Sequencing and de novo draft assemblies of a fathead minnow (Pimephales promelas) reference genome

2015 ◽  
Vol 35 (1) ◽  
pp. 212-217 ◽  
Author(s):  
Frank R. Burns ◽  
Amarin L. Cogburn ◽  
Gerald T. Ankley ◽  
Daniel L. Villeneuve ◽  
Eric Waits ◽  
...  
Keyword(s):  
Fathead Minnow ◽  
Reference Genome ◽  
De Novo ◽  
Pimephales Promelas

scholarly journals De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure

2021 ◽  
Author(s):  
John Martinson ◽  
David C. Bencic ◽  
Gregory P. Toth ◽  
Mitchell S. Kostich ◽  
Robert W. Flick ◽  
...  
Keyword(s):  
Gene Structure ◽  
Fathead Minnow ◽  
Reference Genome ◽  
De Novo ◽  
Gene Annotation ◽  
Pimephales Promelas ◽  
Single Copy ◽  
Model Organisms ◽  
Coding Regions ◽  
Genomic Resource

ABSTRACTThe Fathead Minnow (FHM) is one of the most important and widely used model organisms in aquatic toxicology. The lack of a high-quality and well-annotated FHM reference genome, however, has severely hampered the efforts using modem ‘omics approaches with FHM for environmental toxicogenomics studies. We present here a de novo assembled and nearly complete reference of the fathead minnow genome. Compared to the current fragmented and sparsely annotated FHM genome assembly (FHM1), the new highly contiguous and well-annotated FHM reference genome (FHM2) represents a major improvement, having 95.1% of the complete BUSCOs (Benchmarking Universal Single-Copy Orthologs) and a scaffold N50 of 12.0 Mbps. The completeness of gene annotation for the FHM2 reference genome was demonstrated to be comparable to that of the zebrafish (ZF) GRCz11 reference genome. In addition, our comparative genomics analyses between FHM and ZF revealed highly conserved coding regions between two species while discovering much more compact gene structure in FHM than ZF. This study not only provides insights for assembling a highly repetitive AT-rich genome, but also delivers a critical genomic resource essential for toxicogenomics studies in environmental toxicology.

De Novo Assembly of the Nearly Complete Fathead Minnow Reference Genome Reveals a Repetitive But Compact Genome

2021 ◽  
Author(s):  
John W. Martinson ◽  
David C. Bencic ◽  
Gregory P. Toth ◽  
Mitchell S. Kostich ◽  
Robert W. Flick ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Fathead Minnow ◽  
Reference Genome ◽  
De Novo

Responses in a Fathead Minnow (Pimephales promelas) Lifecycle Test and in Wild White Sucker (Catostomus commersoni) Exposed to a Canadian Bleached Kraft Mill Effluent

2010 ◽  
Vol 45 (2) ◽  
pp. 187-200 ◽  
Author(s):  
Joanne L. Parrott ◽  
L. Mark Hewitt ◽  
Tibor G. Kovacs ◽  
Deborah L. MacLatchy ◽  
Pierre H. Martel ◽  
...  
Keyword(s):  
Egg Production ◽  
Fathead Minnow ◽  
Pimephales Promelas ◽  
Fish Reproduction ◽  
White Sucker ◽  
Catostomus Commersoni ◽  
Liver Size ◽  
Paper Mill Effluent ◽  
Kraft Mill Effluent ◽  
Kraft Mill

Abstract To evaluate currently available bioassays for their use in investigating the causes of pulp and paper mill effluent effects on fish reproduction, the responses of wild white sucker (Catostomus commersoni) collected from the receiving environment at the bleached kraft mill at La Tuque, Quebec, were compared with responses of fathead minnow (Pimephales promelas) exposed to effluent in a laboratory lifecycle test. White sucker collected at effluent exposed sites had increased liver size but none of the reproductive effects that had been documented in earlier field studies at this site. Exposure to 1, 3, 10, 30, and 100% bleached kraft mill effluent (BKME) in the lab led to significantly decreased length, but increased weight and liver size in male fathead minnow. Female length was also decreased and liver size was increased at high effluent exposures. Most effluent concentrations (1 to 30%) significantly increased egg production compared with controls. The fathead minnow lifecycle assay mirrored the effects seen in wild fish captured downstream of the BKME discharge. These results will be used to select short-term fish tests for investigating the causes of and solutions to the effects of mill effluents on fish reproduction.

scholarly journals Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 904
Author(s):  
Saif ur Rehman ◽  
Faiz-ul Hassan ◽  
Xier Luo ◽  
Zhipeng Li ◽  
Qingyou Liu
Keyword(s):  
Selective Breeding ◽  
Reference Genome ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Genomic Diversity ◽  
Production Performance ◽  
Phylogeographic Structure ◽  
Economic Significance ◽  
And Performance

The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

scholarly journals nLethal and sublethal effects of diluted bitumen and conventional oil on fathead minnow (Pimephales promelas) larvae exposed during their early development

2021 ◽  
pp. 105884
Author(s):  
Roxanne Bérubé ◽  
Charles Gauthier ◽  
Thibault Bourdin ◽  
Marilou Bouffard ◽  
Gaëlle Triffault-Bouchet ◽  
...  
Keyword(s):  
Early Development ◽  
Fathead Minnow ◽  
Sublethal Effects ◽  
Pimephales Promelas ◽  
Conventional Oil

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

Environmental Gestagens Activate Fathead Minnow (Pimephales promelas) Nuclear Progesterone and Androgen Receptors in Vitro

2014 ◽  
Vol 48 (14) ◽  
pp. 8179-8187 ◽  
Author(s):  
Laura E. Ellestad ◽  
Mary Cardon ◽  
Ian G. Chambers ◽  
Jennifer L. Farmer ◽  
Phillip Hartig ◽  
...  
Keyword(s):  
Fathead Minnow ◽  
Androgen Receptors ◽  
Pimephales Promelas

Effects of Long-Term Exposure to Carbaryl (Sevin) on Survival, Growth, and Reproduction of the Fathead Minnow (Pimephales promelas)

1972 ◽  
Vol 29 (5) ◽  
pp. 583-587 ◽  
Author(s):  
A. R. Carlson
Keyword(s):  
Life Cycle ◽  
Fathead Minnow ◽  
Pimephales Promelas ◽  
Threshold Concentration ◽  
Fathead Minnows ◽  
Motile Sperm ◽  
High Concentration ◽  
Toxicant Concentration ◽  
Growth And Reproduction

When fathead minnows (Pimephales promelas) were exposed to five concentrations (0.008–0.68 mg/liter) of the insecticide carbaryl for 9 months and throughout a life cycle, the highest concentration prevented reproduction and decreased survival. At the high concentration, testes contained motile sperm and ovaries were in a flaccid condition and appeared to be in a resorptive state. At the 0.68 mg/liter concentration, carbaryl appeared to contribute to mortality of larvae (produced by unexposed parents) within 30 days of hatching. Survival of young grown in the 0.008 mg/liter concentration was reduced. Since no demonstrable effects were noted for survival, growth, or reproduction at the 0.017, 0.062, and 0.21 mg/liter concentrations, this low survival value is considered not due to carbaryl. The 96-hr median tolerance concentration (TL 50) and the lethal threshold concentration (LTC) for 2-month-old fathead minnows were 9.0 mg/liter. The maximum acceptable toxicant concentration (MATC) for fathead minnows exposed to carbaryl in water with a hardness of 45.2 mg/liter and a pH of 7.5 lies between 0.21 and 0.68 mg/liter. The application factors (MATC/96-hr TL50 and MATC/LTC) both lie between 0.023 and 0.075.

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