in intrinsic competition experiments, and guarding behavior in extrinsic competition: Trissolcus cultratus and Trissolcus japonicus

Tara Gariepy
Understanding competition between scelionid parasitoids that exploit the same host may provide insight into strategies that allow co-existence on a shared resource. Competition studies typically focus on interactions between native and exotic parasitoids that do not share an evolutionary history; however, co-evolved parasitoids may be more likely to demonstrate strategies to avoid or exploit a shared resource. We examined intrinsic and extrinsic competition between Asian Trissolcus japonicus Ashmead and T. cultratus Mayr (Hymenoptera: Scelionidae) associated...

A horizontally transmitted Parasitoid Killing Factor protects insects from parasitoids

Martin Erlandson, Edyta Sieminska, Cathy Coutu, Dwayne Hegedus, David Theilmann, Doug Baldwin & Stephanie Harris
Interkingdom competition occurs between hymenopteran parasitoids and insect viruses sharing the same insect hosts. It has been assumed that parasitoid larvae die with the death of infected host or as result of competition for host resources. Herein we describe a gene family, parasitoid killing factor (pkf), that encodes proteins toxic to parasitoids of the Microgastrinae group and determines parasitism success. Pkfs are found in several entomopathogenic DNA virus families and in some lepidopteran genomes. We...

Phylogeny, classification, and character evolution of Acalypha (Euphorbiaceae Acalyphoideae)

Geoffrey Levin, Warren M. Cardinal-McTeague, Victor W. Steinmann & Vernie G. Sagun
Acalypha (Euphorbiaceae Acalyphoideae) is a large, monophyletic genus distributed worldwide in tropical and subtropical regions, with a few species extending into temperate Asia and North America. We reconstructed phylogenetic relationships within the genus using DNA sequences from the plastid ndhF and trnL-F regions and the nuclear ribosomal ITS region, sampling 143 species to represent the geographic, morphologic, and taxonomic diversity with the genus, resulting in a 162 (158 in Acalypha) terminal and 3847 character combined...

Genetic structure and genome-wide association study of a genomic panel of two-row, spring barley (Hordeum vulgare L.) with differential reaction to Fusarium head blight (Fusarium graminearum Schwabe) and deoxynivalenol production

James R. Tucker, Anita L. Brûlé-Babel, Colin W. Hiebert, Roger Larios, William G. Legge, Ana Badea & W. G. Dilantha Fernando
Fusarium head blight (FHB), primarily incited by Fusarium graminearum Schwabe, is the most devastating disease of barley (Hordeum vulgare L.) in Canada. Contaminated grains are unsuitable for use as livestock feed or by the malting industry, primarily due to contamination by mycotoxins such as deoxynivalenol (DON). Reducing DON content has been a long-term goal of barley breeders; however, the complex genetics of resistance and laborious testing required have made it difficult to develop resistant cultivars....

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